diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 82f17b7c4a736..4bd237d97ddf3 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -39,6 +39,7 @@ jobs:
           set -e
           eval "$(conda shell.bash hook)"
           conda activate bioconda
+          source common.sh
           echo '============'
           conda info --all
           conda config --show-sources
@@ -93,15 +94,15 @@ jobs:
 
           eval "$(conda shell.bash hook)"
           conda activate bioconda
+          source common.sh
           if [ -z "$GITHUB_BASE_REF" ] ; then
               export GITHUB_BASE_REF="master"
           fi
           git fetch origin "$GITHUB_BASE_REF"
-          docker pull quay.io/dpryan79/mulled_container:latest
+
           bioconda-utils build recipes config.yml \
             --docker --mulled-test \
             --git-range origin/"$GITHUB_BASE_REF" HEAD
-          docker rmi quay.io/dpryan79/mulled_container:latest
 
       - name: Prepare artifacts
         run: |
@@ -134,14 +135,8 @@ jobs:
         with:
           name: linux-packages
           path: |
-            /tmp/artifacts/packages
+            /tmp/artifacts
 
-      - name: Archive images 
-        uses: actions/upload-artifact@v4
-        with:
-          name: docker-images
-          path: |
-            /tmp/artifacts/images
 
   build-osx-64:
     name: OSX-64 Tests
@@ -149,6 +144,7 @@ jobs:
     strategy:
       fail-fast: true
       max-parallel: 4
+    # Limited concurrency for osx, so first make sure linux can pass
     needs: build-linux
     steps:
       - uses: actions/checkout@v4
@@ -178,19 +174,20 @@ jobs:
           set -e
           eval "$(conda shell.bash hook)"
           conda activate bioconda
+          source common.sh
+          # Sets up OSX SDK
+          run_conda_forge_build_setup
 
           # Clean up lingering build artifacts
           for n in linux-64 osx-64 noarch; do
               rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2
           done
 
-          # The SDK isn't actually cached, so reinstall it
-          run_conda_forge_build_setup
-
           if [ -z "$GITHUB_BASE_REF" ] ; then
               export GITHUB_BASE_REF="master"
           fi
           git fetch origin "$GITHUB_BASE_REF"
+
           bioconda-utils build recipes config.yml \
             --git-range origin/"$GITHUB_BASE_REF" HEAD
 
@@ -210,87 +207,88 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: osx-packages
-          path: |
-            /tmp/artifacts/packages
-
-  build_and_test-osx-arm64:
-    name: OSX-ARM64 Tests
-    runs-on: macOS-14 # M1
-    strategy:
-      fail-fast: true
-      max-parallel: 4
-    needs: build-linux
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      # bail if there's no osx-arm64 recipes
-      - name: Check for Additional Platforms
-        id: additional_platforms
-        run: |
-          result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${GITHUB_JOB}")
-          if [[ ${result} != "build" ]]
-          then
-              echo "No recipes using this platform, skipping rest of job."
-              echo "skip_build=true" >> $GITHUB_OUTPUT
-          fi
-
-      - name: set path
-        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
-
-      - name: Fetch conda install script
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: |
-          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
-
-      - name: Set up bioconda-utils
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: bash install-and-set-up-conda.sh
-
-      - name: Configure conda
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: bash configure-conda.sh
-
-      - name: Build and Test
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        env:
-          # Mimic circleci
-          OSTYPE: "darwin"
-          CI: "true"
-        run: |
-          set -xe
-          eval "$(conda shell.bash hook)"
-          conda activate bioconda
-          source common.sh
-          # Sets up OSX SDK
-          run_conda_forge_build_setup
-
-          if [ -z "$GITHUB_BASE_REF" ] ; then
-              export GITHUB_BASE_REF="master"
-          fi
-          git fetch origin "$GITHUB_BASE_REF"
-
-          bioconda-utils build recipes config.yml \
-            --lint --git-range origin/"$GITHUB_BASE_REF" HEAD
-
-      - name: Prepare artifacts
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: |
-              (
-              rm -rf /tmp/artifacts
-              mkdir -p /tmp/artifacts/packages
-              cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0
-              find -name .cache | xargs rm -rf || true
-              for n in index.html channeldata.json osx-arm64 noarch; do
-                cp -rv $n /tmp/artifacts/packages || true
-              done
-              ) || true
-
-      - name: Archive packages
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        uses: actions/upload-artifact@v4
-        with:
-          name: osx-arm64-packages
           path: |
             /tmp/artifacts
+
+  # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
+  # build_and_test-osx-arm64:
+  #   name: OSX-ARM64 Tests
+  #   runs-on: macOS-14 # M1
+  #   strategy:
+  #     fail-fast: true
+  #     max-parallel: 4
+  #   needs: build-linux
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #       with:
+  #         fetch-depth: 0
+
+  #     # bail if there's no osx-arm64 recipes
+  #     - name: Check for Additional Platforms
+  #       id: additional_platforms
+  #       run: |
+  #         result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${GITHUB_JOB}")
+  #         if [[ ${result} != "build" ]]
+  #         then
+  #             echo "No recipes using this platform, skipping rest of job."
+  #             echo "skip_build=true" >> $GITHUB_OUTPUT
+  #         fi
+
+  #     - name: set path
+  #       run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
+
+  #     - name: Fetch conda install script
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: |
+  #         wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
+
+  #     - name: Set up bioconda-utils
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: bash install-and-set-up-conda.sh
+
+  #     - name: Configure conda
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: bash configure-conda.sh
+
+  #     - name: Build and Test
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       env:
+  #         # Mimic circleci
+  #         OSTYPE: "darwin"
+  #         CI: "true"
+  #       run: |
+  #         set -xe
+  #         eval "$(conda shell.bash hook)"
+  #         conda activate bioconda
+  #         source common.sh
+  #         # Sets up OSX SDK
+  #         run_conda_forge_build_setup
+
+  #         if [ -z "$GITHUB_BASE_REF" ] ; then
+  #             export GITHUB_BASE_REF="master"
+  #         fi
+  #         git fetch origin "$GITHUB_BASE_REF"
+
+  #         bioconda-utils build recipes config.yml \
+  #           --lint --git-range origin/"$GITHUB_BASE_REF" HEAD
+
+  #     - name: Prepare artifacts
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: |
+  #             (
+  #             rm -rf /tmp/artifacts
+  #             mkdir -p /tmp/artifacts/packages
+  #             cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0
+  #             find -name .cache | xargs rm -rf || true
+  #             for n in index.html channeldata.json osx-arm64 noarch; do
+  #               cp -rv $n /tmp/artifacts/packages || true
+  #             done
+  #             ) || true
+
+  #     - name: Archive packages
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       uses: actions/upload-artifact@v4
+  #       with:
+  #         name: osx-arm64-packages
+  #         path: |
+  #           /tmp/artifacts
diff --git a/.github/workflows/master.yml b/.github/workflows/master.yml
index 7e237b314da22..243e3a6ac1dd3 100644
--- a/.github/workflows/master.yml
+++ b/.github/workflows/master.yml
@@ -44,16 +44,12 @@ jobs:
           set -ex
           eval "$(conda shell.bash hook)"
           conda activate bioconda
-          docker pull quay.io/dpryan79/mulled_container:latest
-          # bioconda-utils handle-merged-pr recipes config.yml \
-          #   --repo bioconda/bioconda-recipes \
-          #   --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \
-          #   --quay-upload-target biocontainers \
-          #   --fallback build
-          bioconda-utils build recipes config.yml \
+          bioconda-utils handle-merged-pr recipes config.yml \
+            --repo bioconda/bioconda-recipes \
             --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
-            --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
-          docker rmi quay.io/dpryan79/mulled_container:latest
+            --quay-upload-target biocontainers \
+            --fallback build \
+            --artifact-source github-actions
 
   build-osx-64:
     name: OSX-64 Upload
@@ -99,74 +95,75 @@ jobs:
           # Sets up OSX SDK
           run_conda_forge_build_setup
 
-          # bioconda-utils handle-merged-pr recipes config.yml \
-          #   --repo bioconda/bioconda-recipes \
-          #   --git-range ${BUILD_SOURCEVERSION}~1 ${BUILD_SOURCEVERSION} \
-          #   --fallback build
-          bioconda-utils build recipes config.yml \
-            --anaconda-upload --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA}
-
-  build_and_upload-osx-arm64:
-    name:  OSX-ARM64 Upload
-    if: github.repository == 'bioconda/bioconda-recipes'
-    runs-on: macOS-14 # M1
-    strategy:
-      fail-fast: false
-      max-parallel: 4
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      # bail if there's no osx-arm64 recipes
-      - name: Check for Additional Platforms
-        id: additional_platforms
-        run: |
-          result=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${GITHUB_JOB}")
-          if [[ ${result} != "build" ]]
-          then
-              echo "No recipes using this platform, skipping rest of job."
-              echo "skip_build=true" >> $GITHUB_OUTPUT
-          fi
-
-      - name: set path
-        run: |
-          echo "/opt/mambaforge/bin" >> $GITHUB_PATH
-
-      - name: Fetch conda install script
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: |
-          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
-
-      - name: Set up bioconda-utils
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: bash install-and-set-up-conda.sh
-
-      - name: Configure conda
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        run: bash configure-conda.sh
-
-      - name: Build and Upload
-        if: steps.additional_platforms.outputs.skip_build != 'true'
-        env:
-          QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
-          QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
-          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-          INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          # Mimic circleci
-          OSTYPE: "darwin"
-          CI: "true"
-        run: |
-          set -xe
-          eval "$(conda shell.bash hook)"
-          conda activate bioconda
-          source common.sh
-          # Sets up OSX SDK
-          run_conda_forge_build_setup
-
           bioconda-utils handle-merged-pr recipes config.yml \
-            --repo bioconda/bioconda-recipes \
-            --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
-            --fallback build \
-            --artifact-source github-actions
+          --repo bioconda/bioconda-recipes \
+          --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
+          --fallback build \
+          --artifact-source github-actions
+
+
+  # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
+  # build_and_upload-osx-arm64:
+  #   name:  OSX-ARM64 Upload
+  #   if: github.repository == 'bioconda/bioconda-recipes'
+  #   runs-on: macOS-14 # M1
+  #   strategy:
+  #     fail-fast: false
+  #     max-parallel: 4
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #       with:
+  #         fetch-depth: 0
+
+  #     # bail if there's no osx-arm64 recipes
+  #     - name: Check for Additional Platforms
+  #       id: additional_platforms
+  #       run: |
+  #         result=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${GITHUB_JOB}")
+  #         if [[ ${result} != "build" ]]
+  #         then
+  #             echo "No recipes using this platform, skipping rest of job."
+  #             echo "skip_build=true" >> $GITHUB_OUTPUT
+  #         fi
+
+  #     - name: set path
+  #       run: |
+  #         echo "/opt/mambaforge/bin" >> $GITHUB_PATH
+
+  #     - name: Fetch conda install script
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: |
+  #         wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
+
+  #     - name: Set up bioconda-utils
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: bash install-and-set-up-conda.sh
+
+  #     - name: Configure conda
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       run: bash configure-conda.sh
+
+  #     - name: Build and Upload
+  #       if: steps.additional_platforms.outputs.skip_build != 'true'
+  #       env:
+  #         QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
+  #         QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
+  #         ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+  #         INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #         # Mimic circleci
+  #         OSTYPE: "darwin"
+  #         CI: "true"
+  #       run: |
+  #         set -xe
+  #         eval "$(conda shell.bash hook)"
+  #         conda activate bioconda
+  #         source common.sh
+  #         # Sets up OSX SDK
+  #         run_conda_forge_build_setup
+
+  #         bioconda-utils handle-merged-pr recipes config.yml \
+  #           --repo bioconda/bioconda-recipes \
+  #           --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
+  #           --fallback build \
+  #           --artifact-source github-actions
diff --git a/azure-pipeline-master.yml b/azure-pipeline-master.yml
index 68f8bd157bc35..904519f9f3082 100644
--- a/azure-pipeline-master.yml
+++ b/azure-pipeline-master.yml
@@ -1,6 +1,8 @@
+# Disable Azure checks in favor of GitHub Actions due to memory issues
 pr: none
-trigger:
-  - master
+trigger: none
+# trigger:
+#   - master
 
 jobs:
   - job: "build_and_push_linux"
@@ -39,11 +41,7 @@ jobs:
           bioconda-utils handle-merged-pr recipes config.yml \
             --repo bioconda/bioconda-recipes \
             --git-range $(Build.SourceVersion)~1 $(Build.SourceVersion) \
-            --quay-upload-target biocontainers \
-            --fallback build
-          #bioconda-utils build recipes config.yml \
-          #  --git-range $(Build.SourceVersion)~1 $(Build.SourceVersion) \
-          #  --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
+            --quay-upload-target biocontainers
 
         env:
           QUAY_LOGIN: $(QUAY_LOGIN)
diff --git a/azure-pipeline.yml b/azure-pipeline.yml
index 10df61e7f2a5e..fc2966287e6b3 100644
--- a/azure-pipeline.yml
+++ b/azure-pipeline.yml
@@ -1,10 +1,13 @@
-pr:
-  autoCancel: true
-trigger:
-  branches:
-    exclude:
-      - master
-      - "*"
+# Disable Azure checks in favor of GitHub Actions due to memory issues
+# pr:
+#   autoCancel: true
+pr: none
+trigger: none
+# trigger: 
+  # branches:
+  #   exclude:
+  #     - master
+  #     - "*"
 
 stages:
   - stage: "lint"
@@ -41,6 +44,8 @@ stages:
   - stage: "test_linux"
     jobs:
       - job: "test_linux"
+        ##timeoutInMinutes: 90 # how long to run the job before automatically cancelling
+        ##cancelTimeoutInMinutes: 40 # how much time to give 'run always even if cancelled tasks' before stopping them
         pool:
           vmImage: "ubuntu-latest"
         strategy:
diff --git a/build-fail-blacklist b/build-fail-blacklist
index a176375749eff..c679e4d7a8eee 100644
--- a/build-fail-blacklist
+++ b/build-fail-blacklist
@@ -220,7 +220,6 @@ recipes/unitig-counter
 recipes/probcons
 recipes/spydrpick
 recipes/bctools
-recipes/bayestyper
 recipes/group_humann2_uniref_abundances_to_go
 recipes/isonclust2
 recipes/sibelia
@@ -772,9 +771,6 @@ recipes/perl-gd
 # sha mismatch when downloading source
 recipes/fmlrc2
 
-# tries to download zlib itself, which fails
-recipes/d4binding
-
 # no matching package named `quickersort` found
 recipes/mudskipper
 
diff --git a/recipes/agc/meta.yaml b/recipes/agc/meta.yaml
index 12d3d1e796fbf..86669ebdbf0b7 100644
--- a/recipes/agc/meta.yaml
+++ b/recipes/agc/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 1
+  number: 2
   script: "mkdir -p ${PREFIX}/bin; cp agc ${PREFIX}/bin"
   run_exports:
     - {{ pin_subpackage('agc', max_pin="x") }}
@@ -31,6 +31,7 @@ test:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   skip-lints:
     - should_be_noarch_generic
     - should_not_be_noarch_source
diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml
index d877735467abd..036c9fa58682e 100644
--- a/recipes/aletsch/meta.yaml
+++ b/recipes/aletsch/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "aletsch" %}
-{% set version = "1.1.2" %}
+{% set version = "1.1.3" %}
 
 package:
   name: "{{ name }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz"
-  sha256: "b081cfcbd2f232dcddab4f9c6ce11f15f41e4319e1f977dd955cca240748d4b5"
+  sha256: "74e1b7e2ff2cb065d02f1e0d45d7e87ae332ccfcef86b6a32af88b2a7005c9f7"
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('aletsch', max_pin="x") }}
 
diff --git a/recipes/altamisa/meta.yaml b/recipes/altamisa/meta.yaml
index 04771930e1e2e..ad5adf9bc1821 100644
--- a/recipes/altamisa/meta.yaml
+++ b/recipes/altamisa/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.2.9" %}
-{% set sha256 = "69e6e5e78df917c5be8a84c75f075f7cf992b52bea0dbe3487664b5e22c8bc72" %}
+{% set version = "0.3.0" %}
+{% set sha256 = "d92eb1017b26b6feb4c376456a789e584a53d569010d6a71dbb4aa8dde62c7d9" %}
 
 package:
   name: altamisa
@@ -10,14 +10,17 @@ source:
   sha256: '{{sha256}}'
 
 build:
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   noarch: python
   number: 0
+  run_exports:
+    - {{ pin_subpackage('altamisa', max_pin="x.x") }}
 
 requirements:
   host:
     - python >=3
     - pip
+    - setuptools
   run:
     - python >=3
     - attrs
diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml
index 1bb7752d2c957..f26e9a314b882 100644
--- a/recipes/ampcombi/meta.yaml
+++ b/recipes/ampcombi/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "AMPcombi" %}
-{% set version = "0.2.2" %}
+{% set version = "2.0.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: da9a179851a8f2041d05ccd10dd45b58099e84059e2e66a9ee405d1913471b58
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ampcombi-{{ version }}.tar.gz
+  sha256: 4bef05aa8433d991b76b81cb2338396c064f2ace5c73642411b2a2467524a0eb
 
 build:
   noarch: python
@@ -32,9 +32,10 @@ requirements:
     - backports.tempfile
     - contextlib2
     - openpyxl
+    - numpy ==1.26.4
     - jsonschema
     - python ==3.11
-    - diamond ==2.0.15
+    - colorama ==0.4.6
     - mmseqs2 ==15.6f452
 
 test:
diff --git a/recipes/ampd-up/build.sh b/recipes/ampd-up/build.sh
new file mode 100644
index 0000000000000..073e6f8bc5c05
--- /dev/null
+++ b/recipes/ampd-up/build.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin/
+mkdir -p ${PREFIX}/share/ampd-up/
+mkdir -p ${PREFIX}/share/ampd-up/src/
+mkdir -p ${PREFIX}/share/ampd-up/data/
+cp -r src/. ${PREFIX}/share/ampd-up/src/
+cp -r data/. ${PREFIX}/share/ampd-up/data/
+
+chmod +x ${PREFIX}/share/ampd-up/src/AMPd-Up.py
+
+echo "#!/bin/bash" > ${PREFIX}/bin/AMPd-Up
+echo "${PREFIX}/share/ampd-up/src/AMPd-Up.py \$@" >> ${PREFIX}/bin/AMPd-Up
diff --git a/recipes/ampd-up/meta.yaml b/recipes/ampd-up/meta.yaml
new file mode 100644
index 0000000000000..8bdfaa926fd5a
--- /dev/null
+++ b/recipes/ampd-up/meta.yaml
@@ -0,0 +1,37 @@
+{% set name = "ampd-up" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/bcgsc/AMPd-Up/archive/v{{ version }}.tar.gz
+  sha256: 8fcb73cb2ecb9d513a653434067a6b9e07428c93d56d173a9476ecfe88410621
+
+build:
+  number: 0
+  noarch: python
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python =3.6
+  run:
+    - python =3.6
+    - pytorch <2.0.0
+    - biopython
+    - numpy
+    - pandas
+
+test:
+  commands:
+    - AMPd-Up -h
+
+about:
+  home: https://github.com/bcgsc/AMPd-Up
+  license: GPL-3
+  license_family: GPL
+  license_file: LICENSE
+  summary: De novo antimicrobial peptide sequence generation with recurrent neural networks
diff --git a/recipes/amplici/build.sh b/recipes/amplici/build.sh
new file mode 100644
index 0000000000000..3b7588794ae9a
--- /dev/null
+++ b/recipes/amplici/build.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ `uname` == "Darwin" ]]; then
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+    export CONFIG_ARGS=""
+fi
+
+cd src || exit 1
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_C_COMPILER="${CC}" \
+    -DCMAKE_C_FLAGS="${CFLAGS}" \
+    "${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/amplici/meta.yaml b/recipes/amplici/meta.yaml
new file mode 100644
index 0000000000000..5949ed9ee80c6
--- /dev/null
+++ b/recipes/amplici/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = "2.2" %}
+
+package:
+  name: amplici
+  version: {{ version }}
+
+source:
+  url: https://github.com/DormanLab/AmpliCI/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 273362b5449ec29ff411d4c1aa5f89b1ec1eb361c8a9b69a4d89f4409fbdb70e
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("amplici", max_pin="x") }}
+
+requirements:
+  build:
+    - cmake
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - {{ compiler('fortran') }}
+  host:
+    - zlib
+
+about:
+  home: https://github.com/DormanLab/AmpliCI
+  license: BSD 3-Clause
+  license_family: BSD
+  license_file: LICENSE  
+  summary: "AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs."
+  dev_url: https://github.com/DormanLab/AmpliCI
+
+test:
+  commands:
+    - run_AmpliCI -h
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - xiyupeng
+  identifiers:
+    - biotools:amplici
+    - doi:10.1093/bioinformatics/btaa648
diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml
index 2c4387219f3f6..d6a1f2f98852c 100644
--- a/recipes/annembed/meta.yaml
+++ b/recipes/annembed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.1.6" %}
+{% set version = "0.1.7" %}
 
 package:
   name: annembed
@@ -11,7 +11,7 @@ build:
   skip: True  # [osx]
 source:
   url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz
-  sha256: f60dceb94df46ae2ccc7ed228988a67df254a28f02b9b545baf31ca6e85f7f8d
+  sha256: 487119295d6b42a1e5785172a211658749534102532ab15488357ce37291d88c
 
 requirements:
   build:
diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml
index a9d5122b1c4c3..21f64964882dd 100644
--- a/recipes/arcs/meta.yaml
+++ b/recipes/arcs/meta.yaml
@@ -1,17 +1,17 @@
-{% set version = "1.2.7" %}
+{% set version = "1.2.8" %}
 
 package:
   name: arcs
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('arcs', max_pin="x") }}
 
 source:
   url: https://github.com/bcgsc/arcs/releases/download/v{{ version }}/arcs-{{ version }}.tar.gz
-  sha256: 3162cff3286a033b494ace8050abc96d4083f846cafe921bb0122170f705eca8
+  sha256: 3393151980ee1e031ff47d32e2871745255a08e9e76f27657e868137b4ddd2df
 
 requirements:
   build:
@@ -43,4 +43,4 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
-    - osx-arm64
\ No newline at end of file
+    - osx-arm64
diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
index 321d4a53e99df..4dd54b605147c 100644
--- a/recipes/argo/meta.yaml
+++ b/recipes/argo/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "argo" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.3" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253
+  sha256: c6be3e1efc744a591524979a53895f9cbd70962a1825d8e2b442f5ffb7a3cc6b
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ build:
 requirements:
   host:
     - pip
+    - setuptools
     - python >=3.7
   run:
     - python >=3.7
@@ -36,7 +37,7 @@ about:
   home: https://github.com/xinehc/argo
   license: MIT
   license_family: MIT
-  summary: 'Argo: species-resolved profiling of antibiotic resistant genes with long-read metagenomics'
+  summary: 'Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping'
 
 extra:
   recipe-maintainers:
diff --git a/recipes/argparse2tool/meta.yaml b/recipes/argparse2tool/meta.yaml
index 6ecb346391010..651f50d085b75 100644
--- a/recipes/argparse2tool/meta.yaml
+++ b/recipes/argparse2tool/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "argparse2tool" %}
-{% set version = "0.4.9" %}
+{% set version = "0.5.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,22 +7,24 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: ecd7142c1ce60bf9e1416443ce393907b7f99a9396a0530277c110dcb7106579
+  sha256: 8c6fbf68df690edf80f438b458e6da1f943254b0c4337ac2b732c567c67fde46
 
 build:
   number: 0
   entry_points:
     - argparse2tool_check_path = argparse2tool.check_path:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
+  run_exports:
+    - {{ pin_subpackage('argparse2tool', max_pin="x.x") }}
 
 requirements:
   host:
     - pip
     - python >=3
+    - setuptools
   run:
-    - click
-    - galaxyxml >=0.2.3
+    - galaxyxml >=0.4.6
     - jinja2
     - python >=3
 
diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml
index 59642e631a4cb..619378e41c107 100644
--- a/recipes/artic/meta.yaml
+++ b/recipes/artic/meta.yaml
@@ -1,83 +1,76 @@
 {% set name = "artic" %}
-{% set version = "1.2.4" %}
-{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %}
+{% set version = "1.5.3" %}
+{% set sha256 = "107483f22de571c4aafae91c475e453d939e6a8e85a7e2cd2d23ccbca224ef1c" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version|replace("-", "_") }}
+
 source:
   url: https://github.com/artic-network/fieldbioinformatics/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   noarch: python
   run_exports:
     - {{ pin_subpackage('artic', max_pin='x.x') }}
-  script: python -m pip install --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   entry_points:
     - artic=artic.pipeline:main
     - align_trim=artic.align_trim:main
-    - align_trim_n=artic.align_trim_n:main
     - margin_cons=artic.margin_cons:main
-    - margin_cons_medaka=artic.margin_cons_medaka:main
     - vcfextract=artic.vcfextract:main
     - artic_vcf_merge=artic.vcf_merge:main
     - artic_vcf_filter=artic.vcf_filter:main
     - artic_make_depth_mask=artic.make_depth_mask:main
     - artic_fasta_header=artic.fasta_header:main
     - artic_mask=artic.mask:main
-    - artic_get_stats=artic.artic_mqc:main
+    - artic_get_models=artic.get_models:main
 
 requirements:
   host:
-    - python >=3
+    - python ==3.9
     - pip
+    - setuptools
   run:
-    - python
-    - artic-porechop >=0.3.2pre
-    - artic-tools
-    - longshot
+    - python ==3.9
     - bcftools
     - biopython
     - bwa
+    - clair3
     - clint
     - htslib
-    - medaka >=1.10.0
-    - minimap2 >=2.26
+    - minimap2
     - multiqc
-    - muscle =3.8
-    - nanopolish >=0.14.0
+    - muscle <5.1
     - pandas
-    - pip
     - pysam
     - pytest 
-    - pyvcf
+    - cyvcf2
     - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE
     - requests
     - samtools
     - tqdm
-    - keras-preprocessing >=1.1.2
-
 
 test:
   commands:
     - artic -h
     - align_trim -h
-    - align_trim_n -h
     - margin_cons -h
-    - margin_cons_medaka -h
     - vcfextract -h
     - artic_vcf_merge -h
     - artic_vcf_filter -h
     - artic_make_depth_mask -h
     - artic_fasta_header -h
     - artic_mask -h
-    - artic_get_stats -h
+    - artic_get_models -h
 
 about:
     home: https://github.com/artic-network/fieldbioinformatics
     license: MIT
+    license_family: MIT
     license_file: LICENSE
-    summary: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
-
+    summary: "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore."
+    dev_url: https://github.com/artic-network/fieldbioinformatics
+    doc_url: https://artic.readthedocs.io/en/latest
diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml
index c3bd699301f87..c2dfcf31b66b8 100644
--- a/recipes/arvados-python-client/meta.yaml
+++ b/recipes/arvados-python-client/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.7.4" %}
+{% set version = "3.0.0" %}
 
 package:
   name: arvados-python-client
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz
-  sha256: 932398da39daba88041f1084d19019e7300cac462ef93f181f40aa85562ff275
+  sha256: 7f980029b27a27f0f348f610784757ca6ff419aee6eb903b046c37b719e1b820
 
 build:
   noarch: python
@@ -35,6 +35,7 @@ requirements:
     - protobuf <4.0.0
     - pyparsing <3
     - dataclasses
+    - websockets
 
 test:
   imports:
diff --git a/recipes/ascat/build.sh b/recipes/ascat/build.sh
index f9d84e6bad81d..e459e688553d6 100644
--- a/recipes/ascat/build.sh
+++ b/recipes/ascat/build.sh
@@ -7,10 +7,4 @@ pushd ASCAT
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
 
-$R CMD INSTALL --build .
-
-# Add more build steps here, if they are necessary.
-
-# See
-# http://docs.continuum.io/conda/build.html
-# for a list of environment variables that are set during the build process.
+${R} CMD INSTALL --build . "${R_ARGS}"
diff --git a/recipes/ascat/meta.yaml b/recipes/ascat/meta.yaml
index f5e04994e9813..227ee1e9efa68 100644
--- a/recipes/ascat/meta.yaml
+++ b/recipes/ascat/meta.yaml
@@ -1,20 +1,22 @@
-{% set version = "3.1.1" %}
-{% set sha256 = "7d63c8bb8eb53f463732950f649db01f7055d89801438a2ac5933f16a9ba1042" %}
+{% set version = "3.2.0" %}
+{% set sha256 = "e866c1b4eec503bde643c6922bfc30c03cf2783e903072779d8b81819f17b547" %}
 
 package:
   name: ascat
   version: '{{ version }}'
 
 source:
-  url: https://github.com/Crick-CancerGenomics/ascat/archive/v{{ version }}.tar.gz
+  url: https://github.com/VanLoo-lab/ascat/archive/refs/tags/v{{ version }}.tar.gz
   sha256: '{{ sha256 }}'
 
 build:
-  number: 1
+  number: 0
   noarch: generic
   rpaths:
     - lib/R/lib/
     - lib/
+  run_exports:
+    - {{ pin_subpackage('ascat', max_pin="x") }}
 
 requirements:
   host:
@@ -38,15 +40,14 @@ requirements:
     - bioconductor-genomicranges
     - bioconductor-iranges
 
-
 test:
   commands:
     - $R -e "library(ASCAT)"
 
 about:
-  home: https://www.crick.ac.uk/research/a-z-researchers/researchers-v-y/peter-van-loo/software/
-  license: GPL-3.0
-  license_family: GPL
+  home: https://www.crick.ac.uk/research/a-z-researchers/researchers-v-y/peter-van-loo/software
+  license: GPL-3.0-or-later
+  license_family: GPL3
   summary: |
     ASCAT is a method to derive copy number profiles of tumour cells,
     accounting for normal cell admixture and tumour aneuploidy (Figure 1).
@@ -56,6 +57,7 @@ about:
     whole-genome allele-specific copy number profiles (the number of copies of
     both parental alleles for all SNP loci across the genome).
   dev_url: https://github.com/Crick-CancerGenomics/ascat
+  doc_url: https://github.com/VanLoo-lab/ascat/blob/v{{ version }}/README.md
 
 extra:
   identifiers:
diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh
index 37603d593282b..efc2cd7bd20db 100644
--- a/recipes/aspera-cli/build.sh
+++ b/recipes/aspera-cli/build.sh
@@ -7,7 +7,7 @@ mkdir -p $GEM_HOME
 gem build aspera-cli.gemspec
 gem install --install-dir $GEM_HOME --bindir $GEM_HOME/bin ${PKG_NAME}-${PKG_VERSION}.gem
 gem_path=$GEM_HOME/gems/${PKG_NAME}-${PKG_VERSION}
-cp -r $SRC_DIR/* $gem_path
+cp -rf $SRC_DIR/* $gem_path
 rm $gem_path/{conda_build,build_env_setup}.sh
 tail -n+3 bin/ascli > $gem_path/bin/ascli
 tail -n+3 bin/asession > $gem_path/bin/asession
@@ -25,9 +25,6 @@ EOF
 echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli
 echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession
 
-ln -s $gem_path/bin/* $PREFIX/bin
+ln -sf $gem_path/bin/* $PREFIX/bin
 
-export ASCLI_HOME="$PREFIX/etc/aspera"
-ascli conf ascp install && ascli config ascp info 
-cp $ASCLI_HOME/aspera-license .
-ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin
\ No newline at end of file
+ascli conf ascp install && ascli config ascp info
diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml
index 1004a29c34209..cd0e7cc0d44d1 100644
--- a/recipes/aspera-cli/meta.yaml
+++ b/recipes/aspera-cli/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "aspera-cli" %}
-{% set version = "4.14.0" %}
+{% set version = "4.19.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,17 +7,15 @@ package:
 
 source:
   - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-    sha256: b46df368df71ad926605e85ea4b61b9e48335cce8be31ac04d97ee6f71109f03
+    sha256: e4f9eb47510094132ff02960764254dfc322f1a16c9ad2b8abc60a54e5e21da1
 
 build:
   noarch: generic
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('aspera-cli', max_pin="x") }}
 
 requirements:
-  build:
-    - ruby >=3
   host:
     - ruby >=3
   run:
@@ -26,16 +24,15 @@ requirements:
 test:
   commands:
     - ascli -h
-    - ascp -h
 
 about:
-  home: https://github.com/IBM/aspera-cli
-  license: Apache-2.0
-  license_file: 
-    - LICENSE
-    - aspera-license
-  summary: "Command Line Interface for IBM Aspera products"
-  dev_url: https://github.com/IBM/aspera-cli
+  home: "https://github.com/IBM/aspera-cli"
+  license: "Apache-2.0"
+  license_file: LICENSE
+  license_family: APACHE
+  summary: "Command Line Interface for IBM Aspera products."
+  dev_url: "https://github.com/IBM/aspera-cli"
+  doc_url: "https://www.rubydoc.info/gems/aspera-cli"
 
 extra:
   recipe-maintainers:
diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml
index 280e9327cfdac..8ea909de74f8d 100644
--- a/recipes/assembly_finder/meta.yaml
+++ b/recipes/assembly_finder/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "assembly_finder" %}
-{% set version = "0.7.7" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0c6542253464b8ba406aeddc630f5625db74a5e1e07911534be3add0500a1f02
+  sha256: 8708d9185dccce21808777c79dad1c2b019ca1f416035c2e5e16b0c32928566e
 
 build:
-  number: 1
+  number: 0
   noarch: python
   entry_points:
     - assembly_finder=assembly_finder.__main__:main
diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml
index 19c285b795681..6d7dce2306868 100644
--- a/recipes/aster/meta.yaml
+++ b/recipes/aster/meta.yaml
@@ -1,13 +1,13 @@
-{% set version = "1.16" %}
+{% set version = "1.19" %}
 {% set name = "ASTER" %}
-{% set sha256 = "c6e80de483a0a59fc0d3a74465b1f793e773b9d79cbd20756c6766136ffbb1a7" %}
+{% set sha256 = "f6d7fd58297ab854a6c869ba5d6715d056a82df8254c0d6cba6d9a6db355f054" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('aster', max_pin="x") }}
 
diff --git a/recipes/atlas/build.sh b/recipes/atlas/build.sh
index ac7ce537255b2..95160393b114a 100644
--- a/recipes/atlas/build.sh
+++ b/recipes/atlas/build.sh
@@ -1,14 +1,27 @@
 #!/bin/bash
 
-export CFLAGS="$CFLAGS -I$PREFIX/include"
-export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
-export LD_LIBRARY_PATH="${PREFIX}/lib"
-export LIBRARY_PATH="${PREFIX}/lib"
-export CPATH="${PREFIX}/include"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
-sed -i.bak 's/^GIT_HEADER/#GIT_HEADER/' makefile
+if [[ `uname` == "Darwin" ]]; then
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+    export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+else
+    export CONFIG_ARGS=""
+fi
 
-make CXX=$CXX ARM=false
+cmake . -GNinja \
+    -DCONDA=ON \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_CXX_COMPILER="${CXX}" \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+    "${CONFIG_ARGS}"
 
-mkdir -p $PREFIX/bin
-cp atlas $PREFIX/bin 
+ninja || exit 1
+
+mkdir -p ${PREFIX}/bin
+cp atlas ${PREFIX}/bin || exit 1
+chmod +x ${PREFIX}/bin/atlas
diff --git a/recipes/atlas/meta.yaml b/recipes/atlas/meta.yaml
index 1dbe80ec37fcb..fdf92201097e6 100644
--- a/recipes/atlas/meta.yaml
+++ b/recipes/atlas/meta.yaml
@@ -1,39 +1,65 @@
-{% set version = "0.9.9" %}
+{% set version = "2.0.0" %}
 
-package: 
+package:
   name: atlas
   version: {{ version }}
 
 source:
-  url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz
-  sha256: 7b65eae5ab7ff439accd53febf8caa15ad9d8230278eee31fd5c2e95bf021990
+  url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.6.tar.gz
+  sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3
 
 build:
-  number: 3
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("atlas", max_pin="x") }}
 
 requirements:
-    build:
-      - make
-      - {{ compiler('cxx') }}
-      - zlib
-      - armadillo
-      - libblas
-      - openblas
-    host:
-      - zlib
-      - armadillo
-      - libblas
-      - openblas
-    run:
-      - libblas
-      - zlib
-      - armadillo
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - git
+    - ninja
+    - sysroot_linux-64 =2.17  # [linux]
+  host:
+    - armadillo
+    - fmt
+    - htslib
+    - lapack
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - nlohmann_json
+    - openblas
+    - sysroot_linux-64 =2.17  # [linux]
+    - jsoncpp
+    - zlib
+  run:
+    - armadillo
+    - fmt
+    - htslib
+    - lapack
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - nlohmann_json
+    - openblas
+    - sysroot_linux-64 =2.17  # [linux]
+    - jsoncpp
 
 test:
-    commands:
-      - atlas task=recal | grep Wegmann
-      
+  commands:
+    - atlas | grep "successfully"
+    - atlas simulate
+    - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta
+    - atlas GLF --bam ATLAS_simulations.bam
+    - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta
+    - atlas majorMinor --glf ATLAS_simulations.glf.gz
+    - rm ATLAS_* *.parameters saf.saf.* || exit 1
+
 about:
-  home: https://bitbucket.org/wegmannlab/atlas/wiki/Home
-  license: GPLv3
-  summary: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
+  home: https://atlaswiki.netlify.app
+  license: MPL-2.0
+  summary: "ATLAS: Analysis Tools for Ancient and Low-depth Samples"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml
index ba381bb2d3dea..50b746c7464cd 100644
--- a/recipes/augur/meta.yaml
+++ b/recipes/augur/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "26.0.0" %}
+{% set version = "26.1.0" %}
 
 package:
   name: augur
@@ -6,14 +6,14 @@ package:
 
 source:
   url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
-  sha256: 0040d881eca4d695b75ba87c07a6c7abbdd13cc3e200606d77b38b875348cb07
+  sha256: 74159e9a663ad4f1171b1800dd345dd94777a37dcc74abc754351626f75668c2
 
 build:
   number: 0
   noarch: python
   entry_points:
     - augur = augur.__main__:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage('augur', max_pin='x') }}
 
@@ -21,6 +21,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - bcbio-gff >=0.7.1,<0.8
@@ -38,7 +39,6 @@ requirements:
     - scipy >=1.0.0,<2
     - treetime >=0.11.2,<0.12
     - xopen[zstd] >=1.7.0,<3
-
     - fasttree
     - iqtree
     - mafft
@@ -52,15 +52,18 @@ test:
     - augur --help
 
 about:
-  home: https://github.com/nextstrain/augur
-  license: AGPL-3.0-only
-  summary: 'Process pathogen genome data for the Nextstrain platform'
+  home: "https://github.com/nextstrain/augur"
+  license: "AGPL-3.0-only"
+  summary: 'Process pathogen genome data for the Nextstrain platform.'
   license_family: AGPL
   license_file: LICENSE.txt
+  dev_url: "https://github.com/nextstrain/augur"
+  doc_url: "https://docs.nextstrain.org/projects/augur"
 
 extra:
   identifiers:
     - doi:10.21105/joss.02906
+    - biotools:Augur
   recipe-maintainers:
     - nextstrain-bot
     - huddlej
diff --git a/recipes/augustus/build.sh b/recipes/augustus/build.sh
index 6c55e6ebfea54..d0126d902f5b8 100644
--- a/recipes/augustus/build.sh
+++ b/recipes/augustus/build.sh
@@ -2,34 +2,39 @@
 
 set -x -e
 
-#export CXXFLAGS="${CXXFLAGS} -std=c++11 -stdlib=libstdc++ -stdlib=libc++ -DUSE_BOOST"
-export CXXFLAGS="${CXXFLAGS} -std=c++11  -DUSE_BOOST -I${PREFIX}/include"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -DUSE_BOOST -I${PREFIX}/include"
 
 mkdir -p ${PREFIX}/bin
 mkdir -p ${PREFIX}/scripts
 mkdir -p ${PREFIX}/config
 
 ## Make the software
-
-if [ "$(uname)" = Darwin ] ; then
-    # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
-    sqlite=
+if [[ "$(uname)" = Darwin ]]; then
+	# SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
+	sqlite=
 else
-    sqlite='SQLITE=true'
+	sqlite='SQLITE=true'
 fi
-make \
-    CC="${CC}" \
-    CXX="${CXX}" \
-    INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \
-    LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \
-    INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \
-    LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \
-    INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \
-    LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \
-    COMPGENPRED=true \
-    MYSQL=false \
-    $sqlite
 
+make \
+	CC="${CC}" \
+	CXX="${CXX}" \
+	INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \
+	LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \
+	INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \
+	LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \
+	INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \
+	LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \
+	COMPGENPRED=true \
+	MYSQL=false \
+	"${sqlite}" -j"${CPU_COUNT}"
+
+# Fix perl shebang
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl
+rm -rf ${SRC_DIR}/scripts/*.bak
 
 ## Build Perl
 
@@ -39,7 +44,7 @@ cd perl-build
 # affects tests for Augustus 3.3:
 # https://github.com/Gaius-Augustus/Augustus/commit/7ca3ab
 #sed -i'' -e '1s/perl -w/perl/' *.pl
-cp ${RECIPE_DIR}/Build.PL ./
+cp -f ${RECIPE_DIR}/Build.PL ./
 perl ./Build.PL
 perl ./Build manifest
 perl ./Build install --installdirs site
@@ -49,11 +54,11 @@ cd ..
 
 ## End build perl
 
+chmod 0755 bin/augustus
 mv bin/* $PREFIX/bin/
 mv scripts/* $PREFIX/bin/
 mv config/* $PREFIX/config/
 
-
 ## Set AUGUSTUS variables on env activation
 
 mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d
diff --git a/recipes/augustus/meta.yaml b/recipes/augustus/meta.yaml
index 7faa39e763a44..6eec34c826555 100644
--- a/recipes/augustus/meta.yaml
+++ b/recipes/augustus/meta.yaml
@@ -1,28 +1,31 @@
+{% set name = "augustus" %}
 {% set version = "3.5.0" %}
 {% set sha256 = "5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686" %}
 
 package:
-  name: augustus
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/Gaius-Augustus/Augustus/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
+    - patches/0001-Makefile.patch
     - patches/homGeneMapping.src.makefile.patch
     - patches/utrrnaseq.patch
 
 build:
-  number: 4
+  number: 5
+  run_exports:
+    - {{ pin_subpackage('augustus', max_pin="x") }}
 
 requirements:
   build:
     - make
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
   host:
     - zlib
-    - samtools ==0.1.19
+    - samtools
     - bamtools
     - htslib
     - gsl
@@ -35,7 +38,6 @@ requirements:
     - perl
     - perl-module-build
   run:
-    - zlib
     - boost-cpp
     - gsl
     - lp_solve
@@ -152,8 +154,8 @@ test:
     - fix_in_frame_stop_codon_genes.py --help | grep -Fq 'fix_in_frame_stop_codon_genes.py'
 
 about:
-  home: http://bioinf.uni-greifswald.de/augustus/
-  license: Artistic Licence
+  home: "https://bioinf.uni-greifswald.de/augustus"
+  license: "Artistic Licence"
   license_family: Other
   license_file: "src/LICENSE.TXT"
   summary: 'AUGUSTUS is a gene prediction program for eukaryotes written by Mario
@@ -161,10 +163,13 @@ about:
     it bases its prediction purely on the sequence. AUGUSTUS may also incorporate
     hints on the gene structure coming from extrinsic sources such as EST, MS/MS,
     protein alignments and synthenic genomic alignments.'
+  dev_url: "https://github.com/Gaius-Augustus/Augustus"
+  doc_url: "https://github.com/Gaius-Augustus/Augustus/blob/v{{ version }}/docs/RUNNING-AUGUSTUS.md"
 
 extra:
   identifiers:
     - biotools:augustus
     - doi:10.1093/bioinformatics/btr010
     - usegalaxy-eu:augustus
+    - usegalaxy-eu:augustus_training
   notes: "Builds with sqlite support are currently only available on Linux due to compile issues with macOS."
diff --git a/recipes/augustus/patches/0001-Makefile.patch b/recipes/augustus/patches/0001-Makefile.patch
new file mode 100644
index 0000000000000..29177a5f9654f
--- /dev/null
+++ b/recipes/augustus/patches/0001-Makefile.patch
@@ -0,0 +1,40 @@
+diff --git a/Makefile b/Makefile
+index a26b40c..b2ccb6a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,20 +26,26 @@ clean:
+ 		cd .. && ./pyclean.sh; \
+ 	fi
+ 
+-PREFIX = /usr/local
+-INSTALLDIR = /opt/augustus-$(AUGVERSION)
++# DESTDIR is usually the empty string but can be set for staging
++prefix ?= $(PREFIX)
++bindir = $(DESTDIR)$(prefix)/bin
++INSTALLDIR = $(prefix)/share/augustus-$(AUGVERSION)
+ 
+ install:
+-	if [ ! $(PWD) -ef $(INSTALLDIR) ] ; then \
++	@echo Installing augustus executables into $(bindir)
++# two main ways:
++# 1) make install is executed from anywhere but in INSTALLDIR. Then INSTALLDIR is created if it does not exist and config data is copied.
++# 2) make install is executed in INSTALLDIR. This is done by the singularity file.
++	if [ ! $(CURDIR) -ef $(INSTALLDIR) ] ; then \
+ 		install -d $(INSTALLDIR) && \
+ 		cp -a config bin scripts $(INSTALLDIR) ; \
+ 	fi
+-	ln -sf $(INSTALLDIR)/bin/augustus $(PREFIX)/bin/augustus
+-	ln -sf $(INSTALLDIR)/bin/etraining $(PREFIX)/bin/etraining
+-	ln -sf $(INSTALLDIR)/bin/prepareAlign $(PREFIX)/bin/prepareAlign
+-	ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(PREFIX)/bin/fastBlockSearch
+-	if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(PREFIX)/bin/load2db ; fi
+-	if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(PREFIX)/bin/getSeq ; fi
++	ln -sf $(INSTALLDIR)/bin/augustus $(bindir)/augustus
++	ln -sf $(INSTALLDIR)/bin/etraining $(bindir)/etraining
++	ln -sf $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign
++	ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearch
++	if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi
++	if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fi
+ 
+ # for internal purposes:
+ release:
diff --git a/recipes/augustus/patches/utrrnaseq.patch b/recipes/augustus/patches/utrrnaseq.patch
index 33ed805d73488..4befbfaf97c85 100644
--- a/recipes/augustus/patches/utrrnaseq.patch
+++ b/recipes/augustus/patches/utrrnaseq.patch
@@ -1,6 +1,17 @@
---- a/auxprogs/utrrnaseq/Makefile	2022-09-23 10:06:14.000000000 -0700
-+++ b/auxprogs/utrrnaseq/Makefile	2022-10-08 10:15:31.359607884 -0700
-@@ -29,6 +29,7 @@
+diff --git a/auxprogs/utrrnaseq/Makefile b/auxprogs/utrrnaseq/Makefile
+index 134c5c5..63fa103 100644
+--- a/auxprogs/utrrnaseq/Makefile
++++ b/auxprogs/utrrnaseq/Makefile
+@@ -3,7 +3,7 @@
+ include ../../common.mk
+ 
+ CXX ?= g++
+-CXXFLAGS := -Wall -O0 -pedantic -fmessage-length=0 ${CXXFLAGS}
++CXXFLAGS := -Wall -O3 -pedantic -fmessage-length=0 -std=c++14 ${CXXFLAGS}
+ INCLS   += $(INCLUDE_PATH_BOOST) # set boost include path in INCLUDE_PATH_BOOST, if boost is not installed system-wide
+ LDFLAGS += $(LIBRARY_PATH_BOOST) # set boost library path in LIBRARY_PATH_BOOST, if boost is not installed system-wide
+ 
+@@ -29,6 +29,7 @@ utrrnaseq: $(OBJS)
  	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
  	@echo 'Finished building target: $@'
  	@echo ' '
@@ -8,7 +19,7 @@
  
  $(OBJS): $(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp
  	@echo 'Building file: $<'
-@@ -55,5 +56,6 @@
+@@ -55,5 +56,6 @@ clean_test:
  clean: clean_test
  	rm -rf $(OBJS) $(DEPS) $(OBJ_DIR) utrrnaseq
  	@echo ' '
diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml
index 7285b2b8b581e..f9d27847244f7 100644
--- a/recipes/auspice/meta.yaml
+++ b/recipes/auspice/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.59.0" %}
+{% set version = "2.59.1" %}
 {% set name = "auspice" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://registry.npmjs.org/{{ name }}/-/{{ name }}-{{ version }}.tgz
-  sha256: 3a9d2d0b4bcaf4480977ed05f21dad9776a91ecbb8a205d0365fe4c6004b80c0
+  sha256: 828bc00e27ca3d403332686ab041dd3171c999a1a942b9fe89ba8256daedfecc
 
 build:
   number: 0
diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml
index fa02ae9c72a68..e8647e67bb759 100644
--- a/recipes/bakta/meta.yaml
+++ b/recipes/bakta/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.9.4" %}
+{% set version = "1.10.1" %}
 
 package:
   name: bakta
@@ -6,56 +6,60 @@ package:
 
 source:
   url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
-  sha256: 'ad92853e9d4f022024d393149eb086ad36a7e35f824a5d9efed94c3262f9cf66'
+  sha256: '4a13b7362dd46d44edc175956afda2478122b48bfef4fb9581c198b35fd36296'
 
 build:
   noarch: python
   number: 0
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   entry_points:
     - bakta = bakta.main:main
     - bakta_proteins = bakta.proteins:main
     - bakta_db = bakta.db:main
     - bakta_plot = bakta.plot:main
+    - bakta_io = bakta.json_io:main
   run_exports:
     - {{ pin_subpackage('bakta', max_pin='x.x') }}
 
 requirements:
   host:
-    - python >=3.8, <3.11
+    - python >=3.9,<3.12
     - pip
   run:
-    - python >=3.8, <3.11
+    - python >=3.9,<3.12
     - biopython >=1.78
     - xopen >=1.5.0
     - requests >=2.25.1
     - alive-progress ==3.0.1
     - pyyaml >=6.0
-    - pyrodigal >=3.1.0
+    - pyrodigal >=3.5.0
     - trnascan-se >=2.0.11
     - aragorn >=1.2.41
     - infernal >=1.1.4
     - piler-cr
-    - pyhmmer >=0.10.4
-    - diamond ==2.1.8
+    - pyhmmer >=0.10.15
+    - diamond >=2.1.10
     - blast >=2.14.0
-    - ncbi-amrfinderplus >=3.11.26
-    - circos >=0.69.8
+    - ncbi-amrfinderplus >=4.0.3
+    - pycirclize >=1.7.0
 
 test:
   import:
     - Bio.SeqIO
     - xopen.xopen
-    - pyrodigal
     - requests
     - alive_progress
+    - pyyaml
+    - pyrodigal
+    - pyhmmer
+    - pycirclize
   commands:
     - bakta --help
 
 about:
   home: https://github.com/oschwengers/bakta
-  license: GPLv3
-  license_family: GPL
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
   summary: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
   dev_url: https://github.com/oschwengers/bakta
diff --git a/recipes/bam2plot/meta.yaml b/recipes/bam2plot/meta.yaml
new file mode 100644
index 0000000000000..d11123a8715d4
--- /dev/null
+++ b/recipes/bam2plot/meta.yaml
@@ -0,0 +1,48 @@
+{% set name = "bam2plot" %}
+{% set version = "0.3.6" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz
+  sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541
+
+build:
+  entry_points:
+    - bam2plot=bam2plot.main:cli
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('bam2plot', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - setuptools
+  run:
+    - python >=3.10
+    - pysam >=0.22.0
+    - seaborn >=0.13.2
+    - polars >=0.20.15
+    - mappy >=2.28
+    - pyfastx
+    - pyarrow
+    - mosdepth
+
+test:
+  imports:
+    - bam2plot
+  commands:
+    - bam2plot from_bam --help
+    - bam2plot from_reads --help
+    - bam2plot guci --help
+
+about:
+  home: https://github.com/willros/bam2plot
+  summary: Plot of coverage from bam file
+  license: GPL-3.0-only
+  license_file: LICENSE
diff --git a/recipes/bayestyper/0001-CMakeLists.patch b/recipes/bayestyper/0001-CMakeLists.patch
new file mode 100644
index 0000000000000..6e80f38569139
--- /dev/null
+++ b/recipes/bayestyper/0001-CMakeLists.patch
@@ -0,0 +1,45 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6bc8406..3a9a766 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -42,9 +42,39 @@ else(${BUILD_STATIC} EQUAL 0)
+ endif(${BUILD_STATIC} EQUAL 0)
+ 
+ 
+-FIND_PACKAGE(Boost COMPONENTS iostreams program_options system filesystem serialization REQUIRED)
++# When user specifies boost paths to use, we need to disable searching from the
++# environment and from using cmake's internal boost variables.
++if (BOOST_ROOT OR BOOST_INCLUDEDIR OR BOOST_LIBRARYDIR OR DEFINED ENV{BOOST_ROOT} OR DEFINED ENV{BOOST_INCLUDEDIR} OR DEFINED ENV{BOOST_LIBRARYDIR})
++  # Don't search for system include dirs for boost
++  set(Boost_NO_SYSTEM_PATHS ON)
++  # Disable excessive warning messages when using multiple boost versions
++  set(Boost_NO_WARN_NEW_VERSION ON)
++endif()
++
++# Use the OLD way of looking for Boost
++# The NEW way only respects BOOST_ROOT, not these more-specific variables.
++if (BOOST_INCLUDEDIR OR BOOST_LIBRARYDIR OR DEFINED ENV{BOOST_INCLUDEDIR} OR DEFINED ENV{BOOST_LIBRARYDIR})
++  # Ignore cmake boost variables
++  set(Boost_NO_BOOST_CMAKE ON)
++endif()
++
++set( Boost_USE_STATIC_LIBS OFF )   
++set( Boost_USE_MULTITHREADED TRUE )
++set( Boost_DEBUG ON )
++
++find_package(Boost 1.71.0 COMPONENTS iostreams program_options system filesystem serialization REQUIRED)
+ message(STATUS ${Boost_LIBRARIES})
+ 
++if(Boost_FOUND)
++        include_directories(${Boost_INCLUDE_DIRS})
++        LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
++endif()
++
++MESSAGE("Boost configuration results:")
++MESSAGE("  Boost_INCLUDE_DIRS: ${Boost_INCLUDE_DIR}")
++MESSAGE("  Boost_LIBRARY_DIRS: ${Boost_LIBRARY_DIRS}")
++MESSAGE("  Boost_LIBRARIES: ${Boost_LIBRARIES}")
++
+ add_subdirectory(${CMAKE_SOURCE_DIR}/external/kmc_api)
+ add_subdirectory(${CMAKE_SOURCE_DIR}/src/vcf++)
+ add_subdirectory(${CMAKE_SOURCE_DIR}/src/kmerBloom)
diff --git a/recipes/bayestyper/bayestyper.patch b/recipes/bayestyper/bayestyper.patch
new file mode 100644
index 0000000000000..b7355e3da4a50
--- /dev/null
+++ b/recipes/bayestyper/bayestyper.patch
@@ -0,0 +1,28 @@
+diff --git i/include/vcf++/VcfFile.hpp w/include/vcf++/VcfFile.hpp
+index 4a2f69e..aaf49be 100644
+--- i/include/vcf++/VcfFile.hpp
++++ w/include/vcf++/VcfFile.hpp
+@@ -35,8 +35,8 @@ THE SOFTWARE.
+ #include <string>
+ #include <unordered_set>
+ 
+-#include "boost/iostreams/filtering_stream.hpp"
+-#include "boost/iostreams/filter/gzip.hpp"
++#include <boost/iostreams/filtering_stream.hpp>
++#include <boost/iostreams/filter/gzip.hpp>
+ 
+ #include "Variant.hpp"
+ #include "VcfMetaData.hpp"
+diff --git i/src/vcf++/CMakeLists.txt w/src/vcf++/CMakeLists.txt
+index c8a6142..beddd90 100755
+--- i/src/vcf++/CMakeLists.txt
++++ w/src/vcf++/CMakeLists.txt
+@@ -3,6 +3,8 @@ project(vcf++)
+ SET(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib)
+ 
+ include_directories(${CMAKE_SOURCE_DIR}/include/vcf++ ${Boost_INCLUDE_DIRS})
++message(STATUS "======= DEBUG Boost_INCLUDE_DIRS: " ${Boost_INCLUDE_DIRS})
++message(STATUS "======= DEBUG Boost_LIB_DIRS: " ${Boost_LIB_DIRS})
+ link_directories(${Boost_LIB_DIRS})
+ 
+ add_library(${PROJECT_NAME} VcfFile.cpp Variant.cpp Allele.cpp VcfMetaData.cpp AttributeSet.cpp Sample.cpp Utils.cpp Attribute.cpp JoiningString.cpp Stats.cpp AttributeFilter.cpp SampleAlleleAttributeFilter.cpp FastaReader.cpp FastaRecord.cpp Auxiliaries.cpp Trio.cpp Contig.cpp Regions.cpp)
diff --git a/recipes/bayestyper/build.sh b/recipes/bayestyper/build.sh
index ceeea5f2b87b9..f3f8e30d6657b 100644
--- a/recipes/bayestyper/build.sh
+++ b/recipes/bayestyper/build.sh
@@ -1,10 +1,28 @@
 #!/bin/bash
 
-mkdir build && cd build
-cmake ..
-make
-
 mkdir -p ${PREFIX}/bin
 
-cp ../bin/bayesTyper ${PREFIX}/bin
-cp ../bin/bayesTyperTools ${PREFIX}/bin
+export INCLUDES="-I${PREFIX}/include"
+export CPLUS_INCLUDE_PATH="${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+	export CXXFLAGS="${CXXFLAGS} -Wno-dev -Wno-deprecated-declarations -Wno-unused-command-line-argument"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	-DBOOST_ROOT="${PREFIX}" \
+	"${CONFIG_ARGS}"
+cmake --build build -j "${CPU_COUNT}"
+
+chmod 0755 bin/*
+mv bin/bayesTyper ${PREFIX}/bin
+mv bin/bayesTyperTools ${PREFIX}/bin
diff --git a/recipes/bayestyper/kmer_defs.patch b/recipes/bayestyper/kmer_defs.patch
new file mode 100644
index 0000000000000..eeeb9de5cfb13
--- /dev/null
+++ b/recipes/bayestyper/kmer_defs.patch
@@ -0,0 +1,18 @@
+diff --git a/external/kmc_api/kmer_defs.h b/external/kmc_api/kmer_defs.h
+index 8328822..89ae5e0 100644
+--- a/external/kmc_api/kmer_defs.h
++++ b/external/kmc_api/kmer_defs.h
+@@ -33,7 +33,12 @@
+ 
+ 
+ 	#include <stdio.h>
+-	#include <ext/algorithm>
++    #if defined(__clang__)
++        #include <algorithm>
++    #elif defined(__GNUC__)
++        #include <ext/algorithm>
++        using __gnu_cxx::copy_n;
++    #endif
+ 	#include <iostream>
+ 	using namespace std;
+ 
diff --git a/recipes/bayestyper/meta.yaml b/recipes/bayestyper/meta.yaml
index 1542f4b25824f..88a72501f760c 100644
--- a/recipes/bayestyper/meta.yaml
+++ b/recipes/bayestyper/meta.yaml
@@ -1,16 +1,23 @@
+{% set name = "bayestyper" %}
 {% set version = "1.5" %}
 
 package:
-  name: bayestyper
+  name: {{ name }}
   version: {{ version }}
 
-build:
-  number: 1
-  skip: True # [osx]
-
 source:
   url: https://github.com/bioinformatics-centre/BayesTyper/archive/v{{ version }}.tar.gz
   sha256: 917cd1b1ca7b5cfb6b8327138515ca1ad70878f0c4e8df393fddcbe42f281e14
+  patches:
+    - 0001-CMakeLists.patch
+    - bayestyper.patch
+    - kmer_defs.patch  # [osx]
+    - stdafx.patch  # [osx]
+
+build:
+  number: 3
+  run_exports:
+    - {{ pin_subpackage('bayestyper', max_pin="x") }}
 
 requirements:
   build:
@@ -21,15 +28,25 @@ requirements:
     - zlib
     - boost-cpp
   run:
-    - zlib
     - boost-cpp
 
 about:
-  home: https://github.com/bioinformatics-centre/BayesTyper
+  home: "https://github.com/bioinformatics-centre/BayesTyper"
   license: MIT
-  summary: A method for variant graph genotyping based on exact alignment of k-mers
+  license_family: MIT
+  summary: "A method for variant graph genotyping based on exact alignment of k-mers."
+  dev_url: "https://github.com/bioinformatics-centre/BayesTyper"
+  doc_url: "https://github.com/bioinformatics-centre/BayesTyper/blob/v{{ version }}/README.md"
 
 test:
   commands:
-    - bayesTyper | grep BayesTyper
-    - bayesTyperTools | grep BayesTyperTools
+    - bayesTyper | grep "BayesTyper"
+    - bayesTyperTools | grep "BayesTyperTools"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - biotools:bayestyper
+    - doi:10.1038/s41588-018-0145-5
diff --git a/recipes/bayestyper/stdafx.patch b/recipes/bayestyper/stdafx.patch
new file mode 100644
index 0000000000000..629aa59278f21
--- /dev/null
+++ b/recipes/bayestyper/stdafx.patch
@@ -0,0 +1,10 @@
+diff --git a/external/kmc_api/stdafx.h b/external/kmc_api/stdafx.h
+index 5b8d29d..3610d6c 100644
+--- a/external/kmc_api/stdafx.h
++++ b/external/kmc_api/stdafx.h
+@@ -1,4 +1,4 @@
+ #include <stdio.h>
+-#include <ext/algorithm>
++#include <algorithm>
+ #include <iostream>
+ using namespace std;
diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml
index a69855905a211..3bb585ba8e733 100644
--- a/recipes/bbmap/meta.yaml
+++ b/recipes/bbmap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "BBMap" %}
-{% set version = "39.10" %}
-{% set sha256 = "996aff05765ba5e64547f8a34c56da396ce7b18db96ffe7f1076f2d2f49c6148" %}
+{% set version = "39.11" %}
+{% set sha256 = "bcb80b109757a638d6c767b7ba785fde5111437f7025e0a93dce587cdfaa2795" %}
 
 package:
   name: {{ name|lower }}
@@ -19,13 +19,13 @@ requirements:
   build:
     - {{ compiler('c') }}
   host:
-    - openjdk >=7.0
+    - openjdk >=11.0.1
     - pbzip2
     - bzip2
     - samtools
     - patchelf  # [osx]
   run:
-    - openjdk >=7.0
+    - openjdk >=11.0.1
     - samtools
 
 test:
diff --git a/recipes/beagle/meta.yaml b/recipes/beagle/meta.yaml
index 1f6614412ea25..881555f83e5bc 100644
--- a/recipes/beagle/meta.yaml
+++ b/recipes/beagle/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "beagle" %}
-{% set version = "5.4_27May24.118" %}
-{% set sha256 = "3b8f0b1dd1f56cccf0dbfd6a53b091829e69e3d693834b814af203be911b0009" %}
+{% set version = "5.4_29Oct24.c8e" %}
+{% set sha256 = "938f0b1ab12385e0686790cef52d7b9491c96c0c1837af5c0d62c9a6576a8956" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://faculty.washington.edu/browning/beagle/beagle.27May24.118.jar
+  url: https://faculty.washington.edu/browning/beagle/beagle.29Oct24.c8e.jar
   sha256: {{ sha256 }}
 
 build:
diff --git a/recipes/bftools/meta.yaml b/recipes/bftools/meta.yaml
index 5d716cca12527..cba3893650909 100644
--- a/recipes/bftools/meta.yaml
+++ b/recipes/bftools/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "6.7.0" %}
-{% set sha256 = "7c013b23529d61280e04c3dd312401d7b71fb5892f5e7870f87d37bab5f3988f" %}
+{% set version = "8.0.0" %}
+{% set sha256 = "46c7c53595a2491adc76dc3b7d4089689e5c3817a9bb549a632d08ef137438e7" %}
 
 
 package:
@@ -7,12 +7,14 @@ package:
   version: '{{version}}'
 
 source:
-  url: "http://downloads.openmicroscopy.org/latest/bio-formats{{version}}/artifacts/bftools.zip"
+  url: https://downloads.openmicroscopy.org/bio-formats/{{ version }}/artifacts/bftools.zip
   sha256: '{{sha256}}'
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('bftools', max_pin="x.x") }}
 
 requirements:
   run:
@@ -21,6 +23,8 @@ requirements:
 test:
   commands:
     - bfconvert -version
+    - domainlist
+    - formatlist
     
 about:
   home: https://docs.openmicroscopy.org/bio-formats/{{version}}/users/comlinetools/index.html
diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml
index 89cd9389aeb41..5c3c2a0abef24 100644
--- a/recipes/bigtools/meta.yaml
+++ b/recipes/bigtools/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.5.2" %}
+{% set version = "0.5.3" %}
 
 package:
   name: bigtools
@@ -11,7 +11,7 @@ build:
 
 source:
   url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: "f5b50a4d717f93242541673bbdeb1fa67b8b9175b0f72d8ff5c52f1563b5cd4e"
+  sha256: "092100e9f32fa6b5a6414703d135c333aa6959bf3aa2d608ec54aacab92eb7fb"
 
 requirements:
   build:
diff --git a/recipes/bindash/build.sh b/recipes/bindash/build.sh
index 83f5dedf13ec7..475c433fa14ce 100644
--- a/recipes/bindash/build.sh
+++ b/recipes/bindash/build.sh
@@ -1,7 +1,25 @@
 #!/bin/bash
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 mkdir release && pushd release
-cmake -DCMAKE_BUILD_TYPE=Release ..
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S .. -B . -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include" \
+	"${CONFIG_ARGS}"
+
 make VERBOSE=1 -j ${CPU_COUNT}
+
 install -d $PREFIX/bin
 install bindash $PREFIX/bin
 popd
diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml
index 1b5105f60619d..fbfd4d1282bb2 100644
--- a/recipes/bindash/meta.yaml
+++ b/recipes/bindash/meta.yaml
@@ -10,8 +10,7 @@ source:
   sha256: 6e4bf36fd04195ed0738ea8bf835eca1e400b5ce6eef3902bdf0673955d15166
 
 build:
-  skip: True  # [osx]
-  number: 2
+  number: 3
   run_exports:
       - {{ pin_subpackage('bindash', max_pin="x") }}
 
@@ -25,7 +24,6 @@ requirements:
     - libgomp  # [linux]
     - llvm-openmp  # [osx]
   run:
-    - zlib
     - libgomp  # [linux]
     - llvm-openmp  # [osx]
 
@@ -34,16 +32,18 @@ test:
     - bindash --help 2>&1 | grep sketch
 
 about:
-  home: https://github.com/zhaoxiaofei/bindash
-  license: Apache-2.0
+  home: "https://github.com/zhaoxiaofei/bindash"
+  license: "Apache-2.0"
   license_family: APACHE
   license_file: LICENSE
   summary: "Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop."
-  dev_url: https://github.com/zhaoxiaofei/bindash
+  dev_url: "https://github.com/zhaoxiaofei/bindash"
+  doc_url: "https://github.com/jianshu93/bindash/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - doi:10.1093/bioinformatics/bty651
     - doi:10.1101/2024.03.13.584875
diff --git a/recipes/biobambam/build.sh b/recipes/biobambam/build.sh
index 272f469dffb76..53b04f87a7e43 100644
--- a/recipes/biobambam/build.sh
+++ b/recipes/biobambam/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
 set -eu
-./configure --prefix=${PREFIX}
+
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" \
+	--with-libmaus2 --with-xerces-c --with-gmp \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 make install
diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml
index 482c9c1b272d1..69ad250229d2e 100644
--- a/recipes/biobambam/meta.yaml
+++ b/recipes/biobambam/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "biobambam" %}
-{% set version = "2.0.183" %}
-{% set datestamp = "20210802180148" %}
-{% set sha256hash = "8712ceac509c389111b01dc3429f673dc0f8b77cb2bc48a1ebcf17f6888b2945" %}
+{% set version = "2.0.185" %}
+{% set datestamp = "20221211202123" %}
+{% set sha256 = "e405421e869ac7220c3a7e5da0d24a3c7b4c7b1807e044a439fe68efc88a1f2a" %}
 
 package:
   name: {{ name }}
@@ -9,10 +9,10 @@ package:
 
 source:
   url: https://gitlab.com/german.tischler/biobambam2/-/archive/{{ version }}-release-{{ datestamp }}/biobambam2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
+  sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
@@ -21,19 +21,33 @@ requirements:
   build:
     - make
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
-    - libmaus2 >=2.0.810
+    - libmaus2 >=2.0.813
+    - gmp
+    - xerces-c
+    - zlib
+  run:
+    - libmaus2 >=2.0.813
 
 test:
   commands:
     - bamsormadup --help
     - bamtofastq --help
+
 about:
   home: https://gitlab.com/german.tischler/biobambam2
-  license: GPLv3
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: GPLv3
-  summary: Tools for early stage alignment file processing
+  summary: "Tools for early stage alignment file processing."
+  dev_url: https://gitlab.com/german.tischler/biobambam2
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64
+  identifiers:
+    - biotools:biobambam
diff --git a/recipes/biobb_amber/meta.yaml b/recipes/biobb_amber/meta.yaml
index f9ff0871709c2..6405adf90b517 100644
--- a/recipes/biobb_amber/meta.yaml
+++ b/recipes/biobb_amber/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_amber" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.3" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 11ce0b1a7f7ec912136d31a46bffdc1c85b831686a51b8e9fe5e35cac611f09c
+  sha256: 78dfd40a00c729549fee6f31f96a70dc93e532bd44f267e976cd85e7191e0835
 
 build:
   number: 0
@@ -18,12 +18,12 @@ build:
 
 requirements:
   host:
-    - python >=3.8,<3.11
+    - python >=3.9,<3.11
     - setuptools
     - biobb_common ==5.0.0
     - ambertools ==22.5.0
   run:
-    - python >=3.8,<3.11
+    - python >=3.9,<3.11
     - biobb_common ==5.0.0
     - ambertools ==22.5.0
 
diff --git a/recipes/biobb_analysis/meta.yaml b/recipes/biobb_analysis/meta.yaml
index c96372e9fe1d3..fa8e94b8e8bcf 100644
--- a/recipes/biobb_analysis/meta.yaml
+++ b/recipes/biobb_analysis/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_analysis" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.1" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 8bf930ecd4cff6b3ad3a97a92599913225295725056c5369bd0e7f536bb4008d
+  sha256: 2ecb3df99f6ae37ed68c9849b1224245e526fe66074db0b21957a49128b20ab3
 
 build:
   number: 0
diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml
index 17755ee4702be..9bf342947e649 100644
--- a/recipes/biobb_chemistry/meta.yaml
+++ b/recipes/biobb_chemistry/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_chemistry" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.3" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: c4f3926a8a219410afa1e79feb84b71a2d1bb70bc0700039d52726853113b0e8
+  sha256: cc89a00439b85b71bd37980cbfe00a2dbbf201613298bac731cd3830c6fb4f6e
 
 build:
   number: 0
@@ -22,13 +22,13 @@ requirements:
     - setuptools
     - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools >=22.5
+    - ambertools ==22.5
     - acpype >=2023.10.27
   run:
     - python >=3.9
     - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools >=22.5
+    - ambertools ==22.5
     - acpype >=2023.10.27
 test:
   imports:
diff --git a/recipes/biobb_dna/meta.yaml b/recipes/biobb_dna/meta.yaml
index 7c781adfcf6f3..c22791c934413 100644
--- a/recipes/biobb_dna/meta.yaml
+++ b/recipes/biobb_dna/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_dna" %}
-{% set version = "4.2.4" %}
+{% set version = "5.0.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: f9343a8ec9ca8b0c9c764657979daf2b06b58ee242d30c2f8679416467d5ada4
+  sha256: 9a6c777bcb328d803326cce64b9fa9998b7b46da4fb9ac447a86d9b08e21fb1a
 
 build:
   number: 0
@@ -18,16 +18,16 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - pandas >=1.3.0
     - scikit-learn >=0.24.2
     - curves ==3.0.2
 
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - pandas >=1.3.0
     - scikit-learn >=0.24.2
     - curves ==3.0.2
@@ -51,7 +51,7 @@ about:
     \ [![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_dna)\
     \ [![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_dna)\
     \ [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n\
-    \n# biobb_dna\n\n### Introduction\nBiobb_dna is a package composed of different analyses for nucleic acid trajectories. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ 
+    \n# biobb_dna\n\n### Introduction\nBiobb_dna is a package composed of different analyses for nucleic acid trajectories. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](https://mmb.irbbarcelona.org) at the [BSC](https://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
     \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
diff --git a/recipes/biobb_flexdyn/meta.yaml b/recipes/biobb_flexdyn/meta.yaml
index 4dbcdc7bf02be..77e2a0e97abd7 100644
--- a/recipes/biobb_flexdyn/meta.yaml
+++ b/recipes/biobb_flexdyn/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_flexdyn" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,28 +7,31 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 5cfe112fb35a86fff4d452efb966fa18757bad4ea1f4017b226e765a8e6f776e 
+  sha256: ae30f8f64e851b1e7546c7c212a079839d1e26cf01fb9d4c88bb0eb1f29f6203 
 
 build:
-  number: 0
+  number: 1
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  entry_points:
+    - concoord_dist = biobb_flexdyn.flexdyn.concoord_dist:main
+    - concoord_disco = biobb_flexdyn.flexdyn.concoord_disco:main
+    - imod_imode = biobb_flexdyn.flexdyn.imod_imode:main
+    - imod_imove = biobb_flexdyn.flexdyn.imod_imove:main
+    - imod_imc = biobb_flexdyn.flexdyn.imod_imc:main
+    - nolb_nma = biobb_flexdyn.flexdyn.nolb_nma:main
+    - prody_anm = biobb_flexdyn.flexdyn.prody_anm:main
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   host:
-    - python >=3.8
-    - setuptools
-    - biobb_common ==4.2.0
-    - concoord
-    - prody
-    - imods
-    - nolb
-
+    - python >=3.9,<3.12
+    - pip
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9,<3.12
+    - biobb_common =={{ version }}
+    - scipy >=1.13.0,<1.14.0
     - concoord
     - prody
     - imods
@@ -41,9 +44,11 @@ test:
 
 about:
   home: https://github.com/bioexcel/biobb_flexdyn
-  license: Apache Software License
+  license: Apache-2.0
   license_family: APACHE
-  summary: Biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins. 
+  license_file: LICENSE
+  dev_url: https://github.com/bioexcel/biobb_flexdyn
+  summary: "Biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins."
   description: "# biobb_flexdyn\n\n### Introduction\nBiobb_flexdyn allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ 
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](https://mmb.irbbarcelona.org) at the [BSC](https://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
diff --git a/recipes/biobb_flexserv/meta.yaml b/recipes/biobb_flexserv/meta.yaml
index a766b6d8ff5cd..285ea0dba28b9 100644
--- a/recipes/biobb_flexserv/meta.yaml
+++ b/recipes/biobb_flexserv/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_flexserv" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 62b3ecb6dacca9cd0496dec9e6ebe5e43e4d0e3fcfd8b122a20dda940d49162e 
+  sha256: 90c2b03541d144026f2f6866e8fd166b0440f73a7c34c83f49b81dd826374edc 
 
 build:
   number: 0
diff --git a/recipes/biobb_godmd/meta.yaml b/recipes/biobb_godmd/meta.yaml
index acf1ed0f9ff70..d2e69fa755408 100644
--- a/recipes/biobb_godmd/meta.yaml
+++ b/recipes/biobb_godmd/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_godmd" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: f697f96f216ce439e058d46842a2507ada30221d7048628fb83676ebf5806c50
+  sha256: edb62b0ca1dc5b8ee89f33cd44e8d2aa6e53ba6fd378f6c193aa6adf603fc282
 
 build:
   number: 0
diff --git a/recipes/biobb_mem/meta.yaml b/recipes/biobb_mem/meta.yaml
new file mode 100644
index 0000000000000..7185fd8b7c226
--- /dev/null
+++ b/recipes/biobb_mem/meta.yaml
@@ -0,0 +1,60 @@
+{% set name = "biobb_mem" %}
+{% set version = "5.0.1" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: bb82d828a3be20ca577162aca4ae9a7073598a08f181e079277c7f13f1e1950c
+
+build:
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.9
+    - setuptools
+    - biobb_common ==5.0.0
+    - lipyphilic ==0.10.0
+    - ambertools >=22.5
+    - gromacs
+    - hole2
+  run:
+    - python >=3.9
+    - biobb_common ==5.0.0
+    - lipyphilic ==0.10.0
+    - ambertools >=22.5
+    - gromacs
+    - hole2
+test:
+  imports:
+    - biobb_mem
+    - biobb_mem.mdanalysis_biobb
+    - biobb_mem.lipyphilic_biobb
+    - biobb_mem.ambertools
+
+about:
+  home: https://github.com/bioexcel/biobb_mem
+  license: Apache Software License
+  license_family: APACHE
+  license_file: ''
+  summary: Biobb_mem is the Biobb module for membrane structure analysis.
+  description: "# biobb_mem\n\n### Introduction\nBiobb_mem is the Biobb module for membrane structure analysis.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
+    \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).\n\
+    \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
+    \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
+    Licensed under the\n\
+    [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\
+    \n\
+    ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
+  doc_url: ''
+  dev_url: ''
+
+extra:
+  recipe-maintainers: ''
diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml
index 1211834359a86..d1fd47ce9461f 100644
--- a/recipes/bioblend/meta.yaml
+++ b/recipes/bioblend/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "bioblend" %}
-{% set version = "1.3.0" %}
+{% set version = "1.4.0" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz
-  sha256: e72318e10c29a81c16281d25aaac00989a07fc2900be7479137964232cc4a507
+  sha256: 175d49d288e27d132ff59c870551c87cd95d7747be55ab94807c563291a3fa1d
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - requests >=2.20.0
@@ -66,7 +67,7 @@ test:
 about:
   home: "https://github.com/galaxyproject/bioblend"
   license: MIT
-  summary: 'A Python library for interacting with the Galaxy API'
+  summary: 'A Python library for interacting with the Galaxy API.'
   license_family: MIT
   license_file: LICENSE
   doc_url: "https://bioblend.readthedocs.org/"
diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
index ffb100d77defe..6c446755cddb2 100644
--- a/recipes/bioconda-utils/meta.yaml
+++ b/recipes/bioconda-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.4.0" %}
-{% set sha256 = "ec1e84a87bfc60e2a07116e0a6dbb3ed44c5bbaa39aa152d2d1c43ff1b990603" %}
+{% set version = "3.4.1" %}
+{% set sha256 = "c68f5472d959ce8a01cad58896a00e02ab2ee805007f75a34d138b88f21868b8" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml
index 0a5192523653c..9eb6587182a64 100644
--- a/recipes/bioconductor-bambu/meta.yaml
+++ b/recipes/bioconductor-bambu/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 900e0e67c251f12989154113c54d2b32
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -74,3 +74,6 @@ about:
   description: 'bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.'
   license_file: LICENSE
 
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml
index 99dbefecd9faf..ffe275e39ca5f 100644
--- a/recipes/bioconductor-protgenerics/meta.yaml
+++ b/recipes/bioconductor-protgenerics/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "1.34.0" %}
+{% set version = "1.38.0" %}
 {% set name = "ProtGenerics" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
@@ -11,7 +11,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 5d55c00588169aa089bb457e2d94669a
+  md5: 7e7211a9fa758ca6f1b701c86e892895
 build:
   number: 0
   rpaths:
diff --git a/recipes/bioutils/meta.yaml b/recipes/bioutils/meta.yaml
index 284dd3259c795..bb9c4416b8f04 100644
--- a/recipes/bioutils/meta.yaml
+++ b/recipes/bioutils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "bioutils" %}
-{% set version = "0.6.0" %}
+{% set version = "0.6.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 6487a5565bb798b88202d1f5aa3a4ee6b229151e86dc8ff77cbf0e3b4f4dad4b
+  sha256: 6ad7a9b6da73beea798a935499339d8b60a434edc37dfc803474d2e93e0e64aa
 
 build:
   number: 0
diff --git a/recipes/blaze2/meta.yaml b/recipes/blaze2/meta.yaml
index 098c5e8149ec3..9666e8318c9c3 100644
--- a/recipes/blaze2/meta.yaml
+++ b/recipes/blaze2/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "BLAZE2" %}
-{% set version = "2.5.0" %}
+{% set version = "2.5.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/shimlab/BLAZE/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: f47175997742562add1deb9524e468b6709e40c92f74165a1a0fe1897b2919fc
+  sha256: 3f48c94d061506c4ec4e2a029396d36ffbd1e1e0746d7d3c201f7238b36c10aa
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3
     - pip
+    - setuptools
   run:
     - python >=3
     - fast-edit-distance ==1.2.1
diff --git a/recipes/breakfast/meta.yaml b/recipes/breakfast/meta.yaml
index cf7699d277b38..ae6d83de4c28e 100644
--- a/recipes/breakfast/meta.yaml
+++ b/recipes/breakfast/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "breakfast" %}
-{% set version = "0.4.3" %}
+{% set version = "0.4.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,43 +7,44 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/breakfast-{{ version }}.tar.gz
-  sha256: a241e0d4891c62635f1b99559271fb4b7777ffa60ef67e25be579d6750c01b9c
+  sha256: 5dd370d4d6d92d7b161acc5356b3b6c7f454d9c0665a8abac38e5f6c012d3eee
 
 build:
   entry_points:
     - breakfast = breakfast.console:main
+  run_exports:
+    - {{ pin_subpackage('breakfast', max_pin="x.x") }}
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
 
 requirements:
   host:
     - pip
-    - poetry
-    - python >=3.6,<3.11
+    - poetry-core
+    - python >=3.11,<3.13
   run:
-    - click >=8.1.3,<9.0.0
-    - networkx >=2.8,<3.0
-    - numpy >=1.22.3,<2.0.0
-    - pandas >=1.4.2,<2.0.0
+    - click >=8.1.7,<9.0.0
+    - networkx >=3.4.2,<4.0.0
+    - numpy >=2.1.3,<3.0.0
+    - pandas >=2.2.3,<3.0.0
     - python >=3.9,<3.11
-    - scikit-learn >=1.0.2,<2.0.0
-    - scipy >=1.8.0,<2.0.0
+    - scikit-learn >=1.5.2,<2.0.0
+    - scipy >=1.14.1,<2.0.0
 
 test:
   imports:
     - breakfast
   commands:
-    - pip check
     - breakfast --help
-  requires:
-    - pip
 
 about:
   home: https://github.com/rki-mf1/breakfast
-  summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs'
+  summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs.'
   license: MIT
+  license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/rki-mf1/breakfast
 
 extra:
   recipe-maintainers:
diff --git a/recipes/bubblegun/meta.yaml b/recipes/bubblegun/meta.yaml
new file mode 100644
index 0000000000000..a97e641474c57
--- /dev/null
+++ b/recipes/bubblegun/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "BubbleGun" %}
+{% set version = "1.1.9" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: "https://github.com/fawaz-dabbaghieh/bubble_gun/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: 005d61a1e5774dfec810e612c1b4c5ce6c8d15f80d131237590ef71f62704c94
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - BubbleGun=BubbleGun.main:main
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_compatible('BubbleGun', max_pin="x") }}
+    
+requirements:
+  host:
+    - python >=3.6
+    - pip
+    - setuptools
+  run:
+    - python >=3.6
+
+test:
+  commands:
+    - BubbleGun -h
+
+about:
+  home: "https://github.com/fawaz-dabbaghieh/bubble_gun"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: 'BubbleGun is a tool for detecting bubbles and superbubbles in GFA graphs, and reports them and their nested structures.'
+  doc_url: "https://github.com/fawaz-dabbaghieh/bubble_gun/blob/v{{ version }}/README.md"
+  dev_url: "https://github.com/fawaz-dabbaghieh"
diff --git a/recipes/buscolite/meta.yaml b/recipes/buscolite/meta.yaml
index 7f4e086d17901..847230300e3d8 100644
--- a/recipes/buscolite/meta.yaml
+++ b/recipes/buscolite/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "buscolite" %}
-{% set version = "23.10.26" %}
+{% set version = "24.11.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,14 +7,14 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/buscolite-{{ version }}.tar.gz
-  sha256: c641dc6c702fa198fd6fa661b756aedde4468ea591c8c64f8b8bd9c8a865b72d
+  sha256: f7ef8151b2dd16848ec8bf7e14658a81db3fbe7898e6377a2bb0553cf065f47b
 
 build:
   number: 0
   noarch: python
   entry_points:
     - buscolite = buscolite.__main__:main
-  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   run_exports:
     - {{ pin_subpackage('buscolite', max_pin="x") }}
 
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - hatchling
   run:
     - python >=3.6
     - augustus >=3.5.0
@@ -42,6 +43,7 @@ about:
   license: BSD-2-Clause
   license_family: BSD
   license_file: LICENSE.md
+  dev_url: https://github.com/nextgenusfs/buscolite
 
 extra:
   recipe-maintainers:
diff --git a/recipes/cadd-scripts/meta.yaml b/recipes/cadd-scripts/meta.yaml
index a507661a3f9dc..6c6356301556d 100644
--- a/recipes/cadd-scripts/meta.yaml
+++ b/recipes/cadd-scripts/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.7.1" %}
-{% set sha256 = "c5db00dc26a585cc70500cf535865a4d9e7765db60a71edf1d267af32ae974e4" %}
+{% set version = "1.7.2" %}
+{% set sha256 = "fb2d1deeffe8e1ef5abb042b0bce48f864878b9de80d2a27b16d5a8389e25e20" %}
 
 package:
   name: cadd-scripts
diff --git a/recipes/cat/build.sh b/recipes/cat/build.sh
index 5f93e3be2391b..712695498a8af 100644
--- a/recipes/cat/build.sh
+++ b/recipes/cat/build.sh
@@ -6,7 +6,6 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
 
-
 mv CAT_pack $outdir
 
-ln -s $outdir/CAT_pack/CAT $PREFIX/bin
+ln -s $outdir/CAT_pack/CAT_pack $PREFIX/bin
diff --git a/recipes/cat/meta.yaml b/recipes/cat/meta.yaml
index 81e3fc1cbdc4b..8b24d8e78fd01 100644
--- a/recipes/cat/meta.yaml
+++ b/recipes/cat/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "5.3" %}
-{% set sha256 = "2893ee18b0d5b24a291edd7d8ca1738d40ea189d18ba0fb7aad3e38973a787e7" %}
+{% set version = "6.0.1" %}
+{% set sha256 = "189707d8a0f6fa3ce50ed5fd5e9955b97119b514d38a190d393a701ec652f8fc" %}
 
 package:
   name: cat
   version: {{ version }}
 
 source:
-  url: https://github.com/dutilh/CAT/archive/v{{ version }}.tar.gz
+  url: https://github.com/MGXlab/CAT_pack/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }} 
 
 build:
@@ -14,19 +14,22 @@ build:
   noarch: generic
   run_exports:
     - {{ pin_subpackage("cat", max_pin="x") }}
+
 requirements:
   run:
-    - python 3
+    - python >=3
     - diamond
     - prodigal
 
 test:
   commands:
-    - CAT prepare --help
+    - CAT_pack prepare -h
 
 about:
   summary: |
     CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
-  home: https://github.com/dutilh/CAT
+  home: https://github.com/MGXlab/CAT_pack
   license: MIT
+  license_family: MIT
   license_file: LICENSE.md
+  dev_url: https://github.com/MGXlab/CAT_pack
diff --git a/recipes/cazy_webscraper/meta.yaml b/recipes/cazy_webscraper/meta.yaml
index e46ee87c652f9..33cdc0413839c 100644
--- a/recipes/cazy_webscraper/meta.yaml
+++ b/recipes/cazy_webscraper/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "cazy_webscraper" %}
-{% set version = "2.3.0.3" %}
-{% set sha256 = "82af3a5c13c1f3254bcbc9967c85d38f085c88f18834fb5a84155d5f13e669d9" %}
+{% set version = "2.3.0.4" %}
+{% set sha256 = "4333de1d4f1742798281a2e55c24a2d10c54a708f1908bb31ac02adafbd06e90" %}
 
 package:
   name: {{ name|lower }}
@@ -13,7 +13,7 @@ source:
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   entry_points:
     - cazy_webscraper = cazy_webscraper.cazy_scraper:main
     - cw_get_genbank_seqs = cazy_webscraper.expand.genbank.sequences.get_genbank_sequences:main
@@ -32,6 +32,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - beautifulsoup4
@@ -55,12 +56,13 @@ test:
     - cazy_webscraper --help
 
 about:
-  home: "https://hobnobmancer.github.io/cazy_webscraper/"
+  home: "https://github.com/HobnobMancer/cazy_webscraper"
   dev_url: "https://github.com/HobnobMancer/cazy_webscraper"
   summary: "A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB."
   license: MIT
   license_family: MIT
   license_file: LICENSE
+  doc_url: "https://hobnobmancer.github.io/cazy_webscraper"
 
 extra:
   identifiers:
diff --git a/recipes/cd-hit/build.sh b/recipes/cd-hit/build.sh
index e1aab78924f19..87fadaf02c43c 100644
--- a/recipes/cd-hit/build.sh
+++ b/recipes/cd-hit/build.sh
@@ -1,26 +1,28 @@
-#!/bin/sh
+#!/bin/bash
 
-export CFLAGS="-I$PREFIX/include"
-export CPPFLAGS="-I$PREFIX/include"
-export CXXFLAGS="-I$PREFIX/include"
-export LDFLAGS="-L$PREFIX/lib"
+mkdir -p $PREFIX/bin
+
+export CFLAGS="${CFLAGS} -O3"
+export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include"
+export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include"
+export LDFLAGS="${LDFLAGS} -L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
 sed -i.bak 's/^CC =$//g' Makefile
 sed -i.bak 's/^#LDFLAGS.*//g' Makefile
-
+rm -rf *.bak
 
 if [[ "$OSTYPE" == "darwin"* ]]; then
   #Lines below is commented out until fix provided for OPENMP support on OS X for this program
  
   CCFLAGS="$CCFLAGS -Wl,-rpath ${PREFIX}/lib -L${PREFIX}/lib -I${PREFIX}/include -fopenmp"
   sed -i.bak 's/CCFLAGS = -fopenmp/CCFLAGS += -fopenmp/g' Makefile
+  rm -rf *.bak
   LDFLAGS="$LDFLAGS -stdlib=libc++"
   
   make CC=$CXX openmp=no MAX_SEQ=1000000
 else
   make CC=$GXX MAX_SEQ=1000000
 fi
-
-mkdir -p $PREFIX/bin 
-make install PREFIX=$PREFIX/bin 
+ 
+make install PREFIX="$PREFIX/bin"
diff --git a/recipes/cd-hit/cd-hit.patch b/recipes/cd-hit/cd-hit.patch
new file mode 100644
index 0000000000000..29ac6a70fd2ec
--- /dev/null
+++ b/recipes/cd-hit/cd-hit.patch
@@ -0,0 +1,1093 @@
+diff --git a/FET.pl b/FET.pl
+index 6db320f..bb56529 100755
+--- a/FET.pl
++++ b/FET.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Storable;
+ use strict;
+diff --git a/cd-hit-2d-para.pl b/cd-hit-2d-para.pl
+index 3cab955..e0c43c7 100755
+--- a/cd-hit-2d-para.pl
++++ b/cd-hit-2d-para.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ # =============================================================================
+ # CD-HIT
+ # http://cd-hit.org/
+diff --git a/cd-hit-auxtools/cd-hit-dup-PE-out.pl b/cd-hit-auxtools/cd-hit-dup-PE-out.pl
+index bfe5af3..f035229 100755
+--- a/cd-hit-auxtools/cd-hit-dup-PE-out.pl
++++ b/cd-hit-auxtools/cd-hit-dup-PE-out.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my $script_name = $0;
+ my $script_dir = $0;
+diff --git a/cd-hit-clstr_2_blm8.pl b/cd-hit-clstr_2_blm8.pl
+index 42f1e57..cb75ffb 100755
+--- a/cd-hit-clstr_2_blm8.pl
++++ b/cd-hit-clstr_2_blm8.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ #
+ 
+ my $rep;
+@@ -23,7 +23,10 @@ while($ll=<>){
+       else              { 
+         push(@non_reps, $id);
+         my @lls = split(/\s+/, $ll);
+-        my ($a, $iden) = split(/\//, $lls[-1]);
++        # my ($a, $iden) = split(/\//, $lls[-1]); #### bug, with cd-hit-est-2d, there are +/- sign e.g. 10:1029:30:1042/+/97.35%
++        my @mms = split(/\//, $lls[-1]);
++        my $a = $mms[0];
++        my $iden = $mms[-1];
+         chop($iden); ### removing % sign
+         my ($qb, $qe, $sb, $se) = split(/:/, $a);
+         my $alnln = $qe-$qb+1;
+diff --git a/cd-hit-div.pl b/cd-hit-div.pl
+index e349394..db8d942 100755
+--- a/cd-hit-div.pl
++++ b/cd-hit-div.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #not like cd-hit-div, this script do not sort input
+ #or throw away seq
+diff --git a/cd-hit-para.pl b/cd-hit-para.pl
+index 33f1a1b..6ee3ca1 100755
+--- a/cd-hit-para.pl
++++ b/cd-hit-para.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ # =============================================================================
+ # CD-HIT
+ # http://cd-hit.org/
+diff --git a/clstr2tree.pl b/clstr2tree.pl
+index 73fd37a..56d9fe2 100755
+--- a/clstr2tree.pl
++++ b/clstr2tree.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ $clstr = shift;
+ $fr = shift; # for nr80.clstr $fr = 0.8
+diff --git a/clstr2txt.pl b/clstr2txt.pl
+index 902b083..127537e 100755
+--- a/clstr2txt.pl
++++ b/clstr2txt.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my $no = 0;
+ my $clstr_no = "";
+diff --git a/clstr2xml.pl b/clstr2xml.pl
+index 10d828c..ba8264a 100755
+--- a/clstr2xml.pl
++++ b/clstr2xml.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...]
+ #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results
+diff --git a/clstr_cut.pl b/clstr_cut.pl
+index 498f180..ae0264c 100755
+--- a/clstr_cut.pl
++++ b/clstr_cut.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #keep only top $no proteins in cluster
+ 
+diff --git a/clstr_list.pl b/clstr_list.pl
+index 9c6639b..b997402 100755
+--- a/clstr_list.pl
++++ b/clstr_list.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Storable;
+ use strict;
+diff --git a/clstr_list_sort.pl b/clstr_list_sort.pl
+index e0d20d8..a9bd588 100755
+--- a/clstr_list_sort.pl
++++ b/clstr_list_sort.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Storable;
+ use strict;
+diff --git a/clstr_merge.pl b/clstr_merge.pl
+index 3fe108e..9186777 100755
+--- a/clstr_merge.pl
++++ b/clstr_merge.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # the order of clusters need to be identical
+ my ($master_clstr, @clstr) = @ARGV;
+diff --git a/clstr_merge_noorder.pl b/clstr_merge_noorder.pl
+index f8acdfc..0852aee 100755
+--- a/clstr_merge_noorder.pl
++++ b/clstr_merge_noorder.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # order of clusters don't need to be the same
+ # but then I have to read everything into memory
+diff --git a/clstr_quality_eval.pl b/clstr_quality_eval.pl
+index 62f2a3d..060ab01 100755
+--- a/clstr_quality_eval.pl
++++ b/clstr_quality_eval.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ ## calculate the sensitivity and specificity of clusters
+ ## if the input fasta file has pre-defined classification term
+diff --git a/clstr_quality_eval_by_link.pl b/clstr_quality_eval_by_link.pl
+index 8fba8df..140c05c 100755
+--- a/clstr_quality_eval_by_link.pl
++++ b/clstr_quality_eval_by_link.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ ## calculate the sensitivity and specificity of clusters
+ ## if the input fasta file has pre-defined classification term
+diff --git a/clstr_reduce.pl b/clstr_reduce.pl
+index 990f4ad..3621025 100755
+--- a/clstr_reduce.pl
++++ b/clstr_reduce.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ 
+ $file90 = shift;
+diff --git a/clstr_renumber.pl b/clstr_renumber.pl
+index b542304..c66088d 100755
+--- a/clstr_renumber.pl
++++ b/clstr_renumber.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ $no = 0;
+ while($ll=<>){
+   if ($ll =~ /^>Cluster (\d+)/) {
+diff --git a/clstr_rep.pl b/clstr_rep.pl
+index 0ebeb88..84b86b3 100755
+--- a/clstr_rep.pl
++++ b/clstr_rep.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ $rep = "";
+ $no = 0;
+diff --git a/clstr_reps_faa_rev.pl b/clstr_reps_faa_rev.pl
+index 80a4a8a..3574b2b 100755
+--- a/clstr_reps_faa_rev.pl
++++ b/clstr_reps_faa_rev.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ # output single fasta file
+ # for each cluster output at least $cutoff seqs
+ 
+diff --git a/clstr_rev.pl b/clstr_rev.pl
+index d7efdcc..71134e2 100755
+--- a/clstr_rev.pl
++++ b/clstr_rev.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ # if nr90 from nr100 and
+ #    nr80 from nr90, so I have nr90.clstr and nr80.clstr
+ # but, in nr80.clstr, some gi numbers whose from nr100 are there
+diff --git a/clstr_select.pl b/clstr_select.pl
+index 1b168d9..dc70147 100755
+--- a/clstr_select.pl
++++ b/clstr_select.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #my $by = shift;
+ my $min;
+diff --git a/clstr_select_rep.pl b/clstr_select_rep.pl
+index 80c7b7e..f7c38f4 100755
+--- a/clstr_select_rep.pl
++++ b/clstr_select_rep.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #my $by = shift;
+ my $min;
+diff --git a/clstr_size_histogram.pl b/clstr_size_histogram.pl
+index 01ecb63..b726e46 100755
+--- a/clstr_size_histogram.pl
++++ b/clstr_size_histogram.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ if(@ARGV==0){
+    print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n";
+diff --git a/clstr_size_stat.pl b/clstr_size_stat.pl
+index b234b06..ecda7db 100755
+--- a/clstr_size_stat.pl
++++ b/clstr_size_stat.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ if(@ARGV==0){
+    print "Usage:\n\tclstr_size_stat.pl clstr_file\n";
+diff --git a/clstr_sort_by.pl b/clstr_sort_by.pl
+index 82e9cf8..adb12d8 100755
+--- a/clstr_sort_by.pl
++++ b/clstr_sort_by.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my $sort_by_what = shift;
+    $sort_by_what = "no" unless $sort_by_what;
+diff --git a/clstr_sort_prot_by.pl b/clstr_sort_prot_by.pl
+index 64f19e2..0832b99 100755
+--- a/clstr_sort_prot_by.pl
++++ b/clstr_sort_prot_by.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my $sort_by = shift;
+    $sort_by = "len" unless ($sort_by);
+diff --git a/clstr_sql_tbl.pl b/clstr_sql_tbl.pl
+index f2dba07..68bfd7d 100755
+--- a/clstr_sql_tbl.pl
++++ b/clstr_sql_tbl.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ if(@ARGV==0){
+   print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n";
+diff --git a/clstr_sql_tbl_sort.pl b/clstr_sql_tbl_sort.pl
+index 67d60a8..3dfe9c4 100755
+--- a/clstr_sql_tbl_sort.pl
++++ b/clstr_sql_tbl_sort.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ if(@ARGV==0){
+    print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n";
+diff --git a/make_multi_seq.pl b/make_multi_seq.pl
+index 7b05636..3678654 100755
+--- a/make_multi_seq.pl
++++ b/make_multi_seq.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #note you have to use "-d 0" in the cd-hit run
+ #note you better to use "-g 1" in the cd-hit run
+diff --git a/plot_2d.pl b/plot_2d.pl
+index 418a5cf..91342ca 100755
+--- a/plot_2d.pl
++++ b/plot_2d.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Image::Magick;
+ 
+diff --git a/plot_len1.pl b/plot_len1.pl
+index efcdfe0..e8be6e3 100755
+--- a/plot_len1.pl
++++ b/plot_len1.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ $file90 = shift;
+ $segs = shift;
+diff --git a/psi-cd-hit/cd-hit-div.pl b/psi-cd-hit/cd-hit-div.pl
+index e349394..db8d942 100755
+--- a/psi-cd-hit/cd-hit-div.pl
++++ b/psi-cd-hit/cd-hit-div.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ #not like cd-hit-div, this script do not sort input
+ #or throw away seq
+diff --git a/psi-cd-hit/clstr_select_rep.pl b/psi-cd-hit/clstr_select_rep.pl
+index b465586..63db0ce 100755
+--- a/psi-cd-hit/clstr_select_rep.pl
++++ b/psi-cd-hit/clstr_select_rep.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my $by = shift;
+ my $min;
+diff --git a/psi-cd-hit/clstr_select_seq.pl b/psi-cd-hit/clstr_select_seq.pl
+index fd7bb8b..598b0e9 100755
+--- a/psi-cd-hit/clstr_select_seq.pl
++++ b/psi-cd-hit/clstr_select_seq.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my $by = shift;
+ my $min;
+diff --git a/psi-cd-hit/fetch_fasta_by_ids.pl b/psi-cd-hit/fetch_fasta_by_ids.pl
+index bfdbb26..9c17504 100755
+--- a/psi-cd-hit/fetch_fasta_by_ids.pl
++++ b/psi-cd-hit/fetch_fasta_by_ids.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my ($gi_file, $seq_file) = @ARGV;
+ 
+diff --git a/psi-cd-hit/fetch_fasta_exclude_ids.pl b/psi-cd-hit/fetch_fasta_exclude_ids.pl
+index 90e237e..13d061a 100755
+--- a/psi-cd-hit/fetch_fasta_exclude_ids.pl
++++ b/psi-cd-hit/fetch_fasta_exclude_ids.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ my ($gi_file, $seq_file) = @ARGV;
+ 
+diff --git a/psi-cd-hit/psi-2d.pl b/psi-cd-hit/psi-2d.pl
+index ab3f655..f3884a3 100755
+--- a/psi-cd-hit/psi-2d.pl
++++ b/psi-cd-hit/psi-2d.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ 
+ my $script_name = $0;
+diff --git a/psi-cd-hit/psi-cd-hit-local-old.pl b/psi-cd-hit/psi-cd-hit-local-old.pl
+index f5ab1b1..21fd706 100755
+--- a/psi-cd-hit/psi-cd-hit-local-old.pl
++++ b/psi-cd-hit/psi-cd-hit-local-old.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ ################################################################################
+ ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
+ ################################################################################
+@@ -1138,7 +1138,7 @@ sub write_remote_perl_script {
+ 
+   open(REPERL, "> $remote_perl_script") || die;
+   print REPERL <<EOD;
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ \$host = shift;
+ \$arg = shift;
+ 
+diff --git a/psi-cd-hit/psi-cd-hit-local.pl b/psi-cd-hit/psi-cd-hit-local.pl
+index edc7180..461057f 100755
+--- a/psi-cd-hit/psi-cd-hit-local.pl
++++ b/psi-cd-hit/psi-cd-hit-local.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ ################################################################################
+ ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
+ ################################################################################
+@@ -1372,7 +1372,7 @@ sub write_remote_perl_script {
+ 
+   open(REPERL, "> $remote_perl_script") || die;
+   print REPERL <<EOD;
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ \$host = shift;
+ \$instance = shift;
+ \$arg = shift;
+diff --git a/psi-cd-hit/psi-cd-hit-old.pl b/psi-cd-hit/psi-cd-hit-old.pl
+index bb4f512..4fbf688 100755
+--- a/psi-cd-hit/psi-cd-hit-old.pl
++++ b/psi-cd-hit/psi-cd-hit-old.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ ################################################################################
+ ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
+ ################################################################################
+diff --git a/psi-cd-hit/psi-cd-hit.pl b/psi-cd-hit/psi-cd-hit.pl
+index 6d209c6..3d5912c 100755
+--- a/psi-cd-hit/psi-cd-hit.pl
++++ b/psi-cd-hit/psi-cd-hit.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w
++#!/usr/bin/env perl
+ ################################################################################
+ ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
+ ################################################################################
+diff --git a/usecases/Miseq-16S/16S-ref-db-PE-splice.pl b/usecases/Miseq-16S/16S-ref-db-PE-splice.pl
+index dc51f93..7836d1c 100755
+--- a/usecases/Miseq-16S/16S-ref-db-PE-splice.pl
++++ b/usecases/Miseq-16S/16S-ref-db-PE-splice.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ ## =========================== NGS tools ==========================================
+ ## NGS tools for metagenomic sequence analysis
+ ## May also be used for other type NGS data analysis
+diff --git a/usecases/Miseq-16S/NG-Omics-Miseq-16S.pl b/usecases/Miseq-16S/NG-Omics-Miseq-16S.pl
+index 1059323..0cc747a 100644
+--- a/usecases/Miseq-16S/NG-Omics-Miseq-16S.pl
++++ b/usecases/Miseq-16S/NG-Omics-Miseq-16S.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ ################################################################################
+ # NGS workflow by Weizhong Li, http://weizhongli-lab.org
+ ################################################################################
+diff --git a/usecases/Miseq-16S/NG-Omics-Miseq-16S.py b/usecases/Miseq-16S/NG-Omics-Miseq-16S.py
+index 273e008..6e75dde 100644
+--- a/usecases/Miseq-16S/NG-Omics-Miseq-16S.py
++++ b/usecases/Miseq-16S/NG-Omics-Miseq-16S.py
+@@ -43,6 +43,7 @@ NGS_executions['sh_1'] = {
+ NGS_batch_jobs = {}
+ NGS_batch_jobs['qc'] = {
+   'CMD_opts'         : ['100'],
++  'non_zero_files'   : ['R1.fa.gz','R2.fa.gz'],
+   'execution'        : 'qsub_1',               # where to execute
+   'cores_per_cmd'    : 4,                    # number of threads used by command below
+   'no_parallel'      : 1,                    # number of total jobs to run using command below
+@@ -52,8 +53,11 @@ java -jar $ENV.NGS_prog_trimmomatic PE -threads 4 -phred33 $DATA.0 $DATA.1 $SELF
+ 
+ perl -e '$i=0; while(<>){ if (/^@/) {$i++;  print ">Sample|$SAMPLE|$i ", substr($_,1); $a=<>; print $a; $a=<>; $a=<>;}}' < $SELF/R1.fq > $SELF/R1.fa &
+ perl -e '$i=0; while(<>){ if (/^@/) {$i++;  print ">Sample|$SAMPLE|$i ", substr($_,1); $a=<>; print $a; $a=<>; $a=<>;}}' < $SELF/R2.fq > $SELF/R2.fa &
+-
+ wait
++gzip $SELF/R1.fa &
++gzip $SELF/R2.fa &
++wait
++
+ rm -f $SELF/R1.fq $SELF/R2.fq $SELF/R1-s.fq $SELF/R2-s.fq
+ '''
+ }
+@@ -61,41 +65,74 @@ rm -f $SELF/R1.fq $SELF/R2.fq $SELF/R1-s.fq $SELF/R2-s.fq
+ 
+ NGS_batch_jobs['otu'] = {
+   'injobs'            : ['qc'],
+-  'CMD_opts'          : ['150', '100', '0.97', '0.0001', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1', '75'],
++  'non_zero_files'    : ['seq.99f','seq.99f.2','seq.99f-all.clstr','pool.ok'],
++  'CMD_opts'          : ['150', '100', '0.0005', '75', 'path_to_pooled_sample_dir'],
+   'execution'         : 'qsub_1',               # where to execute
+   'cores_per_cmd'     : 2,                    # number of threads used by command below
+   'no_parallel'       : 1,                    # number of total jobs to run using command below
+   'command'           : '''
+-#### cluster at 100% PE
+-$ENV.CD_HIT_dir/cd-hit-est -i $INJOBS.0/R1.fa -j $INJOBS.0/R2.fa -o $SELF/seq.nr -op $SELF/seq.nr.2 -sf 1 -sc 1 -P 1 -r 0 \\
++
++#### 1. cluster at 100% PE
++$ENV.CD_HIT_dir/cd-hit-est -i $INJOBS.0/R1.fa.gz -j $INJOBS.0/R2.fa.gz -o $SELF/seq.nr -op $SELF/seq.nr.2 -sf 1 -sc 1 -P 1 -r 0 \\
+     -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 1.0  -n 10 -G 1 -b 1  -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.nr.log
+-#### cluster at 99% PE and SE for R1,R2 
+-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr   -o $SELF/seq.chimeric-clstr.R1 -r 0 -cx $CMDOPTS.6 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.chimeric-clstr.R1.log
+-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr.2 -o $SELF/seq.chimeric-clstr.R2 -r 0 -cx $CMDOPTS.6 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.chimeric-clstr.R2.log
++
++#### 2. cluster at 99% PE 
+ $ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -j $SELF/seq.nr.2 -o $SELF/seq.99 -op $SELF/seq.99.2 -P 1 -r 0 \\
+     -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.99 -n 10 -G 1 -b 1  -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.99.log
+-$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-chimeric-and-small.pl -c $CMDOPTS.3 -k $SELF/seq.nr.clstr \\
++
++#### 3. cluster at 99% SE for R1, R2 
++$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr   -o $SELF/seq.chimeric-clstr.R1 -r 0 -cx $CMDOPTS.3 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.chimeric-clstr.R1.log
++$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr.2 -o $SELF/seq.chimeric-clstr.R2 -r 0 -cx $CMDOPTS.3 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.chimeric-clstr.R2.log
++rm -f $SELF/seq.chimeric-clstr.R1    $SELF/seq.chimeric-clstr.R1.log \\
++      $SELF/seq.chimeric-clstr.R2    $SELF/seq.chimeric-clstr.R2.log 
++
++#### 4. 5. filter chimeric sequences and sequences in small clusters
++$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-chimeric-and-small.pl -c $CMDOPTS.2 -k $SELF/seq.nr.clstr \\
+     -i $SELF/seq.chimeric-clstr.R1.clstr -j $SELF/seq.chimeric-clstr.R2.clstr \\
+     -a $SELF/seq.99.clstr -f $SELF/seq.99 -g $SELF/seq.99.2 -o $SELF/seq.99f
+ $ENV.CD_HIT_dir/clstr_rev.pl $SELF/seq.nr.clstr       $SELF/seq.99f.clstr     > $SELF/seq.99f-all.clstr
+-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.99f -j $SELF/seq.99f.2 -o $SELF/seq.97 -op $SELF/seq.97.2 -P 1 -r 0 \\
+-    -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10  -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.97.log
+-$ENV.CD_HIT_dir/cd-hit-est-2d -i $SELF/seq.97 -j $SELF/seq.97.2 -i2 $CMDOPTS.4 -j2 $CMDOPTS.5 -o $SELF/seq.97.ref -op $SELF/seq.97.ref.2 -P 1 -r 0 \\
+-    -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10  -T 1 -M 8000  -d 0 -p 1 > $SELF/seq.97.ref.log
+-$ENV.CD_HIT_dir/clstr_rev.pl $SELF/seq.99f-all.clstr $SELF/seq.97.clstr > $SELF/seq.97-all.clstr
+-$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-nontop-ref.pl < $SELF/seq.97.ref.clstr > $SELF/seq.97.reftop.clstr
+-$ENV.CD_HIT_dir/clstr_merge.pl $SELF/seq.97-all.clstr $SELF/seq.97.reftop.clstr > $SELF/OTU.clstr
+-
+-rm -f $SELF/seq.chimeric-clstr.R1    $SELF/seq.chimeric-clstr.R1.log    $SELF/seq.chimeric-clstr.R2    $SELF/seq.chimeric-clstr.R2.log 
+-rm -f $SELF/seq.97.ref $SELF/seq.97.ref.2 $SELF/seq.97.ref.log
+ mv $SELF/seq.99f.log $SELF/chimeric-small-clusters-list.txt
+ 
++
++####
++if [ ! -e "$CMDOPTS.4" ]; then
++  mkdir -p $CMDOPTS.4
++fi
++
++i="0"
++while [ 1 ]; do
++
++  if [ -e "$CMDOPTS.4/lock" ]; then
++    echo "wait $CMDOPTS.4/lock"
++    sleep 5
++  else
++    date > $CMDOPTS.4/lock
++    
++    cat $SELF/seq.99f                          >> $CMDOPTS.4/seq.99f
++    cat $SELF/seq.99f.2                        >> $CMDOPTS.4/seq.99f.2
++    cat $SELF/seq.99f-all.clstr                >> $CMDOPTS.4/seq.99f-all.clstr
++    cat $SELF/chimeric-small-clusters-list.txt >> $CMDOPTS.4/chimeric-small-clusters-list.txt
++    date > $SELF/pool.ok
++    sleep 1
++
++    rm -f $CMDOPTS.4/lock
++    break
++  fi
++
++  i=$[$i+1]
++  if [ "$i" -gt "50" ]; then
++    echo "wait $CMDOPTS.4/lock for too long"
++    break
++  fi
++done
++
+ '''
+ }
+ 
+ 
+ NGS_batch_jobs['otu-pooled'] = {
+-  'CMD_opts'          : ['150', '100', '0.97', '0.0001', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1', '75'],
++  'CMD_opts'          : ['150', '100', '0.97', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1'],
++  'non_zero_files'    : ['OTU.txt'],
+   'execution'         : 'qsub_1',               # where to execute
+   'cores_per_cmd'     : 2,                    # number of threads used by command below
+   'no_parallel'       : 1,                    # number of total jobs to run using command below
+@@ -103,9 +140,9 @@ NGS_batch_jobs['otu-pooled'] = {
+ #### before running
+ #### concat seq.99f seq.99f.2 seq.99f-all.clstr chimeric-small-clusters-list.txt
+ $ENV.CD_HIT_dir/cd-hit-est -i seq.99f -j seq.99f.2 -o seq.97 -op seq.97.2 -P 1 -r 0 \\
+-    -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10  -T 1 -M 8000  -d 0 -p 1 > seq.97.log
+-$ENV.CD_HIT_dir/cd-hit-est-2d -i seq.97 -j seq.97.2 -i2 $CMDOPTS.4 -j2 $CMDOPTS.5 -o seq.97.ref -op seq.97.ref.2 -P 1 -r 0 \\
+-    -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10  -T 1 -M 8000  -d 0 -p 1 > seq.97.ref.log
++    -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c $CMDOPTS.2  -n 10 -G 1 -b 10  -T 1 -M 8000  -d 0 -p 1 > seq.97.log
++$ENV.CD_HIT_dir/cd-hit-est-2d -i seq.97 -j seq.97.2 -i2 $CMDOPTS.3 -j2 $CMDOPTS.4 -o seq.97.ref -op seq.97.ref.2 -P 1 -r 0 \\
++    -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c $CMDOPTS.2  -n 10 -G 1 -b 10  -T 1 -M 8000  -d 0 -p 1 > seq.97.ref.log
+ $ENV.CD_HIT_dir/clstr_rev.pl seq.99f-all.clstr seq.97.clstr > seq.97-all.clstr
+ $ENV.CD_HIT_dir/usecases/Miseq-16S/filter-nontop-ref.pl < seq.97.ref.clstr > seq.97.reftop.clstr
+ $ENV.CD_HIT_dir/clstr_merge.pl seq.97-all.clstr seq.97.reftop.clstr > OTU.clstr
+diff --git a/usecases/Miseq-16S/NG-Omics-WF.pl b/usecases/Miseq-16S/NG-Omics-WF.pl
+index 2f46255..195583e 100755
+--- a/usecases/Miseq-16S/NG-Omics-WF.pl
++++ b/usecases/Miseq-16S/NG-Omics-WF.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ # =============================== NG-Omics-WF ==================================
+ #  _   _  _____         ____            _              __          ________ 
+ # | \ | |/ ____|       / __ \          (_)             \ \        / /  ____|
+diff --git a/usecases/Miseq-16S/OTU_2_taxon_table.pl b/usecases/Miseq-16S/OTU_2_taxon_table.pl
+new file mode 100755
+index 0000000..86561af
+--- /dev/null
++++ b/usecases/Miseq-16S/OTU_2_taxon_table.pl
+@@ -0,0 +1,158 @@
++#!/usr/bin/env perl
++## =========================== NGS tools ==========================================
++## NGS tools for metagenomic sequence analysis
++## May also be used for other type NGS data analysis
++##
++##                                      Weizhong Li, UCSD
++##                                      liwz@sdsc.edu
++## http://weizhongli-lab.org/
++## ================================================================================
++
++use Getopt::Std;
++getopts("i:o:a:t:r:N:c:P:",\%opts);
++die usage() unless ($opts{o} and $opts{i} and $opts{t});
++
++
++my $otu_table   = $opts{i}; ### e.g. OTU-short.txt
++my $taxon_file  = $opts{t}; ### e.g. OTU-feature.txt
++my $output      = $opts{o};
++
++my ($i, $j, $k, $ll, $cmd);
++
++my @samples = ();
++my @otus = ();
++my %otu_mat = ();
++
++my $fh;
++if ($otu_table eq "-") { $fh = "STDIN";}
++else {
++  open(TMP, $otu_table) || die "can not open $otu_table";
++  $fh = "TMP";
++}
++
++$ll = <$fh>; chop($ll);
++my ($t1, @lls) = split(/\t/, $ll);
++@samples = @lls;
++my $num_samples = $#samples+1;
++
++while($ll=<$fh>){
++  next if ($ll =~ /^#/);
++  next unless ($ll =~ /^otu/i);
++  chop($ll);
++  my ($otu, @v) = split(/\t/, $ll);
++  push(@otus, $otu);
++  for ($i=0; $i<$num_samples; $i++) {
++    $otu_mat{$otu}{$samples[$i]} = $v[$i];
++  }
++}
++
++open(TMP, $taxon_file) || die "can not open $taxon_file";
++my %taxon_info = ();
++while($ll=<TMP>) {
++  chop($ll);
++  next if ($ll =~ /^#/);
++  my ($otu, $taxon, $c) = split(/\t/, $ll);
++  # next unless ($taxon =~ /__/); #### skip unknown OTUs
++
++#OTUID	taxonomy	confidence
++#OTU1	Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__	1.0
++#OTU2	Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16;g__;s__	1.0
++#OTU3	Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Flexispira;s__rappini	1.0
++#OTU4	Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__C21_c20	1.0
++
++  my $k = "unclassified";
++  my $p = "unclassified";
++  my $c = "unclassified";
++  my $o = "unclassified";
++  my $f = "unclassified";
++  my $g = "unclassified";
++  my $s = "unclassified";
++
++  $j = $taxon;
++  if ($j =~ /^k__([^;]+)/) {$k = $1;}
++  if ($j =~ /;k__([^;]+)/) {$k = $1;}
++  if ($j =~ /;p__([^;]+)/) {$p = $1;}
++  if ($j =~ /;c__([^;]+)/) {$c = $1;}
++  if ($j =~ /;o__([^;]+)/) {$o = $1;}
++  if ($j =~ /;f__([^;]+)/) {$f = $1;}
++  if ($j =~ /;g__([^;]+)/) {$g = $1;}
++  if ($j =~ /;s__([^;]+)/) {$s = $1;}
++
++  if ($j =~ /^D_0__([^;]+)/) {$k = $1;}
++  if ($j =~ /;D_0__([^;]+)/) {$k = $1;}
++  if ($j =~ /;D_1__([^;]+)/) {$p = $1;}
++  if ($j =~ /;D_2__([^;]+)/) {$c = $1;}
++  if ($j =~ /;D_3__([^;]+)/) {$o = $1;}
++  if ($j =~ /;D_4__([^;]+)/) {$f = $1;}
++  if ($j =~ /;D_5__([^;]+)/) {$g = $1;}
++  if ($j =~ /;D_6__([^;]+)/) {$s = $1;}
++
++  if (($g ne "unclassified") and ($s ne "unclassified")) {
++    if ( substr($s, 0, length($g)) ne $g) { #### if species name doesn't contain genus name, add
++      $s = "$g $s";
++    }
++  } 
++  $taxon_info{$otu} = [$k,$p,$c,$o,$f,$g,$s];
++
++}
++close(TMP);
++
++my @ranks = qw/kingdom phylum class order family genus species/;
++my %rank_col = qw/kingdom 0 phylum 1 class 2 order 3 family 4 genus 5 species 6/;
++foreach $rank (@ranks) {
++  next if ($rank eq "kingdom");
++
++  my $c = $rank_col{$rank};
++  my $out = "$output.$rank.txt";
++  open(OUT, "> $out") || die "can not write to $out";
++  #### print table header
++  print OUT "#", join("\t", @ranks[0..$c]);
++  print OUT "\t", join("\t", @samples), "\n";
++
++  my %rank_ti_info = ();
++  my %rank_mat = ();
++  my %ti_sum = ();
++  foreach $otu (@otus) {
++    my @ann = @{$taxon_info{$otu}};
++    my $ti = join("|", @ann[0 .. $c] );
++
++    if (not defined($rank_ti_info{$ti})) {
++      $rank_ti_info{$ti} = [ @ann[0 .. $c] ];
++    }
++    foreach $sample (@samples) {
++      $rank_mat{$ti}{$sample} += $otu_mat{$otu}{$sample}; 
++      $ti_sum{$ti} += $otu_mat{$otu}{$sample};
++    }
++  }
++  my @tis = keys %rank_mat;
++     @tis = sort {$ti_sum{$b} <=> $ti_sum{$a} } @tis;
++
++  foreach $ti (@tis) {
++    print OUT join("\t", @{ $rank_ti_info{$ti} } );
++    foreach $sample (@samples) {
++      print OUT "\t", $rank_mat{$ti}{$sample};
++    }
++    print OUT "\n";
++  }
++  close(OUT);
++}
++
++
++sub usage {
++<<EOD
++Given cd-hit-otu pipeline output, this script generate
++taxonomy abundance tables
++
++usage:
++  $0  -i otu_table -t taxon_info_file -o output
++
++  options
++    -i input OTU table from cd-hit-otu 16S pipeline, default STDIN
++       e.g. OTU-short.txt
++    -t taxon info, e.g. OTU-features.txt
++    -o output file
++
++EOD
++}
++########## END usage
++
+diff --git a/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl b/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl
+index e746d60..5c2424c 100755
+--- a/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl
++++ b/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Getopt::Std;
+ my $script_name = $0;
+diff --git a/usecases/Miseq-16S/clstr_2_OTU_table.pl b/usecases/Miseq-16S/clstr_2_OTU_table.pl
+index 0ad13e3..0a4cccb 100755
+--- a/usecases/Miseq-16S/clstr_2_OTU_table.pl
++++ b/usecases/Miseq-16S/clstr_2_OTU_table.pl
+@@ -1,10 +1,21 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ #
+ use Getopt::Std;
+-getopts("i:s:S:o:f:j:",\%opts);
++getopts("i:s:S:o:f:j:b:h:",\%opts);
++
++die usage() unless($opts{o});
+ 
+ my $input             = $opts{i}; $input   = "OTU.clstr" unless $input;
+-my $output            = $opts{o}; $output  = "OTU.txt" unless ($output);
++my $output            = $opts{o};
++my $output_pre        = $output;
++   $output_pre        =~ s/\.([^\.])+$//;
++my $output_meta       = "$output_pre-sample-meta.txt";
++my $output_feature    = "$output_pre-feature.txt";
++my $output_short      = "$output_pre-short.txt";
++my $output_biom       = "$output_pre.biom";
++my $biom_exe          = $opts{b};
++
++
+ my ($i, $j, $k, $str, $cmd, $ll);
+ 
+ my %count = ();
+@@ -31,8 +42,18 @@ while($ll=<TMP>){
+         $count_s{$sample_id}++;
+       }
+       else {
++        $id =~ s/^([^\|]+)\|//;
++        $id =~ s/;\./;/g;
++        $id = "Root;$id";
++        $id =~ s/;D_0__/;k__/;
++        $id =~ s/;D_1__/;p__/;
++        $id =~ s/;D_2__/;c__/;
++        $id =~ s/;D_3__/;o__/;
++        $id =~ s/;D_4__/;f__/;
++        $id =~ s/;D_5__/;g__/;
++        $id =~ s/;D_6__/;s__/;
+         $OTU_2_ann{$OTU} = $id;
+-        $tree_flag = 1 if ($id =~ /\|k__Bacteria;.p__/);
++        $tree_flag = 1 if ($id =~ /;k__Bacteria/);
+       }
+     }
+     else {
+@@ -45,23 +66,34 @@ close(TMP);
+ my @sample_ids = sort keys %sample_id;
+ 
+ open(OUT1, "> $output") || die "can not write $output";
+-print OUT1 "OTU";
++open(OUT2, "> $output_short") || die "can not write $output_short";
++open(OUT3, "> $output_feature") || die "can not write $output_feature";
++
++print OUT1 "#OTUID";
++print OUT2 "#OTUID";
++print OUT3 "#OTUID";
+ foreach $sample_id (@sample_ids){
+   print OUT1 "\t$sample_id";
++  print OUT2 "\t$sample_id";
+ }
+ if ($tree_flag) {
+   print OUT1 "\t", join("\t", qw/Kingdom Phylum Class Order Family Genus Species/);
+ }
+ #print OUT1 "\tTotal\n";
+ print OUT1 "\tAnnotation\n";
++print OUT2 "\n";
++print OUT3 "\ttaxonomy\tconfidence\n";
+ 
+ for ($i=1; $i<=$OTU; $i++){
+-  $ann = "None";
++  $ann = "";
+   if ($OTU_2_ann{$i}) { $ann = $OTU_2_ann{$i}; }
+   print OUT1 "OTU$i";
++  print OUT2 "OTU$i";
++  print OUT3 "OTU$i";
+   foreach $sample_id (@sample_ids){
+     $k = $count{$i}{$sample_id}? $count{$i}{$sample_id} : 0;
+     print OUT1 "\t$k";
++    print OUT2 "\t$k";
+   }
+   if ($tree_flag) {
+     my ($tax_k, $tax_p, $tax_c, $tax_o, $tax_f, $tax_g, $tax_s);
+@@ -76,7 +108,37 @@ for ($i=1; $i<=$OTU; $i++){
+   }
+   #print OUT1 "\t$count_t{$i}";
+   print OUT1 "\t$ann\n";
++  print OUT2 "\n";
++  print OUT3 "\t$ann\t1.0\n";
+ }
+ close(OUT1);
++close(OUT2);
++close(OUT3);
++
++open(OUT, ">$output_meta") || die "can not write to $output_meta";
++print OUT "#SampleID\tGroup\n";
++foreach $sample_id (@sample_ids){
++  print OUT "$sample_id\tnogroup\n";
++}
++close(OUT);
+ 
++if (-e $biom_exe) {
++  $cmd = `$biom_exe convert -i $output_short -o $output_biom --to-hdf5 --observation-metadata-fp $output_feature --sample-metadata-fp $output_meta`;
++}
++
++sub usage {
++<<EOF
++This script converts OTU clusters to tsv format, and if biom is available,
++convert .biom file
++
++Usage:
++$script_name -i OTU.clstr -o OTU.txt
++
++Options:
++    -i input OTU.clstr, by cd-hit-otu-miseq
++    -o output OTU table
++    -b path to biom executible, if provided, will make .biom file
++
++EOF
++}
+ 
+diff --git a/usecases/Miseq-16S/filter-chimeric-and-small.pl b/usecases/Miseq-16S/filter-chimeric-and-small.pl
+index de303fe..3e07d35 100755
+--- a/usecases/Miseq-16S/filter-chimeric-and-small.pl
++++ b/usecases/Miseq-16S/filter-chimeric-and-small.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Getopt::Std;
+ my $script_name = $0;
+diff --git a/usecases/Miseq-16S/filter-chimeric-by-ref.pl b/usecases/Miseq-16S/filter-chimeric-by-ref.pl
+index 5e9b32a..9423398 100755
+--- a/usecases/Miseq-16S/filter-chimeric-by-ref.pl
++++ b/usecases/Miseq-16S/filter-chimeric-by-ref.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Getopt::Std;
+ my $script_name = $0;
+diff --git a/usecases/Miseq-16S/filter-nontop-ref.pl b/usecases/Miseq-16S/filter-nontop-ref.pl
+index 71d8ec3..4200212 100755
+--- a/usecases/Miseq-16S/filter-nontop-ref.pl
++++ b/usecases/Miseq-16S/filter-nontop-ref.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Getopt::Std;
+ my $script_name = $0;
+diff --git a/usecases/Miseq-16S/filter-refonly-cluster.pl b/usecases/Miseq-16S/filter-refonly-cluster.pl
+index c4c8ab6..bba8f12 100755
+--- a/usecases/Miseq-16S/filter-refonly-cluster.pl
++++ b/usecases/Miseq-16S/filter-refonly-cluster.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Getopt::Std;
+ my $script_name = $0;
+diff --git a/usecases/Miseq-16S/greengene-ann1.pl b/usecases/Miseq-16S/greengene-ann1.pl
+index fde835e..cf2fc6b 100755
+--- a/usecases/Miseq-16S/greengene-ann1.pl
++++ b/usecases/Miseq-16S/greengene-ann1.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ ## =========================== NGS tools ==========================================
+ ## NGS tools for metagenomic sequence analysis
+ ## May also be used for other type NGS data analysis
+diff --git a/usecases/Miseq-16S/pool_samples.pl b/usecases/Miseq-16S/pool_samples.pl
+index 44cc208..9e5c3a4 100755
+--- a/usecases/Miseq-16S/pool_samples.pl
++++ b/usecases/Miseq-16S/pool_samples.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ #
+ use Getopt::Std;
+ getopts("s:S:o:f:j:",\%opts);
+diff --git a/usecases/Miseq-16S/silva-ana1.pl b/usecases/Miseq-16S/silva-ann1.pl
+similarity index 98%
+rename from usecases/Miseq-16S/silva-ana1.pl
+rename to usecases/Miseq-16S/silva-ann1.pl
+index 03959a3..19fecc1 100755
+--- a/usecases/Miseq-16S/silva-ana1.pl
++++ b/usecases/Miseq-16S/silva-ann1.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ ## =========================== NGS tools ==========================================
+ ## NGS tools for metagenomic sequence analysis
+ ## May also be used for other type NGS data analysis
+diff --git a/usecases/Miseq-16S/silva-qiime-format-ann1.pl b/usecases/Miseq-16S/silva-qiime-format-ann1.pl
+new file mode 100755
+index 0000000..66e9e39
+--- /dev/null
++++ b/usecases/Miseq-16S/silva-qiime-format-ann1.pl
+@@ -0,0 +1,75 @@
++#!/usr/bin/env perl
++## =========================== NGS tools ==========================================
++## NGS tools for metagenomic sequence analysis
++## May also be used for other type NGS data analysis
++##
++##                                      Weizhong Li, UCSD
++##                                      liwz@sdsc.edu
++## http://weizhongli-lab.org/
++## ================================================================================
++
++use Getopt::Std;
++getopts("i:j:o:r:e:p:q:c:d:N:t:u:d:M:T:S:",\%opts);
++die usage() unless ($opts{i} and $opts{j} and $opts{o});
++my ($i, $j, $k, $cmd);
++my ($ll, $lla, $llb, $id, $ida, $idb, $seq, $seqa, $seqb, $qua, $quaa, $quab);
++my ($len, $lena, $lenb);
++
++my $file1 = $opts{i};
++my $fasta = $opts{j};
++my $output  = $opts{o};
++
++my %id_2_ann;
++open(TMP, $file1) || die "can not open $file1";
++while($ll=<TMP>){
++  chop($ll);
++  my ($id, $txt) = split(/\s+/, $ll, 2);
++  $txt =~ s/ /./g;
++  $id_2_ann{$id} = $txt;
++}
++close(TMP);
++
++my %id_2_seq = ();
++my $id = "";
++open(TMP, $fasta) || die "can not open $fasta";
++while($ll=<TMP>){
++  if ($ll =~ /^>(\S+)/) {
++    chop($ll);
++    $id = $1;
++    $ann = $id_2_ann{$id};
++    $id = "$id|$ann" if ($ann);
++  }
++  else {
++    $id_2_seq{$id} .= $ll;
++  }
++}
++
++close(TMP);
++
++my @ids = keys %id_2_seq;
++   @ids = sort {length($b) <=> length($a) } @ids;
++
++open(OUT, "> $output") || die "can not write to $output";
++foreach $id (@ids) {
++  print OUT ">$id\n$id_2_seq{$id}";
++}
++close(OUT);
++
++
++
++sub usage {
++<<EOD;
++This script formats Qiime comtatible Silva FASTA file for CD-HIT-OTU-MiSeq. You should download Silva sequences
++from https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_xxx_release.zip
++unzip this file
++
++Run this script as $0 -i SILVA_132_QIIME_release/taxonomy/16S_only/99/consensus_taxonomy_7_levels.txt \\
++  -j SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_16S.fna -o silva_132_99_16S_processed.fna
++
++Options:
++======================
++        -i path for SILVA_132_QIIME_release/taxonomy/16S_only/99/consensus_taxonomy_7_levels.txt
++        -j path for SILVA_132_QIIME_release/rep_set/rep_set_16S_only/99/silva_132_99_16S.fna -o silva_132_99_16S_processed.fna
++        -o output FASTA file of formatted Silva reference DB
++EOD
++}
+diff --git a/usecases/miRNA-seq/NG-Omics-miRNA-seq.pl b/usecases/miRNA-seq/NG-Omics-miRNA-seq.pl
+index 010a088..20c8b78 100644
+--- a/usecases/miRNA-seq/NG-Omics-miRNA-seq.pl
++++ b/usecases/miRNA-seq/NG-Omics-miRNA-seq.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ ################################################################################
+ # NGS workflow by Weizhong Li, http://weizhongli-lab.org
+ ################################################################################
+diff --git a/usecases/miRNA-seq/clstr_2_miRNA-table.pl b/usecases/miRNA-seq/clstr_2_miRNA-table.pl
+index a98688a..2f45874 100755
+--- a/usecases/miRNA-seq/clstr_2_miRNA-table.pl
++++ b/usecases/miRNA-seq/clstr_2_miRNA-table.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ #
+ use Getopt::Std;
+ getopts("i:s:S:o:f:j:",\%opts);
+diff --git a/usecases/miRNA-seq/filter-small-cluster.pl b/usecases/miRNA-seq/filter-small-cluster.pl
+index f649797..00dfae4 100755
+--- a/usecases/miRNA-seq/filter-small-cluster.pl
++++ b/usecases/miRNA-seq/filter-small-cluster.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use Getopt::Std;
+ my $script_name = $0;
diff --git a/recipes/cd-hit/meta.yaml b/recipes/cd-hit/meta.yaml
index 8163e48de1d69..b46294a67d0a4 100644
--- a/recipes/cd-hit/meta.yaml
+++ b/recipes/cd-hit/meta.yaml
@@ -8,9 +8,11 @@ package:
 source:
   url: https://github.com/weizhongli/cdhit/archive/V{{ version }}.tar.gz
   sha256: {{ sha256 }}
+  patches:
+    - cd-hit.patch
 
 build:
-  number: 10
+  number: 11
   run_exports:
     - {{ pin_subpackage('cd-hit', max_pin="x") }}
 
@@ -19,22 +21,30 @@ requirements:
     - make
     - {{ compiler('cxx') }}
     - {{ compiler('c') }}
-    - llvm-openmp  # [osx]
-    - libgomp  # [linux]
   host:
     - zlib
-  run:
-    - zlib
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
 
 test:
   commands:
     - cd-hit --help | grep 'Usage' > /dev/null
 
 about:
-  home: https://github.com/weizhongli/cdhit
-  license: GPLv2
-  summary: Clusters and compares protein or nucleotide sequences
+  home: "https://github.com/weizhongli/cdhit"
+  license: "GPL-2.0-or-later"
+  license_family: GPL
+  license_file: "license.txt"
+  summary: "Clusters and compares protein or nucleotide sequences."
+  dev_url: "https://github.com/weizhongli/cdhit"
+  doc_url: "https://github.com/weizhongli/cdhit/wiki"
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - doi:10.1093/bioinformatics/17.3.282
+    - doi:10.1093/bioinformatics/18.1.77
+    - biotools:cd-hit
+    - usegalaxy-eu:cd_hit
diff --git a/recipes/cell2cell/meta.yaml b/recipes/cell2cell/meta.yaml
new file mode 100644
index 0000000000000..5e01f81b216ed
--- /dev/null
+++ b/recipes/cell2cell/meta.yaml
@@ -0,0 +1,62 @@
+{% set name = "cell2cell" %}
+{% set version = "0.7.4" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/cell2cell-{{ version }}.tar.gz
+  sha256: 2e17a1556d90c187434aa492000b2ced0d755cf6d437732f07df42e6670370e0
+
+build:
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 1
+  run_exports:
+    - {{ pin_subpackage("cell2cell", max_pin="x.x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+
+  host:
+    - python <=3.9
+    - cython
+    - pip
+  run:
+    - python <=3.9
+    - numpy >=1.16,<2.0
+    - pandas >=1.0.0
+    - xlrd >=1.1
+    - openpyxl >=2.6.2
+    - networkx >=2.3
+    - matplotlib-base >=3.2.0,<3.7.3
+    - seaborn >=0.11.0
+    - scikit-learn
+    - umap-learn
+    - tqdm
+    - statsmodels
+    - statannotations
+    - tensorly ==0.8.1
+    - kneed
+    - scanpy <=1.9.3
+    - gseapy ==1.0.3
+
+test:
+  imports:
+    - benchmarks
+    - cell2cell
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://github.com/earmingol/cell2cell
+  summary: Inferring cell-cell interactions from transcriptomes with cell2cell
+  license: BSD-3-Clause
+  license_file: LICENSE.txt
+
+extra:
+  recipe-maintainers:
+    - nilchia
diff --git a/recipes/cellprofiler/meta.yaml b/recipes/cellprofiler/meta.yaml
index 813f6bbada87d..e0cde02fab3b5 100644
--- a/recipes/cellprofiler/meta.yaml
+++ b/recipes/cellprofiler/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "CellProfiler" %}
-{% set version = "4.2.7" %}
+{% set version = "4.2.8" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/CellProfiler/{{ name  }}/archive/v{{ version }}.tar.gz
-  sha256: "8bc0819f1e2c215756e7eb5b7f0078949760d707397930eddf002b8bdd452ed3"
+  sha256: "c1352e703ca36af63b6069fda9a0de3b54980ed0d2b7d45d08c84fbeeded03fd"
 
 build:
   number: 0
@@ -23,6 +23,7 @@ requirements:
     - python >=3.8
     - pip
     - pytest
+    - setuptools
   run:
     - python >=3.8
     - boto3 >=1.12.28
diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml
index dccd1d4dbe4d6..196d36ed4e995 100644
--- a/recipes/centrifuger/meta.yaml
+++ b/recipes/centrifuger/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "centrifuger" %}
-{% set version = "1.0.4" %}
+{% set version = "1.0.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
 source:
   url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 5261abcfb3b88126000ae7708702d07704a0ee19d6f54f9f89f0d2e195e24d1d
+  sha256: 1de388229d3ee6a65a58308b5521bef6cbfcdf92628064a39d6b70c7523d68de
 
 requirements:
   build:
diff --git a/recipes/cgat-apps/0001-setup.py.patch b/recipes/cgat-apps/0001-setup.py.patch
new file mode 100644
index 0000000000000..7dc8f129e99f4
--- /dev/null
+++ b/recipes/cgat-apps/0001-setup.py.patch
@@ -0,0 +1,327 @@
+diff --git a/requires.txt b/requires.txt
+deleted file mode 100644
+index e69de29b..00000000
+diff --git a/setup.py b/setup.py
+index 1cc415ea..56d2ccd8 100644
+--- a/setup.py
++++ b/setup.py
+@@ -4,239 +4,73 @@ import os
+ import subprocess
+ import re
+ 
+-########################################################################
+-#######################################################################
+-# Check for dependencies
+-#
+-# Is there a way to do this more elegantly?
+-#     1. Run "pip install numpy"
+-#     2. Wrap inside functions (works for numpy/pysam, but not cython)
+-try:
+-    import numpy
+-except ImportError:
+-    raise ImportError(
+-        "the CGAT code collection requires numpy to be installed "
+-        "before running setup.py (pip install numpy)")
++# Import setuptools at the beginning
++import setuptools
++from setuptools import setup, find_packages, Extension
++from distutils.version import LooseVersion
++from Cython.Distutils import build_ext
+ 
++# Ensure dependencies are installed before setup
+ try:
++    import numpy
+     import Cython
+-except ImportError:
+-    raise ImportError(
+-        "the CGAT code collection requires cython to "
+-        "be installed before running setup.py (pip install cython)")
+-
+-try:
+     import pysam
+-except ImportError:
+-    raise ImportError(
+-        "the CGAT code collection requires pysam to "
+-        "be installed before running setup.py (pip install pysam)")
++except ImportError as e:
++    missing_package = str(e).split("'")[1]
++    raise ImportError(f"{missing_package} must be installed before running setup.py")
+ 
+-########################################################################
+-########################################################################
+-# Import setuptools
+-# Use existing setuptools, otherwise try ez_setup.
+-try:
+-    import setuptools
+-except ImportError:
+-    # try to get via ez_setup
+-    # ez_setup did not work on all machines tested as
+-    # it uses curl with https protocol, which is not
+-    # enabled in ScientificLinux
+-    import ez_setup
+-    ez_setup.use_setuptools()
++# Enforce Python 3 requirement
++if sys.version_info < (3, 6):
++    raise SystemExit("Python 3.6 or later is required to install this package.")
+ 
+-from setuptools import setup, find_packages, Extension
+-
+-from distutils.version import LooseVersion
++# Minimum setuptools version requirement
+ if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
+-    print("Version detected:", LooseVersion(setuptools.__version__))
+-    raise ImportError(
+-        "the CGAT code collection requires setuptools 1.1 higher")
++    raise ImportError("Setuptools version >=1.1 is required")
+ 
+-from Cython.Distutils import build_ext
+-
+-########################################################################
+-########################################################################
+-IS_OSX = sys.platform == 'darwin'
+-
+-########################################################################
+-########################################################################
+-# collect CGAT version
++# Define version and other package information
+ sys.path.insert(0, "cgat")
+ import version
+-
+ version = version.__version__
+ 
+-###############################################################
+-###############################################################
+-# Check for external dependencies
+-#
+-# Not exhaustive, simply execute a representative tool from a toolkit.
+-external_dependencies = (
+-    ("wigToBigWig", "UCSC tools", 255),
+-    ("bedtools", "bedtools", 0),
+-    )
++IS_OSX = sys.platform == 'darwin'
+ 
++# External dependency check
++external_dependencies = [("wigToBigWig", "UCSC tools", 255), ("bedtools", "bedtools", 0)]
+ for tool, toolkit, expected in external_dependencies:
+-    try:
+-        # py3k
+-        from subprocess import DEVNULL
+-    except ImportError:
+-        DEVNULL = open(os.devnull, 'wb')
+-
+-    try:
+-        retcode = subprocess.call(tool, shell=True,
+-                                  stdout=DEVNULL, stderr=DEVNULL)
+-    except OSError as msg:
+-        print(("WARNING: depency check for %s failed: %s" % (toolkit, msg)))
+-
+-    # UCSC tools return 255 when called without arguments
++    retcode = subprocess.call(tool, shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+     if retcode != expected:
+-        print(("WARNING: depency check for %s(%s) failed, error %i" %
+-               (toolkit, tool, retcode)))
+-
+-###############################################################
+-###############################################################
+-# Define dependencies
+-#
+-major, minor1, minor2, s, tmp = sys.version_info
+-
+-if (major == 2 and minor1 < 7) or major < 2:
+-    raise SystemExit("""CGAT requires Python 2.7 or later.""")
+-
+-
+-#####################################################################
+-#####################################################################
+-# Code to install dependencies from a repository
+-#####################################################################
+-# Modified from http://stackoverflow.com/a/9125399
+-#####################################################################
+-def which(program):
+-    """
+-    Detect whether or not a program is installed.
+-    Thanks to http://stackoverflow.com/a/377028/70191
+-    """
+-    def is_exe(fpath):
+-        return os.path.exists(fpath) and os.access(fpath, os.X_OK)
+-
+-    fpath, _ = os.path.split(program)
+-    if fpath:
+-        if is_exe(program):
+-            return program
+-    else:
+-        for path in os.environ['PATH'].split(os.pathsep):
+-            exe_file = os.path.join(path, program)
+-            if is_exe(exe_file):
+-                return exe_file
+-
+-    return None
+-
+-REPO_REQUIREMENT = re.compile(
+-    r'^-e (?P<link>(?P<vcs>git|svn|hg|bzr).+#egg=(?P<package>.+)-(?P<version>\d(?:\.\d)*))$')
+-HTTPS_REQUIREMENT = re.compile(
+-    r'^-e (?P<link>.*).+#(?P<package>.+)-(?P<version>\d(?:\.\d)*)$')
+-install_requires = []
+-dependency_links = []
+-
+-for requirement in (
+-        l.strip() for l in open('requires.txt') if not l.startswith("#")):
+-    match = REPO_REQUIREMENT.match(requirement)
+-    if match:
+-        assert which(match.group('vcs')) is not None, \
+-            ("VCS '%(vcs)s' must be installed in order to "
+-             "install %(link)s" % match.groupdict())
+-        install_requires.append("%(package)s==%(version)s" % match.groupdict())
+-        dependency_links.append(match.group('link'))
+-        continue
++        print(f"WARNING: Dependency check for {toolkit} ({tool}) failed with error code {retcode}")
+ 
+-    if requirement.startswith("https"):
+-        install_requires.append(requirement)
+-        continue
+ 
+-    match = HTTPS_REQUIREMENT.match(requirement)
+-    if match:
+-        install_requires.append("%(package)s>=%(version)s" % match.groupdict())
+-        dependency_links.append(match.group('link'))
+-        continue
+-
+-    install_requires.append(requirement)
+-
+-if major == 2:
+-    install_requires.extend(['web.py>=0.37',
+-                             'xlwt>=0.7.4',
+-                             'matplotlib-venn>=0.5'])
+-elif major == 3:
+-    pass
+-
+-cgat_packages = find_packages(exclude=['tests'])
++# Adjust packages and directories
++cgat_packages = find_packages(include=["cgat", "cgat.*"], exclude=['tests'])
+ cgat_package_dirs = {'cgat': 'cgat'}
+ 
+-##########################################################
+-##########################################################
+-# classifiers
+-classifiers = """
+-Development Status :: 3 - Alpha
+-Intended Audience :: Science/Research
+-Intended Audience :: Developers
+-License :: OSI Approved
+-Programming Language :: Python
+-Topic :: Software Development
+-Topic :: Scientific/Engineering
+-Operating System :: POSIX
+-Operating System :: Unix
+-Operating System :: MacOS
+-"""
+-
+-##########################################################
+-# Cython Extensions
++# Cython extensions and paths
+ conda_includes = [os.path.dirname(sysconfig.get_paths()["include"])]
+ conda_libdirs = [os.path.dirname(sysconfig.get_paths()["stdlib"])]
+-
+-# Connected components cython extension
+ pysam_libraries = pysam.get_libraries()
+-pysam_libdirs = list(set(os.path.dirname(x) for x in
+-                         pysam_libraries)) + conda_libdirs
+-
+-# remove lib and .so and add htslib
+-pysam_libs = ["hts"] + list([os.path.basename(x)[3:-3] for x in
+-                             pysam_libraries])
+-
++pysam_libdirs = list(set(os.path.dirname(x) for x in pysam_libraries)) + conda_libdirs
++pysam_libs = ["hts"] + [os.path.basename(x)[3:-3] for x in pysam_libraries]
+ pysam_dirname = os.path.dirname(pysam.__file__)
+-if IS_OSX:
+-    # linking against bundles does no work (and apparently is not needed)
+-    # within OS X
+-    extra_link_args = []
+-else:
+-    extra_link_args = [os.path.join(pysam_dirname, x) for x in
+-                       pysam.get_libraries()]
+-
+-extra_link_args_pysam = ['-Wl,-rpath,{}'.format(x) for x in pysam_libdirs] +\
+-                        ['-Wl,-rpath,{}'.format(x) for x in conda_libdirs]
++extra_link_args_pysam = [f'-Wl,-rpath,{x}' for x in pysam_libdirs + conda_libdirs]
+ 
+ extensions = [
+     Extension(
+         'cgat.Components',
+-        ['cgat/Components/Components.pyx',
+-         'cgat/Components/connected_components.cpp', ],
+-        library_dirs=[],
+-        libraries=[],
++        ['cgat/Components/Components.pyx', 'cgat/Components/connected_components.cpp'],
++        include_dirs=[os.path.join('cgat', 'Components')] + conda_includes,
+         language="c++",
+     ),
+     Extension(
+         "cgat.NCL.cnestedlist",
+-        ["cgat/NCL/cnestedlist.pyx",
+-         "cgat/NCL/intervaldb.c"],
+-        library_dirs=[],
+-        libraries=[],
++        ["cgat/NCL/cnestedlist.pyx", "cgat/NCL/intervaldb.c"],
+         language="c",
+     ),
+     Extension(
+         "cgat.GeneModelAnalysis",
+         ["cgat/GeneModelAnalysis.pyx"],
+         include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()],
+-        library_dirs=[],
+-        libraries=[],
+         define_macros=pysam.get_defines(),
+         language="c",
+     ),
+@@ -292,11 +126,8 @@ extensions = [
+     ),
+ ]
+ 
+-for e in extensions:
+-    e.cython_directives = {'language_level': "3str"} #all are Python-3
+-
++# Build setup configuration
+ setup(
+-    # package information
+     name='cgat',
+     version=version,
+     description='cgat : the Computational Genomics Analysis Toolkit',
+@@ -306,22 +137,26 @@ setup(
+     platforms=["any"],
+     keywords="computational genomics",
+     long_description='cgat : the Computational Genomics Analysis Toolkit',
+-    classifiers=[_f for _f in classifiers.split("\n") if _f],
++    classifiers=[_f for _f in """
++        Development Status :: 3 - Alpha
++        Intended Audience :: Science/Research
++        Intended Audience :: Developers
++        License :: OSI Approved
++        Programming Language :: Python
++        Topic :: Software Development
++        Topic :: Scientific/Engineering
++        Operating System :: POSIX
++        Operating System :: Unix
++        Operating System :: MacOS
++    """.splitlines() if _f],
+     url="http://www.cgat.org/cgat/Tools/",
+-    # package contents
++    python_requires=">=3.6",
+     packages=cgat_packages,
+     package_dir=cgat_package_dirs,
+     include_package_data=True,
+-    entry_points={
+-        'console_scripts': ['cgat = cgat.cgat:main']
+-    },
+-    # dependencies
+-    install_requires=install_requires,
+-    dependency_links=dependency_links,
+-    # extension modules
++    entry_points={'console_scripts': ['cgat = cgat.cgat:main']},
+     ext_modules=extensions,
+     cmdclass={'build_ext': build_ext},
+-    # other options
+     zip_safe=False,
+     test_suite="tests",
+ )
diff --git a/recipes/cgat-apps/build.sh b/recipes/cgat-apps/build.sh
index 404e4cfe860ef..c2405bcd10101 100644
--- a/recipes/cgat-apps/build.sh
+++ b/recipes/cgat-apps/build.sh
@@ -1,28 +1,16 @@
 #!/bin/bash
 
 # export compiler flags
-#export CFLAGS=${CFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
-#export CPPFLAGS=${CPPFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
-export LDFLAGS=${LDFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
-export CPATH=${CPATH}" -I${PREFIX}/include -L${PREFIX}/lib"
-export C_INCLUDE_PATH=${C_INCLUDE_PATH}:${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${CPLUS_INCLUDE_PATH}:${PREFIX}/include
-export LIBRARY_PATH=${LIBRARY_PATH}:${PREFIX}/lib
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PREFIX}/lib:${PREFIX}/lib/R/lib
-
-# linking htslib, see:
-# http://pysam.readthedocs.org/en/latest/installation.html#external
-# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79
-#export CFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
-#export CPPFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
-#export LDFLAGS="-L$PREFIX/lib"
-
-#export HTSLIB_LIBRARY_DIR=$PREFIX/lib
-#export HTSLIB_INCLUDE_DIR=$PREFIX/include
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
+export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include"
 
 # remove install_requires (no longer required with conda package)
-sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
-sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
+sed -i.bak'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
+sed -i.bak'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
+rm -rf *.bak
 
 # https://bioconda.github.io/linting.html#setup-py-install-args
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt
+$PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/cgat-apps/build_failure.linux-64.yaml b/recipes/cgat-apps/build_failure.linux-64.yaml
deleted file mode 100644
index e3ce08b25b4e4..0000000000000
--- a/recipes/cgat-apps/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: cd4db28503c1e8d834aba9be11a1d56ca31801f1fcbbef8169312e7476bc9123  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: dependency issue
-log: |2-
-    File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems
-      self._maybe_raise_for_conda_build(
-    File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build
-      raise exc
-  conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python[version='>=3.7,<3.8.0a0']"), MatchSpec("alignlib-lite==0.3=py37h3f2a3d2_2")}
-  Encountered problems while solving:
-    - package alignlib-lite-0.3-py37h3f2a3d2_2 requires python >=3.7,<3.8.0a0, but none of the providers can be installed
-
-  Could not solve for environment specs
-  The following packages are incompatible
-   [32malignlib-lite[0m is installable with the potential options
-     [32malignlib-lite 0.3[0m would require
-       [32mpython >=3.7,<3.8.0a0 [0m with the potential options
-          [32mpython [2.7.15|3.5.5|3.6.6|3.7.0][0m would require
-            [32mopenssl >=1.0.2o,<1.0.3a [0m, which can be installed;
-          [32mpython [2.7.15|3.6.6|3.6.7|3.7.0|3.7.1][0m would require
-            [32mopenssl >=1.0.2p,<1.0.3a [0m, which can be installed;
-          [32mpython [2.7.15|3.6.7|...|3.7.6][0m would require
-            [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed;
-            [32mpypy3.6 7.3.0.* [0m with the potential options
-               [32mpypy3.6 7.3.0[0m would require
-                 [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed;
-               [32mpypy3.6 7.3.0[0m would require
-                 [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed;
-               [32mpypy3.6 7.3.0[0m would require
-                  [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed;
-          [32mpython 3.7.10[0m would require
-            [32mpypy3.7 [7.3.4.* |7.3.5.* ][0m with the potential options
-               [32mpypy3.7 [7.3.4|7.3.5][0m would require
-                 [32mopenssl >=1.1.1k,<1.1.2a [0m, which can be installed;
-               [32mpypy3.7 7.3.5[0m would require
-                  [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed;
-          [32mpython [3.6.13|3.6.15|3.7.10|3.7.12][0m would require
-            [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed;
-          [32mpython [3.7.10|3.7.12][0m, which can be installed;
-          [32mpython [3.6.13|3.7.10][0m would require
-            [32mopenssl >=1.1.1j,<1.1.2a [0m, which can be installed;
-          [32mpython [3.6.12|3.7.5|3.7.9][0m would require
-            [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed;
-            [32mpypy3.6 7.3.3.* [0m, which requires
-              [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed;
-            [32mpypy3.7 7.3.3.* [0m, which requires
-               [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed;
-          [32mpython [3.6.10|3.6.11|3.7.6|3.7.8][0m would require
-            [32mopenssl >=1.1.1g,<1.1.2a [0m, which can be installed;
-          [32mpython 3.7.6[0m would require
-            [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed;
-          [32mpython [3.6.11|3.6.12|3.6.9|3.7.8|3.7.9][0m would require
-             [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed;
-             [32mpypy3.6 7.3.2.* [0m, which requires
-                [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed;
-     [32malignlib-lite [0.2.3|0.3][0m would require
-       [32mpython [2.7* |3.6* |>=2.7,<2.8.0a0 |>=3.6,<3.7.0a0 ][0m with the potential options
-          [32mpython [2.7.15|3.5.5|3.6.6|3.7.0][0m, which can be installed (as previously explained);
-          [32mpython [2.7.15|3.6.6|3.6.7|3.7.0|3.7.1][0m, which can be installed (as previously explained);
-          [32mpython [2.7.15|3.6.7|...|3.7.6][0m, which can be installed (as previously explained);
-          [32mpython [3.6.13|3.6.15|3.7.10|3.7.12][0m, which can be installed (as previously explained);
-          [32mpython [3.6.13|3.7.10][0m, which can be installed (as previously explained);
-          [32mpython [3.6.12|3.7.5|3.7.9][0m, which can be installed (as previously explained);
-          [32mpython [3.6.10|3.6.11|3.7.6|3.7.8][0m, which can be installed (as previously explained);
-          [32mpython [3.6.11|3.6.12|3.6.9|3.7.8|3.7.9][0m, which can be installed (as previously explained);
-          [32mpython [2.7.12|2.7.13|...|3.6.5][0m would require
-            [32mopenssl [1.0* |1.0.* ][0m, which can be installed;
-          [32mpython [3.6.10|3.6.9][0m would require
-            [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed;
-            [32mpypy3.6 7.3.1.* [0m, which requires
-               [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed;
-          [32mpython [3.6.10|3.6.9][0m would require
-             [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed;
-     [32malignlib-lite [0.2.3|0.3][0m would require
-       [32mpython [3.4* |3.5* |>=3.5,<3.6.0a0 ][0m, which can be installed (as previously explained);
-     [32malignlib-lite 0.3[0m would require
-       [32mpython_abi 3.10.* *_cp310[0m, which can be installed;
-     [32malignlib-lite 0.3[0m would require
-       [32mpython_abi 3.7.* *_cp37m[0m, which can be installed;
-     [32malignlib-lite 0.3[0m would require
-       [32mpython_abi 3.8.* *_cp38[0m, which can be installed;
-     [32malignlib-lite 0.3[0m would require
-        [32mpython_abi 3.9.* *_cp39[0m, which can be installed;
-   [32mpysam >=0.22.1,<0.23.0a0 [0m is installable with the potential options
-     [32mpysam 0.22.1[0m would require
-       [32mpython_abi 3.8.* *_cp38[0m, which can be installed;
-     [32mpysam 0.22.1[0m would require
-       [32mpython_abi 3.10.* *_cp310[0m, which can be installed;
-     [31mpysam 0.22.1[0m would require
-       [31mopenssl >=3.3.1,<4.0a0 [0m, which conflicts with any installable versions previously reported;
-     [32mpysam 0.22.1[0m would require
-       [32mpython_abi 3.12.* *_cp312[0m, which can be installed;
-     [32mpysam 0.22.1[0m would require
-        [32mpython_abi 3.9.* *_cp39[0m, which can be installed;
-   [31mpython >=3.11,<3.12.0a0 [0m is not installable because there are no viable options
-     [31mpython [3.11.0|3.11.1|...|3.11.9][0m would require
-       [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported;
-     [31mpython 3.11.0[0m would require
-       [32mopenssl >=1.1.1q,<1.1.2a [0m, which can be installed;
-       [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported;
-     [31mpython 3.11.0[0m would require
-        [32mopenssl >=1.1.1s,<1.1.2a [0m, which can be installed;
-        [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported;
-   [31mpython_abi 3.11.* *_cp311[0m is not installable because it conflicts with any installable versions previously reported.
-# Last 100 lines of the build log.
diff --git a/recipes/cgat-apps/build_failure.osx-64.yaml b/recipes/cgat-apps/build_failure.osx-64.yaml
deleted file mode 100644
index 63feff1b5e2d5..0000000000000
--- a/recipes/cgat-apps/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: cd4db28503c1e8d834aba9be11a1d56ca31801f1fcbbef8169312e7476bc9123  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: dependency issue
-log: |2-
-     alignlib-lite 0.3 would require
-       python_abi 3.7.* *_cp37m, which can be installed;
-     alignlib-lite 0.3 would require
-       python >=3.7,<3.8.0a0 , which can be installed;
-     alignlib-lite 0.3 would require
-       python_abi 3.8.* *_cp38, which can be installed;
-     alignlib-lite 0.3 would require
-        python_abi 3.9.* *_cp39, which can be installed;
-   pysam >=0.22.1,<0.23.0a0  is installable with the potential options
-     pysam 0.22.1 would require
-       xz >=5.2.6,<6.0a0 , which conflicts with any installable versions previously reported;
-     pysam 0.22.1 would require
-        python_abi 3.12.* *_cp312, which can be installed;
-   python >=3.11,<3.12.0a0  is not installable because it requires
-     python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
-   python_abi 3.11.* *_cp311 is not installable because it conflicts with any installable versions previously reported.
-
-  During handling of the above exception, another exception occurred:
-
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build
-      create_build_envs(top_level_pkg, notest)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs
-      raise e
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs
-      environ.get_package_records(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions
-      precs = get_package_records(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions
-      precs = get_package_records(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions
-      precs = get_package_records(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions
-      precs = _install_actions(prefix, index, specs)["LINK"]
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions
-      txn = solver.solve_for_transaction(prune=False, ignore_pinned=False)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction
-      unlink_precs, link_precs = self.solve_for_diff(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff
-      final_precs = self.solve_final_state(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state
-      out_state = self._solving_loop(in_state, out_state, index)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop
-      solved = self._solve_attempt(in_state, out_state, index, attempt=attempt)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt
-      new_conflicts = self._maybe_raise_for_problems(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems
-      self._maybe_raise_for_conda_build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build
-      raise exc
-  conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("alignlib-lite==0.2.3=py27_1"), MatchSpec("python=2.7")}
-  Encountered problems while solving:
-    - package alignlib-lite-0.2.3-py27_1 requires python 2.7*, but none of the providers can be installed
-
-  Could not solve for environment specs
-  The following packages are incompatible
-   alignlib-lite is installable with the potential options
-     alignlib-lite [0.2.3|0.3] would require
-       python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
-     alignlib-lite [0.2.3|0.3] would require
-       python 3.4* , which can be installed;
-     alignlib-lite [0.2.3|0.3] would require
-       python [3.5* |>=3.5,<3.6.0a0 ] with the potential options
-          python [3.5.1|3.5.2] would require
-            xz 5.0.* , which can be installed;
-          python [3.5.2|3.5.3|3.5.4|3.5.5], which can be installed;
-     alignlib-lite 0.3 would require
-       python_abi 2.7.* *_cp27m, which can be installed;
-     alignlib-lite 0.3 would require
-       python_abi 3.10.* *_cp310, which can be installed;
-     alignlib-lite 0.3 would require
-       python 3.6* , which can be installed;
-     alignlib-lite 0.3 would require
-       python >=3.6,<3.7.0a0 , which can be installed;
-     alignlib-lite 0.3 would require
-       python_abi 3.6.* *_cp36m, which can be installed;
-     alignlib-lite 0.3 would require
-       python_abi 3.7.* *_cp37m, which can be installed;
-     alignlib-lite 0.3 would require
-       python >=3.7,<3.8.0a0 , which can be installed;
-     alignlib-lite 0.3 would require
-       python_abi 3.8.* *_cp38, which can be installed;
-     alignlib-lite 0.3 would require
-        python_abi 3.9.* *_cp39, which can be installed;
-   pysam >=0.22.1,<0.23.0a0  is installable with the potential options
-     pysam 0.22.1 would require
-       xz >=5.2.6,<6.0a0 , which conflicts with any installable versions previously reported;
-     pysam 0.22.1 would require
-        python_abi 3.12.* *_cp312, which can be installed;
-   python >=3.11,<3.12.0a0  is not installable because it requires
-     python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
-   python_abi 3.11.* *_cp311 is not installable because it conflicts with any installable versions previously reported.
-# Last 100 lines of the build log.
diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml
index 4cf264a7950fe..cc4106af5f493 100644
--- a/recipes/cgat-apps/meta.yaml
+++ b/recipes/cgat-apps/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "cgat-apps" %}
-{% set version = "0.7.2" %}
+{% set version = "0.7.4" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://pypi.io/packages/source/c/cgat/cgat-{{ version }}.tar.gz
-  sha256: 746701d1a6677e8200092894c35c942383123fd8e22ab172f3ef6b2222b8eaef
-
+  url: https://github.com/cgat-developers/cgat-apps/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 3e161597c6e4cf59fc121a8527aeddefd1526f7d13c370d5eaf15b4d3a1894e6
+  patches:
+    - 0001-setup.py.patch
   
 build:
-  number: 2
-  skip: true # [py == 312]
+  number: 0
   run_exports:
     - {{ pin_subpackage('cgat-apps', max_pin="x.x") }}
   entry_points:
@@ -24,11 +24,11 @@ requirements:
     - {{ compiler('cxx') }}
   host:
     - python
-    - cython
+    - pip
+    - cython >=0.29.35
     - numpy
     - pysam
     - htslib
-    - setuptools
   run:
     - python
     - cgatcore
@@ -52,7 +52,6 @@ requirements:
     - ucsc-wigtobigwig
     - coreutils
     - grep
-    - zlib
 
 test:
   imports:
@@ -65,7 +64,10 @@ test:
     - cgat bam2bed -h
 
 about:
-  home: https://cgat-apps.readthedocs.io/en/latest/
+  home: "https://github.com/cgat-developers/cgat-apps"
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: "Computational Genomics Analysis Toolkit"
+  summary: "Computational Genomics Analysis Toolkit."
+  dev_url: "https://github.com/cgat-developers/cgat-apps"
+  doc_url: "https://cgat-apps.readthedocs.io/en/latest"
diff --git a/recipes/chopper/meta.yaml b/recipes/chopper/meta.yaml
index 00dbb1806606e..a044b5c8ae375 100644
--- a/recipes/chopper/meta.yaml
+++ b/recipes/chopper/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('chopper', max_pin="x.x") }}
 
@@ -39,3 +39,7 @@ about:
   license: MIT
   license_file: LICENSE
   summary: A rust command line for filtering and trimming long reads.
+  dev_url: https://github.com/wdecoster/chopper
+  doc_url: https://github.com/wdecoster/chopper#readme
+  notes: |
+    includes native support for Apple Silicon (M1/M2/M3) processors
diff --git a/recipes/clusty/build.sh b/recipes/clusty/build.sh
index abc2ec7057f35..231cb4591de1d 100644
--- a/recipes/clusty/build.sh
+++ b/recipes/clusty/build.sh
@@ -1,10 +1,14 @@
 #!/bin/bash
-#ln -s ${CC} gcc
-#ln -s ${CXX} g++
-#export PATH=$PATH:$(pwd)
+
 uname_S=`uname -s 2>/dev/null || echo not`
 
-if [ "$uname_S" == "Darwin" ]; then make -j${CPU_COUNT}; else make -j${CPU_COUNT} LEIDEN=true; fi
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+if [[ "$uname_S" == "Darwin" ]]; then
+	make -j"${CPU_COUNT}" CXX="${CXX}" LDFLAGS="${LDFLAGS}";
+else
+	make LEIDEN=true -j"${CPU_COUNT}" CXX="${CXX}" LDFLAGS="${LDFLAGS}";
+fi
 
 install -d "${PREFIX}/bin"
-install clusty "${PREFIX}/bin"
+install -v -m 0755 clusty "${PREFIX}/bin"
diff --git a/recipes/clusty/buildfixes.patch b/recipes/clusty/buildfixes.patch
new file mode 100644
index 0000000000000..aa30e082358e0
--- /dev/null
+++ b/recipes/clusty/buildfixes.patch
@@ -0,0 +1,13 @@
+diff --git a/makefile b/makefile
+index 21492fe..009c44f 100644
+--- a/makefile
++++ b/makefile
+@@ -73,7 +73,7 @@ ifeq ($(DYNAMIC_LINK), true)
+ else
+ ifeq ($(uname_S),Darwin)
+     CFLAGS  = -Wall -O3 $(ARCH_FLAGS) -std=c++17 $(DEFINE_FLAGS) $(INCLUDES)
+-    CLINK	= -lm -O3 -std=c++17 $(ABI_FLAGS) -static-libgcc
++    CLINK	= -lm -O3 -std=c++17 $(ABI_FLAGS)
+ else
+     CFLAGS  = -Wall -O3 $(ARCH_FLAGS) -std=c++17 $(DEFINE_FLAGS) $(INCLUDES) -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
+     CLINK	= -lm -static -O3 -std=c++17 $(ABI_FLAGS) -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
diff --git a/recipes/clusty/meta.yaml b/recipes/clusty/meta.yaml
index 280747e80a52c..f0ccb8d26d782 100644
--- a/recipes/clusty/meta.yaml
+++ b/recipes/clusty/meta.yaml
@@ -1,37 +1,42 @@
-{% set version = "1.1.1" %}
+{% set name = "clusty" %}
+{% set version = "1.1.4" %}
 
 package:
-  name: clusty
+  name: {{ name }}
   version: {{ version }}
 
 build:
   number: 0
   run_exports:
-  - {{ pin_subpackage('clusty', max_pin='x.x.x') }}
+  - {{ pin_subpackage('clusty', max_pin='x') }}
 
 source:
   git_url: https://github.com/refresh-bio/clusty.git
   git_rev: v{{ version }}
+  patches:
+    - buildfixes.patch  # [osx]
 
 requirements:
   build:
     - make
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
     - cmake
     - flex
     - bison
 
+test:
+  commands:
+    - clusty > /dev/null
+
 about:
   home: https://github.com/refresh-bio/clusty
   summary: "Clusty is a tool for large-scale data clustering."
-  license: GPL-3
-  license_family: GPL
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
-
-test:
-  commands:
-    - clusty > /dev/null
+  dev_url: https://github.com/refresh-bio/clusty
+  doc_url: "https://github.com/refresh-bio/clusty/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
@@ -39,4 +44,4 @@ extra:
     - osx-arm64
   skip-lints:
     - uses_vcs_url 
-    - missing_hash
\ No newline at end of file
+    - missing_hash
diff --git a/recipes/cmaple/build.sh b/recipes/cmaple/build.sh
index 63ffed49625be..0bf9ec1963687 100644
--- a/recipes/cmaple/build.sh
+++ b/recipes/cmaple/build.sh
@@ -8,13 +8,16 @@ set -ex
 sed -i.bak 's/-mavx/-mno-avx -mno-avx2 -march=nocona -mtune=haswell/' CMakeLists.txt
 
 DCMAKE_ARGS=""
-if [ "$(uname)" == Darwin ]; then
+if [[ "$(uname)" == Darwin ]]; then
 	CC=$(which "$CC")
 	CXX=$(which "$CXX")
 	AR=$(which "$AR")
 	RANLIB=$(which "$RANLIB")
 	DCMAKE_ARGS=(-DCMAKE_C_COMPILER="${CC}" -DCMAKE_CXX_COMPILER="${CXX}"
 		-DCMAKE_CXX_COMPILER_AR="${AR}" -DCMAKE_CXX_COMPILER_RANLIB="${RANLIB}")
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
 fi
 
 case $(uname -m) in
@@ -27,10 +30,12 @@ aarch64)
 esac
 
 mkdir build
-cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" -G Ninja \
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release -G Ninja \
 	"${DCMAKE_ARGS[@]}" \
 	-DBUILD_GMOCK=OFF -DINSTALL_GTEST=OFF \
-	-Wno-dev -Wno-deprecated --no-warn-unused-cli
+	-Wno-dev -Wno-deprecated --no-warn-unused-cli \
+	"${CONFIG_ARGS}"
 
 VERBOSE=1 cmake --build build --target install -j ${JOBS}
 
diff --git a/recipes/cmaple/meta.yaml b/recipes/cmaple/meta.yaml
index 808b5f3f941ee..9866c9e060621 100644
--- a/recipes/cmaple/meta.yaml
+++ b/recipes/cmaple/meta.yaml
@@ -1,19 +1,20 @@
 {% set name = "cmaple" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "68693229053d8c456028b7696ee39770ff55a3eaf3454d7087def08accbf0603" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "72079ac3881840ce6a6d45603202a2ab9a399aa8ebaf51fbdcd85337696e4435" %}
+
 package:
   name: {{ name }}
   version: {{ version | replace("-", "_") }}
+
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
+
 source:
   - url: https://github.com/iqtree/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
     sha256: {{ sha256 }}
-    # Patch necessary to build on arm, can be removed with next release
-    patches:
-      - patch
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -24,6 +25,7 @@ requirements:
   host:
     - libgomp  # [linux]
     - llvm-openmp  # [osx]
+
 test:
   source_files:
     - example/input.fa
@@ -33,6 +35,7 @@ test:
     - cmaple-aa
     # Mulled builds don't work with source_files
     - cmaple -aln example/input.fa  # [osx]
+
 about:
   home: "https://github.com/iqtree/cmaple"
   dev_url: "https://github.com/iqtree/cmaple"
@@ -40,7 +43,8 @@ about:
   license: "GPL-2.0"
   license_family: GPL2
   license_file: LICENSE
-  summary: "MAximum Parsimonious Likelihood Estimation in C/C++"
+  summary: "MAximum Parsimonious Likelihood Estimation in C/C++."
+
 extra:
   additional-platforms:
     - linux-aarch64
diff --git a/recipes/cmaple/patch b/recipes/cmaple/patch
deleted file mode 100644
index afeca4c13e424..0000000000000
--- a/recipes/cmaple/patch
+++ /dev/null
@@ -1,563 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index a58bf79..306b4e8 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,6 +1,6 @@
- ##################################################################
- # CMAPLE cmake build definition
--# Copyright (c) 2022 Nhan Ly-Trong, Chris Bielow, Nicola De Maio, Bui Quang Minh 
-+# Copyright (c) 2022 Nhan Ly-Trong, Chris Bielow, Nicola De Maio, Bui Quang Minh
- ##################################################################
- 
- # Windows example usages:
-@@ -11,10 +11,8 @@
- #
- # cmake -G "Visual Studio 12" <source_dir>          (32-bit version, compiled with MSVC)
- # cmake -G "Visual Studio 12 Win64" <source_dir>    (64-bit version, compiled with MSVC)
--# cmake -G "Visual Studio 12 Win64" -T "Intel C++ Compiler XE 15.0" <source_dir>        (64-bit version, compiled with ICC)
--# cmake -G "MinGW Makefiles" <source_dir> (TDM-GCC)
--# cmake -G "Unix Makefiles" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_MAKE_PROGRAM=mingw32-make <source_dir> (TDM-GCC and clang)
--
-+## using clang.exe as shipped with Visual Studio:
-+# cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -G "Ninja" -DCMAPLE_FLAGS=static ..\cmaple
- 
- # Linux example usages:
- #----------------------
-@@ -63,13 +61,24 @@ set(GCC_MIN_VERSION "5")
- ##############################################################
- # Clang-tidy
- ##############################################################
--message("Setup clang-tidy")
--#set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-header-filter=.;-checks=performance-*")
-+if (USE_CLANG_TIDY)
-+  message("Setup clang-tidy (USE_CLANG_TIDY=ON)")
-+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-header-filter=.;-checks=performance-*")
-+else()
-+  message("No clang-tidy (USE_CLANG_TIDY=OFF)")
-+endif()
-+
- 
- project(cmaple)
- add_definitions(-DCMAPLE)
- set(CMAKE_CXX_STANDARD 20)
--set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE) # Enable IPO (LTO) by default
-+
-+if (((${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm" OR ${CMAKE_SYSTEM_PROCESSOR} MATCHES "aarch") AND (NOT APPLE AND UNIX))
-+    OR WIN32)
-+    set(CMAKE_INTERPROCEDURAL_OPTIMIZATION FALSE) # Disable IPO (LTO) for Linux ARM
-+else()
-+    set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE) # Enable IPO (LTO) by default
-+endif()
- 
- # The version number.
- set (cmaple_VERSION_MAJOR 1)
-@@ -80,14 +89,19 @@ option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)
- option(INSTALL_CMAPLE "Enable installation of CMAPLE. (Projects integrating CMAPLE may want to turn this OFF.)" ON)
- 
- ##################################################################
--# check existence of a few basic functions
-+# check existence of a few basic functions and headers
- ##################################################################
--include (${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
-+include (CheckFunctionExists)
- check_function_exists (gettimeofday HAVE_GETTIMEOFDAY)
- check_function_exists (getrusage HAVE_GETRUSAGE)
- check_function_exists (GlobalMemoryStatusEx HAVE_GLOBALMEMORYSTATUSEX)
- check_function_exists (strndup HAVE_STRNDUP)
- check_function_exists (strtok_r HAVE_STRTOK_R)
-+## find optional headers
-+include (CheckIncludeFile)
-+CHECK_INCLUDE_FILE("unistd.h" CMAPLE_HAS_UNISTDH)
-+
-+
- 
- if (NOT CMAKE_BUILD_TYPE)
-     set(CMAKE_BUILD_TYPE "Release")
-@@ -129,6 +143,8 @@ else()
-     message("Target OS     : Unknown and untested yet")
- endif()
- 
-+# NHANLT: Note: to build a static version, we have to link
-+# the static OpenMP library manually here instead of the dynamic one
- ##################################################################
- # configure OpenMP to build a static version
- ##################################################################
-@@ -136,13 +152,19 @@ if (NOT CMAPLE_FLAGS MATCHES "single")
-     message("OpenMP        : Yes")
- 
-     if(APPLE)
--        if(OSX_NATIVE_ARCHITECTURE STREQUAL "arm64")
-+        if (${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm" OR ${CMAKE_SYSTEM_PROCESSOR} MATCHES "aarch")
-             link_directories(${PROJECT_SOURCE_DIR}/libraries/static/libmac_m1)
-         else()
-             link_directories(${PROJECT_SOURCE_DIR}/libraries/static/libmac)
-         endif()
--    elseif (WIN32 OR UNIX)
--        if (CMAKE_SIZEOF_VOID_P EQUAL 4)
-+    elseif (UNIX AND NOT ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
-+      if (${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm" OR ${CMAKE_SYSTEM_PROCESSOR} MATCHES "aarch")
-+        link_directories(${PROJECT_SOURCE_DIR}/libraries/static/liblinux_arm)
-+      else()
-+        link_directories(${PROJECT_SOURCE_DIR}/libraries/static/lib)
-+      endif()
-+    elseif (WIN32)
-+        if (BINARY32)
-             link_directories(${PROJECT_SOURCE_DIR}/libraries/static/lib32)
-         else()
-             link_directories(${PROJECT_SOURCE_DIR}/libraries/static/lib)
-@@ -169,13 +191,20 @@ endif()
- 
- ## enable 'SSE/AVX' on x86-64, 'neon' on arm to achive faster computations (mainly the Matrix::dotProduct())
- if (CMAKE_CXX_COMPILER_ID MATCHES "Clang|GNU")
--  if(${CMAKE_SYSTEM_PROCESSOR} MATCHES "x86") 
-+  if(${CMAKE_SYSTEM_PROCESSOR} MATCHES "x86")
-     add_compile_options(-msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -msse4.2 -mavx) # needed for simde instructions
--  elseif (${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm")
--    add_compile_options(-neon)  
--  endif() 
-+  elseif (${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm" OR ${CMAKE_SYSTEM_PROCESSOR} MATCHES "aarch")
-+    # NHANLT: Because the option "-neon" is not found,
-+    # I changed it to "-march=native"
-+    #add_compile_options(-neon)
-+    if (NOT APPLE AND UNIX)
-+        add_compile_options(-march=armv8-a)
-+    else()
-+        add_compile_options(-march=native)
-+    endif()
-+  endif()
- elseif (CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
--  if(${CMAKE_SYSTEM_PROCESSOR} MATCHES "x86") 
-+  if(${CMAKE_SYSTEM_PROCESSOR} MATCHES "x86")
-     add_compile_options(/arch:AVX2) ## not really needed, but may be beneficial in other places when in Release mode (i.e. with optimizations turned on)
-   endif()
- endif()
-@@ -244,13 +273,13 @@ FetchContent_MakeAvailable(googletest)
- ##################################################################
- LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}")
- if (NOT TARGET ncl)
--	add_subdirectory(libraries/ncl)
--endif() 
-+    add_subdirectory(libraries/ncl)
-+endif()
- if (NOT TARGET nclextra)
--	add_subdirectory(libraries/nclextra)
--endif() 
-+    add_subdirectory(libraries/nclextra)
-+endif()
- add_subdirectory(utils)
--add_subdirectory(libraries/SIMDe) 
-+add_subdirectory(libraries/SIMDe)
- target_include_directories(cmaple_utils PUBLIC ${SIMDE_INCLUDE_DIRECTORY})
- add_subdirectory(model)
- add_subdirectory(alignment)
-@@ -267,16 +296,17 @@ add_executable(cmaple-aa main/main.cpp)
- 
- if(Backtrace_FOUND)
-   include_directories(${Backtrace_INCLUDE_DIR})
--  target_link_libraries(cmaple ${Backtrace_LIBRARY})
--  target_link_libraries(cmaple-aa ${Backtrace_LIBRARY})
-+  target_link_libraries(cmaple PRIVATE ${Backtrace_LIBRARY})
-+  target_link_libraries(cmaple-aa PRIVATE ${Backtrace_LIBRARY})
- endif(Backtrace_FOUND)
- 
- ##################################################################
- # setup linking flags
- ##################################################################
- 
--target_link_libraries(cmaple maple cmaple_tree cmaple_alignment cmaple_model ncl nclextra cmaple_utils)
--target_link_libraries(cmaple-aa maple-aa cmaple_tree-aa cmaple_alignment-aa cmaple_model-aa ncl nclextra cmaple_utils)
-+target_link_libraries(cmaple PUBLIC maple cmaple_tree cmaple_alignment cmaple_model ncl nclextra cmaple_utils)
-+target_link_libraries(cmaple-aa PUBLIC maple-aa cmaple_tree-aa cmaple_alignment-aa cmaple_model-aa ncl nclextra cmaple_utils)
-+
- 
- ##############################################################
- # add the install targets
-@@ -323,7 +353,20 @@ set(CPACK_SOURCE_IGNORE_FILES
- 
- set (SYSTEM_NAME "${CMAKE_SYSTEM_NAME}")
- if (${CMAKE_SYSTEM_NAME} STREQUAL "Darwin")
--    set (SYSTEM_NAME "MacOSX")
-+    if (IQTREE_FLAGS MATCHES "oldmac")
-+        set (SYSTEM_NAME "macOS10.5")
-+    elseif (${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm" OR ${CMAKE_SYSTEM_PROCESSOR} MATCHES "aarch")
-+        set (SYSTEM_NAME "macOS-arm")
-+    else()
-+        set (SYSTEM_NAME "macOS-intel")
-+    endif()
-+endif()
-+if (NOT APPLE AND UNIX)
-+    if (${CMAKE_SYSTEM_PROCESSOR} MATCHES "arm" OR ${CMAKE_SYSTEM_PROCESSOR} MATCHES "aarch")
-+        set (SYSTEM_NAME "Linux-arm")
-+    else()
-+        set (SYSTEM_NAME "Linux-intel")
-+    endif()
- endif()
- 
- set(CPACK_PACKAGE_FILE_NAME
-diff --git a/alignment/alignment.cpp b/alignment/alignment.cpp
-index 738793d..1b98ce1 100644
---- a/alignment/alignment.cpp
-+++ b/alignment/alignment.cpp
-@@ -875,7 +875,15 @@ void cmaple::Alignment::readMaple(std::istream& aln_stream) {
- 
-       // extract <Type>
-       ssin >> tmp;
--      StateType state = convertChar2State(toupper(tmp[0]));
-+      StateType state;
-+      try
-+      {
-+        state = convertChar2State(toupper(tmp[0]));
-+      }
-+      catch(std::invalid_argument& e)
-+      {
-+        throw std::invalid_argument("Line " + convertIntToString(line_num + 1) + ": " + e.what());
-+      }
- 
-       // extract <Position>
-       ssin >> tmp;
-@@ -1037,9 +1045,8 @@ auto cmaple::Alignment::convertChar2State(char state) -> StateType {
-             return 1;
-         default:
-             {
--                string invalid_state_msg = "Invalid state ";
-+                string invalid_state_msg = "Unrecognized character ";
-                 invalid_state_msg += state;
--                invalid_state_msg += ". Please check and try again!";
-                 throw std::invalid_argument(invalid_state_msg);
-                 return TYPE_INVALID;
-             }
-@@ -1081,9 +1088,8 @@ auto cmaple::Alignment::convertChar2State(char state) -> StateType {
-         case 'V':
-           return 1 + 2 + 4 + 3;  // A or G or C
-         default: {
--          string invalid_state_msg = "Invalid state ";
-+          string invalid_state_msg = "Unrecognized character ";
-           invalid_state_msg += state;
--          invalid_state_msg += ". Please check and try again!";
-           throw std::invalid_argument(invalid_state_msg);
-           // return TYPE_INVALID;  // unrecognize character
-         }
-@@ -1113,9 +1119,8 @@ auto cmaple::Alignment::convertChar2State(char state) -> StateType {
-       loc = strchr(symbols_protein, state);
- 
-       if (loc == nullptr) {
--        string invalid_state_msg = "Invalid state ";
-+        string invalid_state_msg = "Unrecognized character ";
-         invalid_state_msg += state;
--        invalid_state_msg += ". Please check and try again!";
-         throw std::invalid_argument(invalid_state_msg);
-         // return TYPE_INVALID;  // unrecognize character
-       }
-@@ -1130,9 +1135,8 @@ auto cmaple::Alignment::convertChar2State(char state) -> StateType {
- 
-         if (!loc)
-         {
--            string invalid_state_msg = "Invalid state ";
-+            string invalid_state_msg = "Unrecognized character ";
-             invalid_state_msg += state;
--            invalid_state_msg += ". Please check and try again!";
-             throw std::invalid_argument(invalid_state_msg);
-             return TYPE_INVALID; // unrecognize character
-         }
-@@ -1141,9 +1145,8 @@ auto cmaple::Alignment::convertChar2State(char state) -> StateType {
-     case cmaple::SeqRegion::SEQ_AUTO:
-     case cmaple::SeqRegion::SEQ_UNKNOWN:
-     default: {
--      string invalid_state_msg = "Invalid state ";
-+      string invalid_state_msg = "Unrecognized character ";
-       invalid_state_msg += state;
--      invalid_state_msg += ". Please check and try again!";
-       throw std::invalid_argument(invalid_state_msg);
-       // return TYPE_INVALID;
-     }
-diff --git a/cmaple.doxy b/cmaple.doxy
-index 3beaee7..da2a488 100644
---- a/cmaple.doxy
-+++ b/cmaple.doxy
-@@ -48,13 +48,13 @@ PROJECT_NAME           = CMAPLE
- # could be handy for archiving the generated documentation or if some version
- # control system is used.
- 
--PROJECT_NUMBER         = 1
-+PROJECT_NUMBER         = 1.0.0
- 
- # Using the PROJECT_BRIEF tag one can provide an optional one line description
- # for a project that appears at the top of each page and should give viewer a
- # quick idea about the purpose of the project. Keep the description short.
- 
--PROJECT_BRIEF          = "CMaple phylogenetic software"
-+PROJECT_BRIEF          = "C++ MAximum Parsimonious Likelihood Estimation"
- 
- # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
- # in the documentation. The maximum height of the logo should not exceed 55
-diff --git a/cmaple_config.h.in b/cmaple_config.h.in
-index 2729eea..4090d2b 100644
---- a/cmaple_config.h.in
-+++ b/cmaple_config.h.in
-@@ -15,5 +15,7 @@
- #cmakedefine HAVE_STRNDUP
- #cmakedefine HAVE_STRTOK_R
- 
-+#cmakedefine CMAPLE_HAS_UNISTDH
-+
- /* does the platform provide backtrace functions? */
- #cmakedefine Backtrace_FOUND
-diff --git a/libraries/static/liblinux_arm/libomp.a b/libraries/static/liblinux_arm/libomp.a
-new file mode 100644
-index 0000000..bf95783
-Binary files /dev/null and b/libraries/static/liblinux_arm/libomp.a differ
-diff --git a/libraries/static/libmac_m1/libomp.a b/libraries/static/libmac_m1/libomp.a
-index bdff3e4..0c72cdc 100644
-Binary files a/libraries/static/libmac_m1/libomp.a and b/libraries/static/libmac_m1/libomp.a differ
-diff --git a/maple/cmaple.cpp b/maple/cmaple.cpp
-index c9f898d..9e21c9f 100644
---- a/maple/cmaple.cpp
-+++ b/maple/cmaple.cpp
-@@ -150,11 +150,6 @@ void cmaple::runCMAPLE(cmaple::Params &params)
-         std::ostream null_stream(nullptr);
-         std::ostream& out_stream = cmaple::verbose_mode >= cmaple::VB_MED ? std::cout : null_stream;
-         tree.infer(tree_search_type, params.shallow_tree_search, out_stream);
--
--        // Write the normal tree file
--        ofstream out = ofstream(output_treefile);
--        out << tree.exportNewick(tree_format);
--        out.close();
-         
-         // Compute branch supports (if users want to do so)
-         if (params.compute_aLRT_SH)
-@@ -169,21 +164,19 @@ void cmaple::runCMAPLE(cmaple::Params &params)
-             tree.computeBranchSupport(static_cast<int>(params.num_threads), params.aLRT_SH_replicates, params.aLRT_SH_half_epsilon + params.aLRT_SH_half_epsilon, allow_replacing_ML_tree, out_stream);
- 
-             // write the tree file with branch supports
--            ofstream out_tree_branch_supports = ofstream(prefix + ".aLRT_SH.treefile");
-+            /*ofstream out_tree_branch_supports = ofstream(prefix + ".aLRT_SH.treefile");
-             out_tree_branch_supports << tree.exportNewick(tree_format, true);
--            out_tree_branch_supports.close();
-+            out_tree_branch_supports.close();*/
-         }
-         
-         // If needed, apply some minor changes (collapsing zero-branch leaves into less-info sequences, re-estimating model parameters) to make the processes of outputting then re-inputting a tree result in a consistent tree
-         if (params.make_consistent)
--        {
-             tree.makeTreeInOutConsistent();
--            
--            // Overwrite the normal tree file
--            ofstream overwrite_out = ofstream(output_treefile);
--            overwrite_out << tree.exportNewick(tree_format);
--            overwrite_out.close();
--        }
-+        
-+        // Write the normal tree file
-+        ofstream out = ofstream(output_treefile);
-+        out << tree.exportNewick(tree_format);
-+        out.close();
-         
-         // output log-likelihood of the tree
-         if (cmaple::verbose_mode > cmaple::VB_QUIET) {
-@@ -205,10 +198,10 @@ void cmaple::runCMAPLE(cmaple::Params &params)
-         // Show information about output files
-         std::cout << "Analysis results written to:" << std::endl;
-         std::cout << "Maximum-likelihood tree:       " << output_treefile << std::endl;
--        if (params.compute_aLRT_SH) {
-+        /*if (params.compute_aLRT_SH) {
-           std::cout << "Tree with aLRT-SH values:      "
-                     << prefix + ".aLRT_SH.treefile" << std::endl;
--        }
-+        }*/
-         std::cout << "Screen log file:               " << prefix + ".log" << std::endl << std::endl;
-         
-         // show runtime
-diff --git a/model/model_aa.nexus b/model/model_aa.nexus
-index e52e032..6da7af0 100644
---- a/model/model_aa.nexus
-+++ b/model/model_aa.nexus
-@@ -208,7 +208,9 @@ model VT=
- 0.5411769916657778 0.8912614404565405 1.0894926581511342 0.7447620891784513 2.1579775140421025 0.9183596801412757 0.5818111331782764 0.3374467649724478 7.7587442309146040 0.8626796044156272 1.2452243224541324 0.7835447533710449 1.0899165770956820 10.3848523331334590 0.4819109019647465 0.9547229305958682 0.8564314184691215 4.5377235790405388
- 4.6501894691803214 0.7807017855806767 0.4586061981719967 0.4594535241660911 2.2627456996290891 0.6366932501396869 0.8940572875547330 0.6193321034173915 0.5333220944030346 14.8729334615190609 3.5458093276667237 0.7801080335991272 4.0584577156753401 1.7039730522675411 0.5985498912985666 0.9305232113028208 3.4242218450865543 0.5658969249032649 1.0000000000000000
- 0.0770764620135024 0.0500819370772208 0.0462377395993731 0.0537929860758246 0.0144533387583345 0.0408923608974345 0.0633579339160905 0.0655672355884439 0.0218802687005936 0.0591969699027449 0.0976461276528445 0.0592079410822730 0.0220695876653368 0.0413508521834260 0.0476871596856874 0.0707295165111524 0.0567759161524817 0.0127019797647213 0.0323746050281867 0.0669190817443274;
--
-+)"
-+// Visual studio needs regular breaks in long strings, to avoid C2026 "string too big"
-+R"(
- model BLOSUM62=
- 0.735790389698
- 0.485391055466 1.297446705134
-@@ -390,7 +392,9 @@ model HIVW=
- 0.0050000 0.0050000 5.0647500 2.2815400 8.3483500 0.0050000 0.0050000 0.0050000 47.4889000 0.1145120 0.0050000 0.0050000 0.5791980 4.1272800 0.0050000 0.9331420 0.4906080 0.0050000
- 24.8094000 0.2794250 0.0744808 2.9178600 0.0050000 0.0050000 2.1995200 2.7962200 0.8274790 24.8231000 2.9534400 0.1280650 14.7683000 2.2800000 0.0050000 0.8626370 0.0050000 0.0050000 1.3548200
- 0.0377494 0.0573210 0.0891129 0.0342034 0.0240105 0.0437824 0.0618606 0.0838496 0.0156076 0.0983641 0.0577867 0.0641682 0.0158419 0.0422741 0.0458601 0.0550846 0.0813774 0.0195970 0.0205847 0.0515638;
--
-+)"
-+// Visual studio needs regular breaks in long strings, to avoid C2026 "string too big"
-+R"(
- model JTTDCMUT=
- 0.531678
- 0.557967 0.451095
-@@ -503,7 +507,9 @@ model MTINV=
- 0.021939769224089 0.182762501894970 1.139165041333800 0.192759935895995 1.342951983818990 0.476209340516188 0.137649645940120 0.072268115092742 2.321701900318870 0.177138315144646 0.161052630578922 0.348477651608884 0.393193176722666 3.234681510126880 0.081395316441860 0.345719568712117 0.174898633040519 0.636664640334042
- 2.751362222454670 0.072153227138698 0.065420927831618 0.088077392769029 1.555396905840990 0.065221940911213 0.231186486525368 0.396428077428706 0.008043434782625 8.542589373962890 1.075872855650690 0.056252073499162 1.509852171058890 0.534676724129225 0.162975872809625 0.377288666084473 1.885338569864270 0.128598566560553 0.080346083861554
- 0.031742312696925 0.010900704360282 0.061579224631690 0.016149206459683 0.013570105428042 0.014644105857642 0.022311208924484 0.047847519139008 0.011641804656722 0.094322337728935 0.149407059762824 0.044438717775487 0.077262530905012 0.102287040914816 0.026290210516084 0.105939042375617 0.042869117147647 0.020701008280403 0.046556718622687 0.059540023816010;
--
-+)"
-+// Visual studio needs regular breaks in long strings, to avoid C2026 "string too big"
-+R"(
- model Q.PFAM=
- 0.531344742
- 0.266631781 0.610524242
-@@ -635,7 +641,9 @@ model Q.MAMMAL=
- 0.091694198 0.139818982 0.655149301 0.420781565 5.685285320 0.126113134 0.070592995 0.083304052 7.287086510 0.172110578 0.176288430 0.080506454 0.165573576 5.877878503 0.112513257 0.458878972 0.102291161 0.645002709
- 4.300445029 0.107177686 0.082093349 0.228482448 0.278600785 0.094238794 0.325642029 0.868890049 0.081513165 12.950251994 1.879650916 0.097391390 7.158497660 0.733119107 0.145626117 0.152049202 0.573328824 0.113423271 0.125003102
- 0.067997000 0.055503000 0.036288000 0.046867000 0.021435000 0.050281000 0.068935000 0.055323000 0.026410000 0.041953000 0.101191000 0.060037000 0.019662000 0.036237000 0.055146000 0.096864000 0.057136000 0.011785000 0.024730000 0.066223000;
--
-+)"
-+// Visual studio needs regular breaks in long strings, to avoid C2026 "string too big"
-+R"(
- model Q.PLANT=
- 0.061995451
- 0.071787018 0.324146307
-@@ -725,7 +733,9 @@ model NQ.BIRD=
- 0.003367 0.003420 0.025103 0.019062 0.118842 0.002325 0.001636 0.002267 0.172299 0.003816 0.011255 0.001973 0.001121 0.149120 0.003758 0.041478 0.002483 0.002546 -0.568642 0.002770
- 0.353020 0.003671 0.001550 0.011216 0.004391 0.002838 0.025621 0.063330 0.001568 0.600920 0.192704 0.003462 0.154474 0.028747 0.004789 0.007272 0.022534 0.001180 0.000311 -1.483598
- 0.066333 0.053982 0.037723 0.047442 0.022723 0.049236 0.071640 0.058487 0.025459 0.045195 0.100085 0.061369 0.020983 0.038111 0.053610 0.089423 0.053556 0.012287 0.027118 0.065238;
--
-+)"
-+// Visual studio needs regular breaks in long strings, to avoid C2026 "string too big"
-+R"(
- model NQ.INSECT=
- -1.158307 0.010073 0.016374 0.018148 0.024562 0.031278 0.050686 0.115871 0.007708 0.016759 0.030487 0.021161 0.017635 0.007697 0.047195 0.387388 0.180867 0.001003 0.005193 0.168222
- 0.016988 -0.864366 0.028327 0.009011 0.016427 0.091271 0.017198 0.023080 0.063484 0.009987 0.026047 0.441579 0.010386 0.003027 0.013118 0.047581 0.024505 0.004420 0.007183 0.010747
-@@ -817,7 +827,9 @@ model NQ.YEAST=
- 0.008246 0.005644 0.022807 0.004919 0.019212 0.007773 0.004189 0.001883 0.119939 0.010396 0.023220 0.003733 0.004427 0.375273 0.002243 0.021838 0.007934 0.015523 -0.669995 0.010796
- 0.198675 0.005913 0.007857 0.004763 0.020689 0.009495 0.019917 0.008777 0.004253 0.727245 0.155452 0.012278 0.043536 0.027573 0.012496 0.016617 0.125934 0.001048 0.008587 -1.411103
- 0.062250 0.044391 0.048928 0.052085 0.009471 0.039753 0.068567 0.039996 0.018745 0.069961 0.114036 0.081245 0.018619 0.047434 0.030178 0.090883 0.054691 0.008448 0.033789 0.066530;
--
-+)"
-+// Visual studio needs regular breaks in long strings, to avoid C2026 "string too big"
-+R"(
- model FLAVI=
- 0.077462
- 0.078037 0.000020
-diff --git a/tree/tree.cpp b/tree/tree.cpp
-index 5290594..e130697 100644
---- a/tree/tree.cpp
-+++ b/tree/tree.cpp
-@@ -6991,8 +6991,10 @@ PositionType cmaple::Tree::count_aRLT_SH_branch(
-     lh_diff_3 += site_lh_diff_3[j];
-     lh_diff_3 += site_lh_root_diff_3[j];
-   }
-+#ifdef DEBUG
-   assert(isinf(lh_diff_2) || fabs(lh_diff_2 - nodelh.getLhDiff2()) < 1e-3);
-   assert(isinf(lh_diff_3) || fabs(lh_diff_3 - nodelh.getLhDiff3()) < 1e-3);
-+#endif
- 
- // iterate a number of replicates
- #pragma omp parallel reduction(+ : sh_count)
-@@ -8848,8 +8850,17 @@ void cmaple::Tree::expandTreeByOneLessInfoSeq(PhyloNode& node,
-   // add a new node representing the less-info-seq
-   // the default min_blength in CMAPLE is not small enough -> I set it at
-   // min_blength * 0.1 for a higher accuracy when calculating aLRT-SH
--  const RealNumType new_min_blength =
-+  RealNumType new_min_blength =
-       (params->fixed_min_blength == -1) ? min_blength * 0.1 : min_blength;
-+    
-+ // if the two sequences are identical set the new blength at 0
-+    if (lower_regions->compareWithSample(*node.getPartialLh(TOP),
-+        static_cast<PositionType>(aln->ref_seq.size()), aln) == 1 &&
-+        node.getPartialLh(TOP)->compareWithSample(*lower_regions,
-+        static_cast<PositionType>(aln->ref_seq.size()), aln) == 1)
-+         new_min_blength = 0;
-+    
-+  // connect the new node to the tree
-   connectNewSample2Branch<num_states>(
-       lower_regions, seq_name_index, node_index, node, top_distance, 0,
-       new_min_blength, best_child_regions, upper_left_right_regions);
-diff --git a/utils/CMakeLists.txt b/utils/CMakeLists.txt
-index 524f20e..1a400be 100644
---- a/utils/CMakeLists.txt
-+++ b/utils/CMakeLists.txt
-@@ -7,6 +7,14 @@ matrix.h
- logstream.h logstream.cpp
- )
- 
-+if(CLANG AND WIN32)
-+    if (BINARY32)
-+        target_link_libraries(cmaple_utils ${PROJECT_SOURCE_DIR}/libraries/static/lib32/libiomp5md.dll)
-+    else()
-+        target_link_libraries(cmaple_utils ${PROJECT_SOURCE_DIR}/libraries/static/lib/libiomp5md.dll)
-+    endif()
-+endif()
-+
- #find_package(OpenMP)
- #if(OpenMP_CXX_FOUND)
- #    if(ZLIB_FOUND)
-diff --git a/utils/matrix.h b/utils/matrix.h
-index cc72203..7b3b2ba 100644
---- a/utils/matrix.h
-+++ b/utils/matrix.h
-@@ -79,7 +79,7 @@ inline double horiz_sum(simde__m256d v) {
-   vlow = simde_mm_add_pd(vlow, vhigh);     // reduce down to 128
- 
-   simde__m128d high64 = simde_mm_unpackhi_pd(vlow, vlow);
--  return  simde_mm_cvtsd_f64(_mm_add_sd(vlow, high64));  // reduce to scalar
-+  return  simde_mm_cvtsd_f64(simde_mm_add_sd(vlow, high64));  // reduce to scalar
- }
- 
- 
-diff --git a/utils/operatingsystem.cpp b/utils/operatingsystem.cpp
-index b8715d9..08d9a63 100644
---- a/utils/operatingsystem.cpp
-+++ b/utils/operatingsystem.cpp
-@@ -8,10 +8,10 @@
- #include "operatingsystem.h"
- #include <sstream>
- #include <string>
--#if defined(WIN32) || defined(WIN64)
--#include <io.h>  //for _isatty
--#else
-+#if defined(CMAPLE_HAS_UNISTDH)
- #include <unistd.h>  //for isatty
-+#else
-+#include <io.h>  //for _isatty
- #endif
- 
- auto getOSName() -> std::string {
-@@ -32,9 +32,9 @@ auto getOSName() -> std::string {
- }
- 
- auto isStandardOutputATerminal() -> bool {
--#if defined(WIN32) || defined(WIN64)
--  return _isatty(fileno(stdout));
--#else
-+#if defined(CMAPLE_HAS_UNISTDH)
-   return isatty(fileno(stdout));
-+#else
-+  return _isatty(fileno(stdout));
- #endif
- }
-diff --git a/utils/operatingsystem.h b/utils/operatingsystem.h
-index 35ac951..37dfe92 100644
---- a/utils/operatingsystem.h
-+++ b/utils/operatingsystem.h
-@@ -9,6 +9,7 @@
- #define operatingsystem_h
- 
- #include <string>
-+#include <cmaple_config.h>
- 
- std::string getOSName();
- bool isStandardOutputATerminal();
-diff --git a/utils/tools.cpp b/utils/tools.cpp
-index a8b1c4e..9992a93 100644
---- a/utils/tools.cpp
-+++ b/utils/tools.cpp
-@@ -881,8 +881,8 @@ void cmaple::parseArg(int argc, char* argv[], Params& params) {
-           outError(e.what());
-         }
- 
--        if (params.fixed_min_blength <= 0) {
--          outError("<NUMBER> following -min-bl must be positive!");
-+        if (params.fixed_min_blength <= 1e-12) {
-+          outError("<NUMBER> following -min-bl must be at least 1e-12!");
-         }
- 
-         continue;
diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml
index f39326c930829..d4ce6da29663e 100644
--- a/recipes/cnvkit/meta.yaml
+++ b/recipes/cnvkit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cnvkit" %}
-{% set version = "0.9.11" %}
+{% set version = "0.9.12" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz
-  sha256: 1763936427184270108fd51219ebc82f542e28339bdec587579b8745f61179a8
+  sha256: 39d65ba3d9c541dfd80986ace298b2d521067d1b81edef7169196b8dcc5d63d5
 
 build:
   noarch: python
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - bioconductor-dnacopy
@@ -49,13 +50,13 @@ test:
     - cnvkit.py -h
 
 about:
-  home: https://github.com/etal/cnvkit
-  license: Apache-2.0
+  home: "https://github.com/etal/cnvkit"
+  license: "Apache-2.0"
   license_family: APACHE
   license_file: LICENSE
-  summary: Copy number variant detection from high-throughput sequencing
-  dev_url: https://github.com/etal/cnvkit
-  doc_url: https://cnvkit.readthedocs.io/en/stable/
+  summary: "Copy number variant detection from high-throughput sequencing."
+  dev_url: "https://github.com/etal/cnvkit"
+  doc_url: "https://cnvkit.readthedocs.io/en/stable"
 
 extra:
   identifiers:
diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml
index aae452e0234c9..63f3ec5de23da 100644
--- a/recipes/cogent3/meta.yaml
+++ b/recipes/cogent3/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cogent3" %}
-{% set version = "2024.7.19a7" %}
+{% set version = "2024.7.19a9" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: c880f7aaa08a1a79cf364650810a2f0e477443f48c01a3101883bb3e327d0148
+  sha256: 5f1ab042294f718a77e0d8fa8adf3b20fefe9ef5a47b1c2092e50e8560883afa
 
 build:
   noarch: python
diff --git a/recipes/commec/meta.yaml b/recipes/commec/meta.yaml
index 676f15e6479c5..fa1f52d5008cb 100644
--- a/recipes/commec/meta.yaml
+++ b/recipes/commec/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "commec" %}
-{% set version = "0.1.2" %}
-{% set sha256 = "33e99060dca151cb9d5481f47e02f1b5276b2cdf61804e7093f0cfc32bef1188" %}
+{% set version = "0.2.0" %}
+{% set sha256 = "d2d47a84a04194caca22984097d06d5c737af81a4833aa4f824243ee3c511351" %}
 
 package:
   name: "{{ name }}"
@@ -15,30 +15,29 @@ build:
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
-    # consider using "x.x.x" rather than "x.x", or "x" considering alpha software and liklihood of change.
-    - {{ pin_subpackage('commec', max_pin="x.x") }}
+    - {{ pin_subpackage('commec', max_pin="x.x.x") }}
 
 requirements:
   host:
-    - python >=3.1
-    - pip >=24
+    - python =3.12
+    - pip
   run:
-    - python >=3.1
     # Runtime Python dependencies
-    - biopython >=1.8
-    - numpy >=2.0.0
-    - pandas >=2.2
-    - pytaxonkit >=0.8
+    - biopython
+    - numpy
+    - pandas
+    - pytaxonkit
     # Runtime non-Python dependencies
-    - bedtools >=2.31
+    - bedtools
     - blast >=2.16
-    - emboss >=6.6
-    - diamond >=0.9
-    - hmmer >=3.4
-    - infernal >=1.1
-    - parallel >=20240722
-    - perl-list-moreutils >=0.430
-    - taxonkit >=0.17
+    - emboss
+    - diamond >=2.1
+    - hmmer
+    - infernal
+    - parallel
+    - perl-list-moreutils
+    - taxonkit
+    - wget
 
 test:
   commands:
diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml
index 334ffd72b4937..cb8b5698bca2c 100644
--- a/recipes/cooltools/meta.yaml
+++ b/recipes/cooltools/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cooltools" %}
-{% set version = "0.7.0" %}
+{% set version = "0.7.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 8b26d4857cc76b2dd3d1097b85f828cf6d5f1cf85b0cfd4b67a310e33e7ece1c
+  sha256: 1f12494add7b1271b71e418d10d060e1dac906a021fc2bd691e91f5599010051
 
 build:
-  number: 2
+  number: 0
   entry_points:
     - cooltools = cooltools.cli:cli
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
diff --git a/recipes/coptr/meta.yaml b/recipes/coptr/meta.yaml
new file mode 100644
index 0000000000000..cbc6774b24785
--- /dev/null
+++ b/recipes/coptr/meta.yaml
@@ -0,0 +1,50 @@
+{% set name = "coptr" %}
+{% set version = "1.1.4" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/coptr-{{ version }}.tar.gz
+  sha256: 62cd4c58d64864aa721c5fe069fe993108acc5c74e893bf8c46b008f3b8667a0
+
+build:
+  entry_points:
+    - coptr = coptr.cli:cli
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 3
+  run_exports:
+   - {{ pin_subpackage("coptr", max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.7,<=3.8
+    - setuptools
+    - pip
+  run:
+    - bowtie2 >=2.4.1
+    - python >=3.7,<=3.8
+    - numpy >=1.19.1,<=1.24.4
+    - pysam >=0.16.0.1
+    - scipy >=1.5.2,<2.0.0
+    - matplotlib-base >=3.3.2
+
+test:
+  imports:
+    - coptr
+  commands:
+    - coptr --help
+
+about:
+  home: https://github.com/tyjo/coptr
+  summary: Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: COPYING
+  dev_url: https://github.com/tyjo/coptr
+
+extra:
+  recipe-maintainers:
+    - ramirobarrantes
diff --git a/recipes/core-snp-filter/build.sh b/recipes/core-snp-filter/build.sh
index 925e2597f08cd..fa0e15cc32d86 100644
--- a/recipes/core-snp-filter/build.sh
+++ b/recipes/core-snp-filter/build.sh
@@ -1,10 +1,5 @@
 #!/bin/bash -euo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo"
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 cargo install --verbose --path . --root $PREFIX
-
diff --git a/recipes/core-snp-filter/meta.yaml b/recipes/core-snp-filter/meta.yaml
index ef9674854c75e..076de9705643a 100644
--- a/recipes/core-snp-filter/meta.yaml
+++ b/recipes/core-snp-filter/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.1.1" %}
+{% set version = "0.2.0" %}
 
 package:
   name: core-snp-filter
@@ -6,16 +6,18 @@ package:
 
 source:
   url: https://github.com/rrwick/Core-SNP-filter/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 6ac542524a22c2c66edba69a937ae637a4a1e62105379ba79708ad74187feed9
+  sha256: 5fa0357c4429e52644a9bdd5dfa4be3a3fc6889073f7678ed5a47f8a7f267c3d
 
 build:
-  number: 1
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('core-snp-filter', max_pin="x.x") }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - rust >=1.39
+    - {{ compiler('rust') }}
     - pkg-config
     - clangdev
     - make
diff --git a/recipes/corneto/meta.yaml b/recipes/corneto/meta.yaml
new file mode 100644
index 0000000000000..fe7defc856845
--- /dev/null
+++ b/recipes/corneto/meta.yaml
@@ -0,0 +1,46 @@
+{% set name = "corneto" %}
+{% set version = "1.0.0a0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/corneto-{{ version }}.tar.gz
+  sha256: 966d50762f92047ea4e5d1a136607f20ae9ec1d585530a24ad5c95e700b24180
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("corneto", max_pin="x.x.x") }}
+
+requirements:
+  host:
+    - python >=3.9
+    - poetry-core >=1.0.0
+    - pip
+  run:
+    - python >=3.9
+    - numpy >=1.15,<2.0.0
+    - cvxpy-base >=1.5.0,<2.0.0
+    - scipy >=1.11.0,<2.0.0
+
+test:
+  imports:
+    - corneto
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://github.com/saezlab/corneto/
+  summary: 'CORNETO: A Unified Framework for Omics-Driven Network Inference'
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - nilchia
diff --git a/recipes/crabs/meta.yaml b/recipes/crabs/meta.yaml
index dc99ff1d3a676..94c42f1d7d137 100644
--- a/recipes/crabs/meta.yaml
+++ b/recipes/crabs/meta.yaml
@@ -1,42 +1,41 @@
+{% set name = "crabs" %}
+{% set version = "1.0.7" %}
+{% set sha256 = "24c8fe8a1d2dd8b47c4d8818ecdcfd908f10ceafd8c1a21d9f255d10927a3535" %}
+
 package:
-  name: crabs
-  version: "0.1.1"
+  name: {{ name|lower }}
+  version: {{ version }}
 
 source:
-  url: https://github.com/gjeunen/reference_database_creator/files/8028374/crabs_v0.1.1.tar.gz
-  md5: 6c2e82fb5e191cb750c5d6a41fa24b61
+  url: https://github.com/gjeunen/reference_database_creator/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
 
 build:
   number: 0
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
-  build:
-
   host:
-    - python >=3.6.10
+    - python >=3.6
     - pip
-    - argparse
-    - biopython =1.78
-    - tqdm
-    - numpy
-    - pandas >=0.23.4
-    - matplotlib-base
-    - wget
-
+    - setuptools
   run:
-    - python >=3.6.10
-    - argparse
-    - biopython =1.78
+    - python >=3.6
+    - biopython
     - tqdm
     - numpy
     - pandas >=0.23.4
     - matplotlib-base
     - wget
-    - muscle >=3.8.31
+    - muscle
     - cutadapt >=3.4
     - vsearch >=2.13.3
+    - rich
+    - rich-click
+    - requests
 
 test:
   commands:
@@ -44,6 +43,8 @@ test:
 
 about:
   home: https://github.com/gjeunen/reference_database_creator
-  license: MIT License
-  summary: Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses
-
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses."
+  dev_url: https://github.com/gjeunen/reference_database_creator
diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml
index ae53c0a7a5a9d..d5c0ba6599b6c 100644
--- a/recipes/cramino/meta.yaml
+++ b/recipes/cramino/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.14.5" %}
+{% set version = "0.15.0" %}
 
 package:
   name: cramino
@@ -12,11 +12,15 @@ build:
 
 source:
   url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz
-  sha256: d3b31ab76808ca76171e2539cfe30e66fe24cbd4af4ff9a941c282a0bc438032
+  sha256: 731d4232e8a5503f704825b04e8ff081294381a1324fec3e59771ca773c68465
 
 requirements:
   build:
     - {{ compiler('c') }}
+    - {{ compiler('rust') }}
+    - {{ compiler('cxx') }}
+    - clangdev
+    - llvmdev
     - rust >=1.60
     - cmake
     - make
diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml
index 86f0aee7a9418..93700fa5b0691 100644
--- a/recipes/csvtk/meta.yaml
+++ b/recipes/csvtk/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.30.0" %}
+{% set version = "0.31.0" %}
 # This package should be migrated to conda-forge due to general utility
 # In that case it needs to be built from source
 package:
@@ -6,19 +6,19 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('csvtk', max_pin='x.x') }}
   
 source:
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx and x86_64]
-    md5: c415255e265ba0cd547806fdbda05652 # [osx and x86_64]
+    md5: 5a23d000a1fc068360e1aeb439f3ae25 # [osx and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_arm64.tar.gz # [arm64]
-    md5: dd8a84c301d378ab7ff28c85d37fbefa # [arm64]
+    md5: 6aa24ce286910e83d95d28a21905f1d8 # [arm64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux and x86_64]
-    md5: 8f5877d4fbea89609d64bd2679956476 # [linux and x86_64]
+    md5: 09bc8c3288f028239c94d4c935ac7a6f # [linux and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_arm64.tar.gz # [aarch64]
-    md5: 2a6dd840291d23971ff538eaf3de00ec # [aarch64]
+    md5: f7a5b8839459d7d55685056331670eec # [aarch64]
 
 test:
   commands:
diff --git a/recipes/cuttlefish/build.sh b/recipes/cuttlefish/build.sh
index 8cc1be2aece0d..d232e1650bf24 100644
--- a/recipes/cuttlefish/build.sh
+++ b/recipes/cuttlefish/build.sh
@@ -1,24 +1,25 @@
 #!/bin/bash
 
-mkdir build
-cd build
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include"
 
-unamestr=`uname`
-
-if [ "$unamestr" == 'Darwin' ];
-then
-  export MACOSX_DEPLOYMENT_TARGET=10.15
-  export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
-  export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
-else 
-  # It's dumb and absurd that the KMC build can't find the bzip2 header <bzlib.h>
-  export C_INCLUDE_PATH="$PREFIX/include"
-  export CPLUS_INCLUDE_PATH="$PREFIX/include"
+if [[ `uname` == 'Darwin' ]]; then
+	export MACOSX_DEPLOYMENT_TARGET=10.11
+	export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	# It's dumb and absurd that the KMC build can't find the bzip2 header <bzlib.h>
+	export C_INCLUDE_PATH="$PREFIX/include"
+	export CPLUS_INCLUDE_PATH="$PREFIX/include"
+	export CONFIG_ARGS=""
 fi
 
-cmake \
-    -DINSTANCE_COUNT=64 \
-    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-    -DCONDA_BUILD=ON \
-    ..
-make install
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	-DINSTANCE_COUNT=64 \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	"${CONFIG_ARGS}"
+cmake --build build/ --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/cuttlefish/build_failure.osx-64.yaml b/recipes/cuttlefish/build_failure.osx-64.yaml
deleted file mode 100644
index 5478b7be1ea8e..0000000000000
--- a/recipes/cuttlefish/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 88d29dc5a3f896af86f91bbb69279e4bd0a02dfb550bb0080c44599f527cd38d  # The commit at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  kmc_core/kb_sorter.h:231:3: note: in instantiation of member function 'CKmerBinSorter<2>::Compact' requested here
-                  Compact();
-                  ^
-  kmc_core/kb_sorter.h:1321:7: note: in instantiation of member function 'CKmerBinSorter<2>::ProcessBins' requested here
-          kbs->ProcessBins();
-               ^
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: (skipping 22 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
-      { return          static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); }
-                        ^
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<4>::ProcessStage2' requested here
-                                  return app_1->ProcessStage2(stage2Params);
-                                                ^
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<5>::ProcessStage2' requested here
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<6>::ProcessStage2' requested here
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<7>::ProcessStage2' requested here
-  kmc_core/kmc_runner.cpp:424:16: note: in instantiation of member function 'KMC::CApplication<8>::ProcessStage2' requested here
-                          return app->ProcessStage2(stage2Params);
-                                      ^
-  In file included from kmc_core/kmc_runner.cpp:12:
-  In file included from kmc_core/kmc.h:30:
-  In file included from kmc_core/kb_sorter.h:33:
-  kmc_core/kxmer_set.h:282:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
-                  data.push(move(sub_array_desc_copy));
-                            ^
-                            std::
-  kmc_core/kxmer_set.h:304:10: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
-                  desc = move(data.front());
-                         ^
-                         std::
-  kmc_core/kxmer_set.h:572:35: note: in instantiation of member function 'CSubArrayDescGenerator<2>::GetNext' requested here
-                  while (sub_array_desc_generator.GetNext(desc, out_start))
-                                                  ^
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of member function 'CKXmerMerger<2>::operator()' requested here
-      { return          static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); }
-                        ^
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of function template specialization 'std::reference_wrapper<CKXmerMerger<2>>::operator()<>' requested here
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/bind.h:295:27: note: in instantiation of function template specialization 'std::__apply_functor<std::reference_wrapper<CKXmerMerger<2>>, std::tuple<>, std::tuple<>>' requested here
-              return _VSTD::__apply_functor(__f_, __bound_args_, __indices(),
-                            ^
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of function template specialization 'std::__bind<std::reference_wrapper<CKXmerMerger<2>>>::operator()<>' requested here
-      { return          static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); }
-                        ^
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/function.h:185:26: note: (skipping 40 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
-          return _Invoker::__call(__f_.first(),
-                           ^
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<4>::ProcessStage2' requested here
-                                  return app_1->ProcessStage2(stage2Params);
-                                                ^
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<5>::ProcessStage2' requested here
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<6>::ProcessStage2' requested here
-  kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<7>::ProcessStage2' requested here
-  kmc_core/kmc_runner.cpp:424:16: note: in instantiation of member function 'KMC::CApplication<8>::ProcessStage2' requested here
-                          return app->ProcessStage2(stage2Params);
-                                      ^
-  In file included from kmc_core/kmc_runner.cpp:12:
-  In file included from kmc_core/kmc.h:15:
-  In file included from kmc_core/params.h:21:
-  kmc_core/libs/ntHash/ntHashWrapper.h:110:7: warning: private field 'convert' is not used [-Wunused-private-field]
-          char convert[256] = {
-               ^
-  127 warnings generated.
-  [ 12%] Performing install step for 'prj_kmc'
-  [ 14%] Completed 'prj_kmc'
-  [ 14%] Built target prj_kmc
-  [ 16%] Building CXX object src/CMakeFiles/cfcore_static.dir/kmc_api/kmc_file.cpp.o
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/src/kmc_api/kmc_file.cpp:12:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/include/kmc_api/stdafx.h:3:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/iostream:43:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/ios:221:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__locale:18:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/mutex:191:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/shared_ptr.h:22:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/allocation_guard.h:14:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/allocator_traits.h:14:
-  In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/construct_at.h:23:
-  /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/new:355:14: error: no member named 'aligned_alloc' in the global namespace
-      return ::aligned_alloc(__alignment, __size > __rounded_size ? __size : __rounded_size);
-             ~~^
-  1 error generated.
-  make[2]: *** [src/CMakeFiles/cfcore_static.dir/build.make:76: src/CMakeFiles/cfcore_static.dir/kmc_api/kmc_file.cpp.o] Error 1
-  make[1]: *** [CMakeFiles/Makefile2:130: src/CMakeFiles/cfcore_static.dir/all] Error 2
-  make: *** [Makefile:136: all] Error 2
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
-      sys.exit(main())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
-      call_conda_build(action, config)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
-      result = api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
-      packages_from_this = build(metadata, stats,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build
-      utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/conda_build.sh']' returned non-zero exit status 2.
-# Last 100 lines of the build log.
diff --git a/recipes/cuttlefish/meta.yaml b/recipes/cuttlefish/meta.yaml
index d76c858dd233d..f2cef96e5af21 100644
--- a/recipes/cuttlefish/meta.yaml
+++ b/recipes/cuttlefish/meta.yaml
@@ -6,7 +6,9 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
+  number: 3
+  run_exports:
+    - {{ pin_subpackage('cuttlefish', max_pin="x") }}
 
 source:
   url: https://github.com/COMBINE-lab/cuttlefish/archive/refs/tags/v{{ version }}.tar.gz
@@ -14,20 +16,14 @@ source:
 
 requirements:
   build:
-    - autoconf
     - cmake >=3.14.0
     - make
     - {{ compiler('cxx') }}
     - {{ compiler('c') }}
-    - zlib
-    - bzip2
   host:
     - jemalloc >=5.1.0
     - zlib
     - bzip2
-  run:
-    - bzip2
-    - zlib
 
 test:
   commands:
@@ -36,17 +32,21 @@ test:
     - cuttlefish version
 
 about:
-  home: https://github.com/COMBINE-lab/cuttlefish
-  license: BSD-3-Clause
+  home: "https://github.com/COMBINE-lab/cuttlefish"
+  license: "BSD-3-Clause"
+  license_family: BSD
   license_file: LICENSE
-  summary: Construction of the compacted de Bruijn graph efficiently
-  dev_url: https://github.com/COMBINE-lab/cuttlefish
-  doc_url: https://github.com/COMBINE-lab/cuttlefish#readme
+  summary: "Construction of the compacted de Bruijn graph efficiently."
+  dev_url: "https://github.com/COMBINE-lab/cuttlefish"
+  doc_url: "https://github.com/COMBINE-lab/cuttlefish/blob/v{{ version }}/README.md"
 
 extra:
+  additional-platforms:
+    - osx-arm64
   recipe-maintainers:
     - jamshed
     - rob-p
   identifiers:
     - doi:10.1093/bioinformatics/btab309
     - doi:10.1186/s13059-022-02743-6
+    - biotools:cuttlefish
diff --git a/recipes/cytoscape/meta.yaml b/recipes/cytoscape/meta.yaml
index 068d4c8f5ba8c..f21b013c9dc0e 100644
--- a/recipes/cytoscape/meta.yaml
+++ b/recipes/cytoscape/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "cytoscape" %}
-{% set version = "3.10.2" %}
-{% set sha256 = "561380f7429aa806941027897fd1ca902597c4dadf4bf1bbd3141a39f2bd3f3e" %}
+{% set version = "3.10.3" %}
+{% set sha256 = "99a2d2f9559222ff0ef2136365517da8202fa4a7a89ec0860f8caf1db0ed40f7" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/d4binding/build.sh b/recipes/d4binding/build.sh
index 564717ff7b0ef..7f2be26f82917 100644
--- a/recipes/d4binding/build.sh
+++ b/recipes/d4binding/build.sh
@@ -1,12 +1,14 @@
-#!/bin/bash -e
+#!/bin/bash
 
-set -x
+set -xe
 
 # TODO: Remove the following export when pinning is updated and we use
 #       {{ compiler('rust') }} in the recipe.
 export \
-    CARGO_NET_GIT_FETCH_WITH_CLI=true \
-    CARGO_HOME="${BUILD_PREFIX}/.cargo"
+	CARGO_NET_GIT_FETCH_WITH_CLI=true \
+	CARGO_HOME="${BUILD_PREFIX}/.cargo"
+
+cp $RECIPE_DIR/build_htslib.sh d4-hts/build_htslib.sh
 
 cd d4binding 
 ./install.sh
diff --git a/recipes/d4binding/build_htslib.sh b/recipes/d4binding/build_htslib.sh
new file mode 100644
index 0000000000000..e3a214a0d2ec0
--- /dev/null
+++ b/recipes/d4binding/build_htslib.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+
+if [ "${DOCS_RS}" = "1" ]
+then
+	exit 0
+fi
+
+set -ex
+
+pushd ${OUT_DIR}
+
+HTSLIB_VERSION=${1}
+
+rm -rf ${OUT_DIR}/htslib
+
+git clone -b ${HTSLIB_VERSION} http://github.com/samtools/htslib.git
+
+cd htslib
+
+cat > config.h << CONFIG_H
+#define HAVE_LIBBZ2 1
+#define HAVE_DRAND48 1
+CONFIG_H
+
+perl -i -pe 's/hfile_libcurl\.o//g' Makefile
+	
+function is_musl() {
+	if [ ! -z $(echo $TARGET | grep musl) ]; then 
+		return 0
+	else
+		return 1
+	fi
+}
+
+is_musl && perl -i -pe 's/gcc/musl-gcc/g' Makefile
+
+
+if [ "x${ZLIB_SRC}" != "x" ]
+then
+	tar xz ${ZLIB_SRC}
+else
+	curl -L 'http://github.com/madler/zlib/archive/refs/tags/v1.2.11.tar.gz' | tar xz
+fi
+cd zlib-1.2.11
+is_musl && CC=musl-gcc ./configure || ./configure
+make libz.a
+cp libz.a ..
+cd ..
+
+#The original file in the repo is lacking -L in the curl command so it doen't work
+curl -L http://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz | tar xz
+cd bzip2-1.0.8
+is_musl && perl -i -pe 's/gcc/musl-gcc/g' Makefile
+is_musl || perl -i -pe 's/CFLAGS=/CFLAGS=-fPIC /g' Makefile
+make
+cp libbz2.a ..
+cd ..
+
+perl -i -pe 's/CPPFLAGS =/CPPFLAGS = -Izlib-1.2.11 -Ibzip2-1.0.8/g' Makefile
+
+is_musl || perl -i -pe 's/CFLAGS *=/CFLAGS = -fPIC/g' Makefile
+
+make -j8 lib-static
\ No newline at end of file
diff --git a/recipes/d4binding/meta.yaml b/recipes/d4binding/meta.yaml
index cbbb959e092d6..3fc0131d181c8 100644
--- a/recipes/d4binding/meta.yaml
+++ b/recipes/d4binding/meta.yaml
@@ -1,29 +1,32 @@
-{% set version = "0.3.4" %}
+{% set name = "d4binding" %}
+{% set version = "0.3.11" %}
 
 package:
-  name: d4binding
+  name: {{ name }}
   version: {{ version }}
 
 build:
   number: 1
+  run_exports:
+    - {{ pin_subpackage("d4binding", max_pin="x.x") }}
 
 source:
-  # TODO: use formal release number when 0.3.5 is released
-  url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}-3.tar.gz
-  sha256: 05e1a410b77c34d7d188e69ef607eaa9f0babcc9817c558362203fc3f1f2219c
+  url: https://github.com/38/d4-format/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - rust >=1.30
-    - gcc #[not osx]
+    - gcc  # [not osx]
     - clangdev
     - pkg-config
     - make
     - cmake
   run:
     - starcode
+
 test:
   commands:
     - "true"
@@ -31,9 +34,14 @@ test:
 about:
   home: https://github.com/38/d4-format
   license: MIT
+  license_family: MIT
   summary: |
-    The C/C++ binding for the D4 file format
+    The C/C++ binding for the D4 file format.
+  dev_url: https://github.com/38/d4-format
+
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - haohou
   skip-lints:
diff --git a/recipes/d4tools/meta.yaml b/recipes/d4tools/meta.yaml
index 185f9b3671124..17f8a4c9838dc 100644
--- a/recipes/d4tools/meta.yaml
+++ b/recipes/d4tools/meta.yaml
@@ -1,7 +1,8 @@
+{% set name = "d4tools" %}
 {% set version = "0.3.11" %}
 
 package:
-  name: d4tools
+  name: {{ name }}
   version: {{ version }}
 
 source:
@@ -9,7 +10,7 @@ source:
   sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('d4tools', max_pin="x.x") }}
 
@@ -35,7 +36,7 @@ about:
   license: MIT
   license_family: MIT
   summary: |
-    The D4 command line utility program
+    The D4 command line utility program.
   dev_url: https://github.com/38/d4-format
 
 extra:
diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml
index 3567fa738173f..e5b4758821a09 100644
--- a/recipes/dajin2/meta.yaml
+++ b/recipes/dajin2/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "DAJIN2" %}
-{% set version = "0.5.5" %}
+{% set version = "0.5.5.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dajin2-{{ version }}.tar.gz
-  sha256: c0260f99ad631b505b0f0fa010ce7b3ef2f081bcb371ed452bd886dd34592ac1
+  sha256: ee5dd13234cb15fd03c32d31a6397431fe28376a0142ae2cb9e7142c1bba4712
 
 build:
   entry_points:
diff --git a/recipes/dapcy/meta.yaml b/recipes/dapcy/meta.yaml
index 42b3650aeadb4..36e07f1d35ced 100644
--- a/recipes/dapcy/meta.yaml
+++ b/recipes/dapcy/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "dapcy" %}
-{% set version = "0.1.1" %}
+{% set version = "1.0.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,11 +7,11 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dapcy-{{ version }}.tar.gz
-  sha256: b62440ea8523f05597cd0a889b9eafb68192bd4e481048e859b772ac654ccb93
+  sha256: 056bd071a7f1089d8453d7fcde853baff77f86ca489869268c6ad2ae04810c71
 
 build:
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   number: 0
   run_exports:
     - {{ pin_subpackage('dapcy', max_pin="x.x") }}
@@ -20,6 +20,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - bed-reader
@@ -29,7 +30,7 @@ requirements:
     - pandas
     - scikit-learn
     - scipy
-    - seaborn
+    - seaborn-base
     - sgkit
     - aiohttp
     - cyvcf2
@@ -39,16 +40,14 @@ requirements:
 test:
   imports:
     - dapcy
-  commands:
-    - pip check
-  requires:
-    - pip
 
 about:
   home: https://gitlab.com/uhasselt-bioinfo/dapcy
-  summary: An sklearn implementation of discriminant analysis of principal components (DAPC) for population genetics
+  summary: "An sklearn implementation of discriminant analysis of principal components (DAPC) for population genetics."
   license: MIT
+  license_family: MIT
   license_file: LICENSE
+  dev_url: https://gitlab.com/uhasselt-bioinfo/dapcy
 
 extra:
   recipe-maintainers:
diff --git a/recipes/decom/meta.yaml b/recipes/decom/meta.yaml
index 7656ee92299a7..d093e6eac17ec 100644
--- a/recipes/decom/meta.yaml
+++ b/recipes/decom/meta.yaml
@@ -2,7 +2,7 @@
 {% set version = "0.0.32" %}
 
 package:
-  name: decom
+  name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
@@ -10,10 +10,8 @@ source:
   sha256: c9efaa97b7abfe6f19f01a199ca6c7a7b32ec699f886d226667b8b5fe562dd88
 
 build:
-  run_exports:
-    - {{ pin_subpackage('decom', max_pin="x") }}
-  number: 0
   noarch: python
+  number: 2
   entry_points:
     - decOM = decOM.__main__:main
     - decOM-aOralOut = decOM.aOralOut.__main__:main
@@ -21,24 +19,38 @@ build:
     - decOM-LOO = decOM.LOO.__main__:main
     - decOM-CV = decOM.CV.__main__:main
     - decOM-MST = decOM.MST.__main__:main
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  run_exports:
+    - {{ pin_subpackage('decom', max_pin='x.x.x') }}
 
 requirements:
   host:
     - pip
-    - python
+    - setuptools
+    - python >=3.9,<3.13
   run:
+    - python >=3.9,<3.13
+    - setuptools
     - colorama
-    - dask >=2021.12.0
-    - importlib_resources >=5.4.0
-    - python-kaleido
     - numpy >=1.7
     - pandas
     - plotly >=5.5.0
-    - python
+    - dask >=2021.12.0
+    - importlib_resources >=5.4.0
+    - python-kaleido
     - git
+    - kmtricks >=1.4.0
 
 test:
+  imports:
+    - decOM
+    - decOM.CV
+    - decOM.LOO
+    - decOM.MST
+    - decOM.aOralOut
+    - decOM.data
+    - decOM.format
+    - decOM.modules
   commands:
     - decOM --help
     - decOM-aOralOut --help
@@ -52,10 +64,12 @@ about:
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: "decOM: Similarity-based microbial source tracking for contamination assessment of ancient oral samples using k-mer-based methods"
-  doc_url: "https://github.com/CamilaDuitama/decOM" 
-  dev_url: "https://camiladuitama.github.io/gradfolio/"
+  summary: "decOM: Microbial source tracking of ancient oral samples using k-mers."
+  description: |
+    decOM is a similarity-based microbial source tracking tool for contamination assessment of ancient oral samples using k-mer-based methods.
+  doc_url: https://github.com/CamilaDuitama/decOM 
+  dev_url: https://github.com/CamilaDuitama/decOM
 
 extra:
   recipe-maintainers:
-    - CamilaDuitama
+    - CamilaDuitama
\ No newline at end of file
diff --git a/recipes/deepchopper-cli/build.sh b/recipes/deepchopper-cli/build.sh
new file mode 100644
index 0000000000000..406a030b71a26
--- /dev/null
+++ b/recipes/deepchopper-cli/build.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# -e = exit on first error
+# -x = print every executed command
+set -ex
+
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y
+
+export PATH="$HOME/.cargo/bin:$PATH"
+
+cd py_cli
+
+maturin build --interpreter "${PYTHON}" --release --strip -b bin --out dist
+
+$PYTHON -m pip install dist/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/deepchopper-cli/meta.yaml b/recipes/deepchopper-cli/meta.yaml
new file mode 100644
index 0000000000000..45fceb4596974
--- /dev/null
+++ b/recipes/deepchopper-cli/meta.yaml
@@ -0,0 +1,56 @@
+{% set name = "deepchopper-cli" %}
+{% set version = "1.2.6" %}
+{% set sha256 = "2ea385c3bb6e95f2d76627c2c6a859cfdab7f3402bd4589b1e787d301df1fbd1" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepchopper_cli-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True  # [py < 310]
+  run_exports:
+    - {{ pin_subpackage("deepchopper-cli", max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - {{ compiler('c') }}
+    - make
+    - cmake
+  host:
+    - python
+    - pip
+    - maturin >=1.2.1,<2
+    - setuptools-rust
+    - setuptools
+  run:
+    - python
+
+
+test:
+  commands:
+    - deepchopper-chop -h
+    
+about:
+  home: https://github.com/ylab-hi/DeepChopper
+  license: Apache-2.0
+  license_family: Apache
+  license_file: LICENSE
+  summary: 'A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.'
+  description: |
+    DeepChopper is a genomic language model designed to identify artificial sequences.
+    It provides functionality for encoding FASTQ files, making predictions, and chopping sequences.
+  doc_url: https://github.com/ylab-hi/DeepChopper
+  dev_url: https://github.com/ylab-hi/DeepChopper
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - yangyangli
diff --git a/recipes/deepchopper/build.sh b/recipes/deepchopper/build.sh
new file mode 100644
index 0000000000000..57474c5448ba7
--- /dev/null
+++ b/recipes/deepchopper/build.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# -e = exit on first error
+# -x = print every executed command
+set -ex
+
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y
+
+export PATH="$HOME/.cargo/bin:$PATH"
+
+maturin build --interpreter "${PYTHON}" --release --strip
+
+$PYTHON -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/deepchopper/meta.yaml b/recipes/deepchopper/meta.yaml
new file mode 100644
index 0000000000000..a94a5edd37044
--- /dev/null
+++ b/recipes/deepchopper/meta.yaml
@@ -0,0 +1,75 @@
+{% set name = "deepchopper" %}
+{% set version = "1.2.6" %}
+{% set sha256 = "f264d1d451a9ad28073af0c2be95f177b71c39fa63a726408592bf412f56e4fe" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True  # [py < 310]
+  run_exports:
+    - {{ pin_subpackage("deepchopper", max_pin="x") }}
+  entry_points:
+    - deepchopper = deepchopper.cli:app
+    
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - {{ compiler('c') }}
+    - make
+    - cmake
+  host:
+    - python
+    - pip
+    - maturin >=1.2.1,<2
+    - setuptools-rust
+    - setuptools
+  run:
+    - python
+    - pytorch >=2.1.0
+    - lightning >=2.1.2
+    - torchmetrics >=1.2.0
+    - rich >=13.7.0
+    - transformers >=4.37.2
+    - safetensors >=0.4.2
+    - datasets ==2.14.2
+    - evaluate >=0.4.1
+    - typer >=0.12.0
+    - gradio ==5.0.1
+    - fastapi ==0.112.2
+    - scikit-learn >=1.5.2
+    - hydra-core >=1.3.2
+    - omegaconf >=2.3.0
+    - python-multipart ==0.0.12
+    - deepchopper-cli >=1.2.5
+
+test:
+  imports:
+    - deepchopper
+  commands:
+    - deepchopper --help
+
+about:
+  home: https://github.com/ylab-hi/DeepChopper
+  license: Apache-2.0
+  license_family: Apache
+  license_file: LICENSE
+  summary: 'A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.'
+  description: |
+    DeepChopper is a genomic language model designed to identify artificial sequences.
+    It provides functionality for encoding FASTQ files, making predictions, and chopping sequences.
+  doc_url: https://github.com/ylab-hi/DeepChopper
+  dev_url: https://github.com/ylab-hi/DeepChopper
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - yangyangli
diff --git a/recipes/derna/build.sh b/recipes/derna/build.sh
index 7898ddc35f18f..0b6e4d0faf8a5 100644
--- a/recipes/derna/build.sh
+++ b/recipes/derna/build.sh
@@ -2,12 +2,21 @@
 
 set -xe
 
+mkdir -p $PREFIX/bin
+
 export C_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 
-mkdir build
-cd build
-cmake ..
-make -j ${CPU_COUNT}
-mkdir -p $PREFIX/bin
-cp derna $PREFIX/bin
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+cmake --build build  -j ${CPU_COUNT} -v
+chmod 0755 build/derna
+mv build/derna $PREFIX/bin
diff --git a/recipes/derna/meta.yaml b/recipes/derna/meta.yaml
index ffafda5a12a70..193695a14d649 100644
--- a/recipes/derna/meta.yaml
+++ b/recipes/derna/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.3" %}
+{% set version = "1.0.4" %}
 
 package:
   name: derna
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://github.com/elkebir-group/derna/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: d7e2fdbe733d03f9e617ea325a43283c0e4e298780253cf2e7da7ad07d3aafc5
+  sha256: eb5fabf0e01d9507ceca3fc687e8c67a9cec91c77e75d2c4f7d310ac926a79cb
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('derna', max_pin="x") }}
 
@@ -25,12 +25,13 @@ test:
     - derna -h
 
 about:
-  home: https://github.com/elkebir-group/derna
+  home: "https://github.com/elkebir-group/derna"
   license: BSD-3-Clause
   license_family: BSD
   license_file: LICENSE
   summary: "RNA sequence design for a target protein sequence."
-  dev_url: https://github.com/elkebir-group/derna
+  dev_url: "https://github.com/elkebir-group/derna"
+  doc_url: "https://github.com/elkebir-group/derna/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml
index f3d95856ef974..8d8264f4816ff 100644
--- a/recipes/dnaio/meta.yaml
+++ b/recipes/dnaio/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "1.2.2" %}
+{% set version = "1.2.3" %}
 
 package:
   name: dnaio
   version: {{ version }}
 
 source:
-  url: https://files.pythonhosted.org/packages/1e/69/b11040d6cb619f2c879904dfd5f703c15d5ed05d20afc556318de9bc476b/dnaio-1.2.2.tar.gz
-  sha256: 55e1c8e5b86056ce3bb3a3eff643ebc9910a5d6d0d5c10a27eb4d5b6525117d5
+  url: https://files.pythonhosted.org/packages/ca/23/1afaeadecfe4712769db4b609ca4aeb4246f6a47a9ab39801cb6a5aa8c2e/dnaio-1.2.3.tar.gz
+  sha256: aad456d9f6272339958b2c5af32fd64d77a50aca12e394e7a143b4129d49b0b9
 
 build:
   number: 0
@@ -20,11 +20,11 @@ requirements:
     - {{ compiler('c') }}
   host:
     - pip
-    - python
+    - python >=3.9
     - cython
     - setuptools-scm
   run:
-    - python
+    - python >=3.9
     - xopen >=1.4.0
 
 test:
diff --git a/recipes/doubletdetection/meta.yaml b/recipes/doubletdetection/meta.yaml
new file mode 100644
index 0000000000000..4b1d68ee91681
--- /dev/null
+++ b/recipes/doubletdetection/meta.yaml
@@ -0,0 +1,66 @@
+{% set name = "doubletdetection" %}
+{% set version = "4.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/doubletdetection-{{ version }}.tar.gz
+  sha256: 77273d543a7c9b4f4e795b7b664c28bce0613b3a3a7c7f5137974012400a0a6c
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('doubletdetection', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.6,<4.0
+    - poetry >=1.0
+    - setuptools
+    - poetry-core
+    - pip
+  run:
+    - python >=3.6.1,<4.0
+    - anndata >=0.6
+    - ipywidgets
+    - leidenalg
+    - louvain
+    - matplotlib-base >=3.1
+    - numpy >=1.14.2
+    - pandas >=0.22.0
+    - phenograph
+    - scanpy >1.4.4
+    - scipy >=1.0.1
+    - tqdm
+  run_constrained:
+    - black >=20.8b1
+    - flake8 >=3.7.7
+    - furo *
+    - myst-parser *
+    - nbsphinx *
+    - nbsphinx-link *
+    - pre-commit >=2.7.1
+    - pytest >=4.4
+    - sphinx >=4.1,<4.4
+    - sphinx-autodoc-typehints *
+
+test:
+  imports:
+    - doubletdetection
+
+about:
+  home: https://github.com/JonathanShor/DoubletDetection
+  summary: Method to detect and enable removal of doublets from single-cell RNA-sequencing.
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE.txt
+  dev_url: https://github.com/JonathanShor/DoubletDetection
+  doc_url: https://doubletdetection.readthedocs.io
+
+extra:
+  recipe-maintainers:
+    - LeonHafner
diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml
index 43bc3d576002f..2e02cdc953848 100644
--- a/recipes/dupsifter/meta.yaml
+++ b/recipes/dupsifter/meta.yaml
@@ -1,17 +1,17 @@
-{% set version = '1.2.1.20240119' %}
+{% set version = '1.3.0.20241113' %}
 
 package:
   name: dupsifter
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('dupsifter', max_pin='x') }}
 
 source:
   url: https://github.com/huishenlab/dupsifter/releases/download/v{{ version }}/release-source.zip
-  sha256: ca3db67e36f9a3d054acf9fbaf0dee1037781d468d7f094ea5d3852610448e7a
+  sha256: 270f1c2dfc2152d8ed63b6660aea9eca0398ff34529c606fd0ae30b1858ebb08
   patches:
     - patch
 
@@ -25,16 +25,10 @@ requirements:
     - xz
     - zlib
     - libdeflate
-    - openssl # [not osx]
+    - openssl  # [not osx]
     - pthread-stubs
   run:
-    - libcurl
-    - bzip2
-    - xz
-    - zlib
-    - libdeflate
-    - openssl # [not osx]
-    - pthread-stubs
+    - openssl  # [not osx]
 
 test:
   commands:
@@ -43,4 +37,11 @@ test:
 about:
   home: https://github.com/huishenlab/dupsifter
   license: MIT
-  summary: A tool for PCR duplicate marking of WGBS (and WGS) data
+  license_family: MIT
+  summary: A tool for PCR duplicate marking of WGBS (and WGS) data.
+  dev_url: https://github.com/huishenlab/dupsifter
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml
index b26c1ef097798..68c313634959b 100644
--- a/recipes/dxpy/meta.yaml
+++ b/recipes/dxpy/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "dxpy" %}
-{% set version = "0.384.0" %}
+{% set version = "0.385.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 17e29e9f58843c2639d53ea02b0dfd5c9940ad4ff20ab9e4df895a664f07e392
+  sha256: 6e0d06e9704e9845967caaf301e918496056ad58e15bd610fb02c3c4d775adcf
 
 build:
   number: 0
diff --git a/recipes/eagle2/0001-Use-CXX-and-flags.patch b/recipes/eagle2/0001-Use-CXX-and-flags.patch
new file mode 100644
index 0000000000000..ffe333a43d662
--- /dev/null
+++ b/recipes/eagle2/0001-Use-CXX-and-flags.patch
@@ -0,0 +1,5 @@
+--- src/Makefile
++++ src/Makefile
+@@ -1,99 +1,99 @@
+-O = DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o memcpy.o
++O = DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o
diff --git a/recipes/eagle2/build.sh b/recipes/eagle2/build.sh
new file mode 100644
index 0000000000000..73c8f41b3773f
--- /dev/null
+++ b/recipes/eagle2/build.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+set -euo pipefail
+
+echo "Building Eagle2 version ${PKG_VERSION}"
+
+cd src || exit 1
+
+sed -i.bak 's/memcpy.o//g' Makefile
+
+# Set up environment variables for building
+export BOOST_INSTALL_DIR=$PREFIX
+export HTSLIB_DIR=$PREFIX/lib
+export BLAS_DIR=$PREFIX/lib
+export ZLIB_STATIC_DIR=$PREFIX/lib
+
+# Run make
+make CC=${CXX} \
+    -e -j ${CPU_COUNT} \
+    CFLAGS="$CXXFLAGS -Wno-unused-result -std=c++11" \
+    BOOST_INSTALL_DIR=$BOOST_INSTALL_DIR \
+    HTSLIB_DIR=$HTSLIB_DIR \
+    BLAS_DIR=$BLAS_DIR \
+    ZLIB_STATIC_DIR=$ZLIB_STATIC_DIR \
+    LIBSTDCXX_STATIC_DIR=${PREFIX}/lib \
+    linking=dynamic
+
+echo "Installing Eagle2..."
+mkdir -p "${PREFIX}/bin"
+install -m 755 eagle "${PREFIX}/bin/"
+echo "Eagle2 installation completed successfully"
+
+cd .. || exit 1
\ No newline at end of file
diff --git a/recipes/eagle2/meta.yaml b/recipes/eagle2/meta.yaml
new file mode 100644
index 0000000000000..84092b0410a33
--- /dev/null
+++ b/recipes/eagle2/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = "2.4.1" %}
+
+package:
+  name: eagle2
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('eagle2', max_pin='x.x.x') }}
+
+source:
+  url: https://github.com/poruloh/Eagle/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 85804bfe972186ccb66e602856d6e04044302e5c0dbf9309849b0cde981e3432
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - htslib >=1.9
+    - bzip2
+    - zlib
+    - boost-cpp >=1.58
+    - openblas >=0.2.19
+  run:
+    - {{ pin_compatible('bzip2') }}
+    - {{ pin_compatible('zlib') }}
+    - {{ pin_compatible('boost-cpp') }}
+    - {{ pin_compatible('openblas') }}
+
+
+test:
+  commands:
+    - eagle -h
+
+about:
+  home: https://github.com/poruloh/Eagle
+  license: GPL-3.0-or-later
+  summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.
+  description:
+    Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new
+    very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas;
+    a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that
+    explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar
+    speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option.
+    (The Eagle1 algorithm can be accessed via the --v1 flag.) Eagle v2.3+ supports phasing sequence data with or without
+    a reference and also supports phasing chrX.
\ No newline at end of file
diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml
index f06b115b8bb5c..2753d1c68df3b 100644
--- a/recipes/ebi-eva-common-pyutils/meta.yaml
+++ b/recipes/ebi-eva-common-pyutils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ebi-eva-common-pyutils" %}
-{% set version = "0.6.10" %}
+{% set version = "0.6.11" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz
-  sha256: f143c703e31f40c94ebe366ba5f8a8247b6c825590ac157a7f5495f36aa7accb
+  sha256: 503f15c55b8438295727661486d610e87b7e9c9ca159ff8e373d0533094eb93b
 
 build:
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
diff --git a/recipes/emu-pca/build_failure.osx-64.yaml b/recipes/emu-pca/build_failure.osx-64.yaml
deleted file mode 100644
index faf6c61b044ce..0000000000000
--- a/recipes/emu-pca/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: c8fdd7d1be49e7c2e5e03c78e8ef8e5da084a2de40931b17429baec27d330480  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-    ERROR: Failed building wheel for emu
-  ERROR: Could not build wheels for emu, which is required to install pyproject.toml-based projects
-  Extracting download
-  source tree in: /opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-      utils.check_call_env(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
-  export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_build_env
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work/conda_build.sh']' returned non-zero exit status 1.
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work
-  INFO: activate_clang_osx-64.sh made the following environmental changes:
-  AR=x86_64-apple-darwin13.4.0-ar
-  AS=x86_64-apple-darwin13.4.0-as
-  CC=x86_64-apple-darwin13.4.0-clang
-  CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/emu-pca-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
-  CLANG=x86_64-apple-darwin13.4.0-clang
-  CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
-  CMAKE_PREFIX_PATH=:$PREFIX
-  CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
-  CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
-  CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9
-  DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/emu-pca-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  HOST=x86_64-apple-darwin13.4.0
-  INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
-  LD=x86_64-apple-darwin13.4.0-ld
-  LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
-  LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
-  LIBTOOL=x86_64-apple-darwin13.4.0-libtool
-  LIPO=x86_64-apple-darwin13.4.0-lipo
-  MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
-  NM=x86_64-apple-darwin13.4.0-nm
-  NMEDIT=x86_64-apple-darwin13.4.0-nmedit
-  OBJC=x86_64-apple-darwin13.4.0-clang
-  OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  OTOOL=x86_64-apple-darwin13.4.0-otool
-  PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
-  RANLIB=x86_64-apple-darwin13.4.0-ranlib
-  REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
-  SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
-  SEGEDIT=x86_64-apple-darwin13.4.0-segedit
-  SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
-  SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
-  SIZE=x86_64-apple-darwin13.4.0-size
-  STRINGS=x86_64-apple-darwin13.4.0-strings
-  STRIP=x86_64-apple-darwin13.4.0-strip
-  _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
-  ac_cv_func_malloc_0_nonnull=yes
-  ac_cv_func_realloc_0_nonnull=yes
-  build_alias=x86_64-apple-darwin13.4.0
-  host_alias=x86_64-apple-darwin13.4.0
-  Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12)
-  Non-user install because user site-packages disabled
-  Ignoring indexes: https://pypi.org/simple
-  Created temporary directory: /private/tmp/pip-build-tracker-pcf71fuv
-  Initialized build tracking at /private/tmp/pip-build-tracker-pcf71fuv
-  Created build tracker: /private/tmp/pip-build-tracker-pcf71fuv
-  Entered build tracker: /private/tmp/pip-build-tracker-pcf71fuv
-  Created temporary directory: /private/tmp/pip-install-_4p1fpa8
-  Created temporary directory: /private/tmp/pip-ephem-wheel-cache-pg6d97ox
-  Processing $SRC_DIR
-    Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-pcf71fuv'
-    Created temporary directory: /private/tmp/pip-modern-metadata-x9ykve7d
-    Preparing metadata (pyproject.toml): started
-    Preparing metadata (pyproject.toml): finished with status 'done'
-    Source in $SRC_DIR has version 1.0, which satisfies requirement emu==1.0 from file://$SRC_DIR
-    Removed emu==1.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-pcf71fuv'
-  Created temporary directory: /private/tmp/pip-unpack-ylygux9m
-  Building wheels for collected packages: emu
-    Created temporary directory: /private/tmp/pip-wheel-f2hnm5l2
-    Destination directory: /private/tmp/pip-wheel-f2hnm5l2
-    Building wheel for emu (pyproject.toml): started
-    Building wheel for emu (pyproject.toml): finished with status 'error'
-  Failed to build emu
-  Exception information:
-  Traceback (most recent call last):
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
-      status = run_func(*args)
-               ^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
-      return func(self, options, args)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 429, in run
-      raise InstallationError(
-  pip._internal.exceptions.InstallationError: Could not build wheels for emu, which is required to install pyproject.toml-based projects
-  Removed build tracker: '/private/tmp/pip-build-tracker-pcf71fuv'
-# Last 100 lines of the build log.
diff --git a/recipes/emu-pca/meta.yaml b/recipes/emu-pca/meta.yaml
index 3606b1fe2ba7c..f299b78443ca6 100644
--- a/recipes/emu-pca/meta.yaml
+++ b/recipes/emu-pca/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "emu-pca" %}
-{% set version = "1.0" %}
+{% set version = "1.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,12 +7,15 @@ package:
 
 source:
   url: 'https://github.com/Rosemeis/emu/archive/refs/tags/v{{ version }}.tar.gz'
-  md5: b79e9a2f72b8b83361a5542edc1c4ca7
+  sha256: a309849df3cbd2255718ba27d413b931b835ed869a67a93cd20320d1a04d31fb
 
 build:
-  number: 1
+  number: 0
+  skip: True  # [py < 310]
   script: 
-    - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation"
+    - "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir"
+  entry_points:
+    - emu=emu.main:main
   run_exports:
     {{ pin_subpackage('emu-pca', max_pin="x") }}
 
@@ -37,4 +40,3 @@ about:
   license_file: LICENSE
   summary: EM-PCA for Ultra-low Coverage Sequencing Data.
   dev_url: https://github.com/Rosemeis/emu
-
diff --git a/recipes/ensembl-utils/meta.yaml b/recipes/ensembl-utils/meta.yaml
index 77bbd0f6413b6..a0579103ab9f5 100644
--- a/recipes/ensembl-utils/meta.yaml
+++ b/recipes/ensembl-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ensembl-utils" %}
-{% set version = "0.5.1" %}
+{% set version = "0.6.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ensembl_utils-{{ version }}.tar.gz
-  sha256: 613d0f9584993aaacab42379b57b0ccbeac9f9269a99c186dddf84d396bc3c86
+  sha256: ee2841af4da1b7f10d2fa88ab844f72dad17042de473759971f4ec1d870a0506
 
 build:
   entry_points:
diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml
index 5592412e043df..4560bc3ab2097 100644
--- a/recipes/ensembl-vep/meta.yaml
+++ b/recipes/ensembl-vep/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ensembl-vep" %}
-{% set version = "113.0" %}
+{% set version = "113.2" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz
-  sha256: 5bb9aa8098d36c75076204693e13ef38b43c57dfce3d7d0169d119a5b4f87164
+  sha256: 4c91eee225c79b6b333c82adfc8661d23bdc2aa95cd94880015509bacdf51a71
 
 build:
   number: 0
diff --git a/recipes/eva-sub-cli/meta.yaml b/recipes/eva-sub-cli/meta.yaml
index 2b0ae04c0c9d7..16804ac314b7b 100644
--- a/recipes/eva-sub-cli/meta.yaml
+++ b/recipes/eva-sub-cli/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "eva-sub-cli" %}
-{% set version = "0.4" %}
+{% set version = "0.4.1" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz
-  sha256: be4d4109d9879ad94ccc01a3bd534ff6077775f126977dfb3f2d6fd9cfb251ba
+  sha256: a7db73bdbdbfe27b8970bc4fef71bcf5714189f30ac453d303820c0839f13fe3
 
 build:
   number: 0
@@ -22,7 +22,7 @@ requirements:
     - nextflow >=21.10.0
     - python >=3.8
     - nodejs >=10.19.1
-    - vcf-validator >=0.9.7
+    - vcf-validator >=0.10.0
     - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2
@@ -35,7 +35,7 @@ requirements:
     - nextflow >=21.10.0
     - python >=3.8
     - nodejs >=10.19.1
-    - vcf-validator >=0.9.7
+    - vcf-validator >=0.10.0
     - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2
diff --git a/recipes/evofr/meta.yaml b/recipes/evofr/meta.yaml
index fb083c92d9933..a378a5c246003 100644
--- a/recipes/evofr/meta.yaml
+++ b/recipes/evofr/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.1.23" %}
+{% set version = "0.1.25" %}
 
 package:
   name: evofr
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz
-  sha256: ac159419119c000e403b5801d8b6dfef215bcbeca6f30f3bf13b66b90b64ad17
+  sha256: 7360736349cad3a665acc80f4e6d3c4fe205a991dae2e35ab86d56b66214bf30
 
 build:
   number: 0
diff --git a/recipes/fairy/meta.yaml b/recipes/fairy/meta.yaml
index 5eb8910ec915f..02f9abd665509 100644
--- a/recipes/fairy/meta.yaml
+++ b/recipes/fairy/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.5.5" %}
+{% set version = "0.5.7" %}
 
 package:
   name: fairy
@@ -11,7 +11,7 @@ build:
 
 source:
   url: https://github.com/bluenote-1577/fairy/archive/v{{ version }}.tar.gz
-  sha256: 2d36fb115f3c069d4788c46f03ed054dc9b8f73228ed1b04d6b1d6bfd8c4124c
+  sha256: 4a4583f0efa3b818d6c3cef43e1f732b307554465ba76f3916f51e4ae02baefc
 
 requirements:
   build:
diff --git a/recipes/famsa/meta.yaml b/recipes/famsa/meta.yaml
index aff435a23945f..57b63bd57adeb 100644
--- a/recipes/famsa/meta.yaml
+++ b/recipes/famsa/meta.yaml
@@ -1,22 +1,22 @@
-{% set version = "2.2.2" %}
-{% set sha256 = "9e1d96b80ff0010852dcab24f8691bf2deb7415838c001f0362ec72fd0ac2d44" %}
+{% set version = "2.2.3" %}
 
 package:
   name: famsa
   version: {{ version }}
 
 build:
-  number: 3
+  number: 0
   run_exports:
     - {{ pin_subpackage('famsa', max_pin='x') }}
 
 source:
-  url: https://github.com/refresh-bio/FAMSA/archive/v{{ version }}.tar.gz
-  sha256: {{ sha256 }}
+  git_url: https://github.com/refresh-bio/FAMSA.git
+  git_rev: v{{ version }}
 
 requirements:
   build:
     - {{ compiler('cxx') }}
+    - cmake
     - make
 
 test:
@@ -25,10 +25,11 @@ test:
 
 about:
   home: https://github.com/refresh-bio/FAMSA
-  summary: "Algorithm for large-scale multiple sequence alignments"
+  summary: "Algorithm for large-scale multiple sequence alignments."
   license: GPL-3.0-only
-  license_family: GPL
+  license_family: GPL3
   license_file: LICENSE
+  dev_url: https://github.com/refresh-bio/FAMSA
 
 extra:
   additional-platforms:
@@ -37,3 +38,6 @@ extra:
   identifiers:
     - doi:10.1038/srep33964
     - biotools:famsa
+  skip-lints:
+    - uses_vcs_url
+    - missing_hash
diff --git a/recipes/fastk/meta.yaml b/recipes/fastk/meta.yaml
index a3a85c9b9151d..72a5ad1be313e 100644
--- a/recipes/fastk/meta.yaml
+++ b/recipes/fastk/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "FASTK" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "92f3f4633fc702f20b6d3c07c6fe10b002d746b25154e090f0115ac7d2791863" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "28a2de98ede77d4b4476596851f92413a9d99a1d3341afc6682d5333ac797f07" %}
 
 package:
   name: {{ name|lower }}
@@ -13,7 +13,7 @@ source:
     - patch
 
 build:
-  number: 1
+  number: 0
   skip: true # [osx]
   run_exports:
     - {{ pin_subpackage("fastk", max_pin="x") }}
@@ -39,4 +39,4 @@ about:
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64
diff --git a/recipes/fastp/meta.yaml b/recipes/fastp/meta.yaml
index 148491c023d63..1cbcc0d55e8d7 100644
--- a/recipes/fastp/meta.yaml
+++ b/recipes/fastp/meta.yaml
@@ -1,4 +1,4 @@
-{% set version="0.23.4" %}
+{% set version="0.24.0" %}
 
 package:
   name: fastp
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://github.com/OpenGene/fastp/archive/v{{ version }}.tar.gz
-  sha256: 4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5
+  sha256: 42445973c57be9209c753027e99781261c69381013813c576ad447e413ff3d04
 
 build:
-  number: 5
+  number: 0
   run_exports:
     - {{ pin_subpackage("fastp", max_pin="x.x") }}
 
diff --git a/recipes/fastqe/meta.yaml b/recipes/fastqe/meta.yaml
index 37ee551c6f5e4..fbd3629b123aa 100644
--- a/recipes/fastqe/meta.yaml
+++ b/recipes/fastqe/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "fastqe" %}
-{% set version = "0.3.1" %}
+{% set version = "0.3.3" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: "5b2e60d3d48d9abc5807ebaa9b51c5326b2130b118e0852cd40a35179460379c"
+  sha256: "6ddcef4a9d25e22d7391ea6f6234181f3ec22c0767d07c90cb2c66deb4ec3881"
   patches:
     - patch
 
@@ -16,14 +16,18 @@ build:
   number: 0
   entry_points:
     - fastqe = fastqe.fastqe:main
-  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir --use-pep517 -vvv
+  run_exports:
+    - {{ pin_subpackage('fastqe', max_pin="x.x") }}
 
 requirements:
   host:
-    - python
+    - python >=3.7
     - pip
+    - twine >=1.11.0
+    - setuptools
   run:
-    - python
+    - python >=3.7
     - biopython >=1.66
     - pyemojify
 
@@ -35,7 +39,8 @@ test:
 
 about:
   home: https://github.com/lonsbio/fastqe
-  license: MIT
-  license_family: MIT
-  summary: A emoji based bioinformatics command line tool
+  license: BSD-3-Clause
+  license_family: BSD
+  license_file: LICENSE.txt
+  summary: "A emoji based bioinformatics command line tool."
   description: "The program reads one or more input FASTQ files.\nFor each file it computes the minimum, maximum and mean FASTQ quality score at each position across all reads in a file.\n\nFor some reason, it then represents these as emoji."
diff --git a/recipes/fc/build.sh b/recipes/fc/build.sh
new file mode 100644
index 0000000000000..6725e40accbf6
--- /dev/null
+++ b/recipes/fc/build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+set -xe
+make CXX="${CXX}" INCLUDES="-I$PREFIX/include" CFLAGS+="${CFLAGS} -g -Wall -O2 -L$PREFIX/lib"
+#chmod +x ./bin/fc-virus
+chmod 777 ./bin/fc-virus
+mkdir -p ${PREFIX}/bin
+cp -f ./bin/fc-virus ${PREFIX}/bin
diff --git a/recipes/fc/meta.yaml b/recipes/fc/meta.yaml
new file mode 100644
index 0000000000000..15c1e2335f04d
--- /dev/null
+++ b/recipes/fc/meta.yaml
@@ -0,0 +1,37 @@
+{% set name = "fc" %}
+{% set version = "1.0.1" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: "https://github.com/qdu-bioinfo/fc-virus/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: "0f3b5f76ca17c90c7553d35280de6c0248802fad088a7fe653652653e3170944"
+
+build:
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage("fc", max_pin="x") }}
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - boost-cpp
+
+test:
+  commands:
+    - fc-virus --help
+
+about:
+  home: "https://github.com/qdu-bioinfo/fc-virus"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies."
+  dev_url: "https://github.com/qdu-bioinfo/fc-virus"
diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml
index ec8d76b58f4d5..49f78563a49ec 100644
--- a/recipes/fgbio-minimal/meta.yaml
+++ b/recipes/fgbio-minimal/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio-minimal
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic
diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml
index 496337cbe9149..04b43d63f15a4 100644
--- a/recipes/fgbio/meta.yaml
+++ b/recipes/fgbio/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic
diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml
index 69a4df4c53ebc..7ae34895a723c 100644
--- a/recipes/fgpyo/meta.yaml
+++ b/recipes/fgpyo/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "fgpyo" %}
-{% set version = "0.7.1" %}
+{% set version = "0.8.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 0d0b0d6f2e365c136830e803e4a6d56fe20c6d615a4b857b423f19c51b700bab
+  sha256: 7a08d718addd7e9e412fb192d83670a9c683daa1d340710af9c833bedce6546a
 
 build:
   noarch: python
diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml
index 4d064dba5f553..5620d4693947c 100644
--- a/recipes/fgsv/meta.yaml
+++ b/recipes/fgsv/meta.yaml
@@ -1,5 +1,5 @@
-{% set version="0.2.0" %}
-{% set sha256="c2f9536a677e7e99f251cada1338f611cea40477deca144f0c6928505755eb37" %}
+{% set version="0.2.1" %}
+{% set sha256="e3f15c7f1a97c009be65663405194faedf473c2636a3c3d742f463030caba860" %}
 
 
 package:
diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml
index 2a13e6f52bfd5..bd4ad503eaa77 100644
--- a/recipes/fibertools-rs/meta.yaml
+++ b/recipes/fibertools-rs/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.5.4" %}
+{% set version = "0.6.0" %}
 {% set name = "fibertools-rs" %}
 {% set build_number = "0" %}
 
@@ -8,7 +8,7 @@ package:
   
 source:  
   url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz
-  sha256: d0dc8523b9c0f2c2b368fb450d6cf6f45e13fb53bdbbd1847f1bb748fb5af42b
+  sha256: 4f33fb470766ed325f83767cf766e7795afcfc1af8dae4e807876b1560efc193
 
 build:
   run_exports:
diff --git a/recipes/flexiformatter/meta.yaml b/recipes/flexiformatter/meta.yaml
new file mode 100644
index 0000000000000..ee19abf265226
--- /dev/null
+++ b/recipes/flexiformatter/meta.yaml
@@ -0,0 +1,51 @@
+{% set name = "flexiformatter" %}
+{% set version = "1.0.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flexiformatter-{{ version }}.tar.gz
+  sha256: fc117809168051e2ba4bfe83c69065de7f65efff7e3941e94552c88e4c6cb3a2
+
+build:
+  entry_points:
+    - flexiformatter = flexiformatter.reformat_flexiplex_tags:app
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.7
+    - pip
+    - setuptools
+  run:
+    - python >=3.7
+    - typer >=0.9.0
+    - simplesam
+    - samtools
+
+test:
+  imports:
+    - flexiformatter
+    - simplesam
+  commands:
+    - flexiformatter --help
+    - samtools --help
+  requires:
+    - pip
+
+about:
+  home: "https://github.com/ljwharbers/flexiformatter"
+  summary: Moving flexiplex barcode and UMI to bam tags
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - ljwharbers
diff --git a/recipes/flippyr/meta.yaml b/recipes/flippyr/meta.yaml
index c45b1fd060bad..87decc35c99b6 100644
--- a/recipes/flippyr/meta.yaml
+++ b/recipes/flippyr/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "flippyr" %}
-{% set version = "0.5.3" %}
-{% set sha256 = "2d7354138bc77a63242369c440175de39ca2dc414a8ef3a506b0abe7e9473a35" %}
+{% set version = "0.6.1" %}
+{% set sha256 = "65bc37f44c8df60c33c1f82638034df874050204cd832918ba7b41d78a1d8452" %}
 
 package:
   name: {{ name|lower }}
@@ -14,7 +14,7 @@ requirements:
   build:
     - python
     - setuptools
-
+    - pip
   run:
     - python
     - pyfaidx
@@ -23,9 +23,11 @@ requirements:
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
+  script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir"
   entry_points:
     - flippyr = flippyr:main
+  run_exports:
+    - {{ pin_subpackage('flippyr', max_pin="x.x") }}
 
 test:
   commands:
diff --git a/recipes/fmsi/meta.yaml b/recipes/fmsi/meta.yaml
index 5db343b3713d3..a8ed730318cfc 100644
--- a/recipes/fmsi/meta.yaml
+++ b/recipes/fmsi/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.3.0" %}
-{% set sha256 = "441d9f5808c7568ae237b5bb45db9328185fee43628eb0a4407ae7da0bdcf3bc" %}
+{% set version = "0.3.1" %}
+{% set sha256 = "c36a21cf134e3aa6172898ebaa01319e2b00f496b1e5bfd81b624908173ba93f" %}
 
 package:
   name: fmsi
diff --git a/recipes/freyja/meta.yaml b/recipes/freyja/meta.yaml
index c6dd548925fd5..4e579935046e6 100644
--- a/recipes/freyja/meta.yaml
+++ b/recipes/freyja/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.5.1" %}
+{% set version = "1.5.2" %}
 {% set name = "Freyja" %}
 
 package:
@@ -6,8 +6,8 @@ package:
   version: {{ version }}
 
 build:
-  number: 1
-  script: "python -m pip install . --no-deps"
+  number: 0
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   entry_points:
     - freyja=freyja._cli:cli
@@ -16,12 +16,13 @@ build:
 
 source:
   url:  https://github.com/andersen-lab/{{ name }}/archive/v{{ version }}.tar.gz
-  sha256: e9007c144857cb8aefe5a834e50c097d1ed685439c9c25f188e38d0c736084d8
+  sha256: e1703f2bff4bd747f80b7b3ebd97a8b06dc1b149d4306323c0408ee4cfeddab9
 
 requirements:
   host:
     - python >=3.7
     - pip
+    - setuptools
   run:
     - python >=3.7
     - click
@@ -40,8 +41,10 @@ requirements:
     - epiweeks
     - pysam
     - biopython
-    - seaborn
+    - seaborn-base
     - pyarrow
+    - sphinx
+    - sphinx_rtd_theme
 
 test:
   commands:
@@ -53,3 +56,4 @@ about:
   license_family: BSD
   license_file: LICENSE
   summary: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics."
+  dev_url: https://github.com/andersen-lab/Freyja
diff --git a/recipes/gadma/meta.yaml b/recipes/gadma/meta.yaml
index e993392fac055..57ee11d2b03b5 100644
--- a/recipes/gadma/meta.yaml
+++ b/recipes/gadma/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gadma" %}
-{% set version = "2.0.0" %}
+{% set version = "2.0.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 1e891b87749261ce9c1866fd3e0ac389306096e3b940eb364101448efeca4cfd
+  sha256: f7b610d0d347e97afb30e6b5f9a814c19e479203838de31aa2e44f7427073db5
 
 build:
   number: 0
@@ -19,27 +19,31 @@ build:
     - gadma-get_confidence_intervals = gadma.get_confidence_intervals:main
     - gadma-get_confidence_intervals_for_ld = gadma.get_confidence_intervals_for_ld:main
     - gadma-precompute_ld_data = gadma.precompute_ld_data:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   run_exports:
     - {{ pin_subpackage('gadma', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3.6,<3.9
+    - python >=3.6
     - pip
     - setuptools-scm
+    - setuptools
   run:
-    - python >=3.6,<3.9
+    - python >=3.6
     - dadi
+    - demes
+    - demesdraw
+    - h5py ==3.10.0
     - matplotlib-base
     - mpmath
     - nlopt
     - numpy
-    - pandas
+    - pandas <=2.2.2
     - pillow
-    - ruamel.yaml
-    - scipy
+    - ruamel.yaml ==0.16.12
+    - scipy <1.14
     - networkx
     - moments
     - scikit-allel
@@ -69,6 +73,7 @@ about:
   license_file: LICENSE
   summary: "Genetic Algorithm for Demographic Inference"
   doc_url: https://gadma.readthedocs.io/en/latest/
+  dev_url: "https://github.com/ctlab/GADMA"
 
 extra:
   identifiers:
diff --git a/recipes/gaftools/meta.yaml b/recipes/gaftools/meta.yaml
new file mode 100644
index 0000000000000..ad29e06c99ed9
--- /dev/null
+++ b/recipes/gaftools/meta.yaml
@@ -0,0 +1,42 @@
+{% set name = "gaftools" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "b04c1f7df479ab9a179b1709dec97dce054787f5fab8f2c2c38eb03df2e4a416" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  noarch: python
+  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv
+  run_exports:
+    - {{ pin_compatible('gaftools', max_pin="x") }}
+
+
+requirements:
+  host:
+    - python >=3.6
+    - pip
+    - setuptools
+  run:
+    - python >=3.6
+    - pysam
+    - pywfa ==0.5.1
+
+test:
+  commands:
+    - gaftools -h
+
+about:
+  home: "https://github.com/marschall-lab/gaftools"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: 'gaftools is a fast and comprehensive toolkit designed for processing pangenome alignments in GAF format'
+  doc_url: "https://gaftools.readthedocs.io/en/latest/index.html"
+  dev_url: "https://github.com/marschall-lab"
diff --git a/recipes/galaxy-data/meta.yaml b/recipes/galaxy-data/meta.yaml
index c8e6406f0d915..5f303645dfb7e 100644
--- a/recipes/galaxy-data/meta.yaml
+++ b/recipes/galaxy-data/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.1.2" %}
-{% set sha256 = "d75e5e9e954773c683cb54a655da0c9733f1c6b0f6e691fedb6a1edc6e4aede2" %}
+{% set version = "24.1.3" %}
+{% set sha256 = "e5f32420a9fd33ea4fb896dcbbbb754a4be23f39c48d3a196aac2bde1d70d53a" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:
@@ -26,6 +26,7 @@ requirements:
   host:
     - pip
     - python >=3.8
+    - setuptools
   run:
     - python >=3.8
     - galaxy-files >={{ galaxy_version }}
diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml
index 83a3987023337..ff499c78ddae3 100644
--- a/recipes/galaxy-files/meta.yaml
+++ b/recipes/galaxy-files/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.1.2" %}
-{% set sha256 = "39f25b6f9a2f48625bf21fe0021e90768f598db1113867960420afc5988a4e70" %}
+{% set version = "24.1.3" %}
+{% set sha256 = "563e5b7973dfb7ae294533c72af9e3d5d0105c7a64e27b6d57a1a59594aec680" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:
@@ -21,6 +21,7 @@ requirements:
   host:
     - pip
     - python >=3.7
+    - setuptools
   run:
     - galaxy-util >={{ galaxy_version }}
     - fs
diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml
index 0581ff15a3a22..caa0ec7b368e2 100644
--- a/recipes/galaxy-objectstore/meta.yaml
+++ b/recipes/galaxy-objectstore/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.1.2" %}
-{% set sha256 = "1079e628fb89125792781e9a62711e8281f3cd34eff0cd5ce8ed452d6c06cb3e" %}
+{% set version = "24.1.3" %}
+{% set sha256 = "dcc9bd7b17e283b436b1660c5cf525c18de83d0fb709bbd0ca1f6cf868428dc5" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:
diff --git a/recipes/galaxy-schema/meta.yaml b/recipes/galaxy-schema/meta.yaml
index 2cb94358c1d1f..eeeaccd63064e 100644
--- a/recipes/galaxy-schema/meta.yaml
+++ b/recipes/galaxy-schema/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "galaxy-schema" %}
-{% set version = "24.1.2" %}
-{% set sha256 = "526d9c7e211da145f4169272a69b4a512304110da3dd9df61d0d305991db5309" %}
+{% set version = "24.1.3" %}
+{% set sha256 = "ab9c6ad72a514e2328fcf9f907db8e99e1bcd0853c319828248a08da11d4784a" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - galaxy-util >={{ galaxy_version }}
diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml
index f588a9884779c..18eb0e910083e 100644
--- a/recipes/gatk4/meta.yaml
+++ b/recipes/gatk4/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "GATK4" %}
-{% set version = "4.5.0.0" %}
-{% set sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %}
+{% set version = "4.6.1.0" %}
+{% set sha256 = "ac7015c3f0ef1852745ca0ef647adbf8ddef5db63ab485b00bc1ffe654814155" %}
 
 package:
   name: {{ name|lower }}
@@ -18,21 +18,21 @@ build:
 
 requirements:
   host:
-    - r-base =3.6
+    - r-base =4.3.1
     - r-gplots
     - r-ggplot2
     - r-gsalib
     - r-reshape
-    - gcnvkernel =0.8
+    - gcnvkernel =0.9
   run:
     - openjdk >=17,<18
     - python
-    - r-base =3.6
+    - r-base =4.3.1
     - r-gplots
     - r-ggplot2
     - r-gsalib
     - r-reshape
-    - gcnvkernel =0.8
+    - gcnvkernel =0.9
 
 test:
   commands:
diff --git a/recipes/gb-io/build.sh b/recipes/gb-io/build.sh
deleted file mode 100644
index a8f3305257de7..0000000000000
--- a/recipes/gb-io/build.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash -e
-
-set -ex
-
-# Use a custom temporary directory as home on macOS.
-# (not sure why this is useful, but people use it in bioconda recipes)
-if [ `uname` == Darwin ]; then
-  export HOME=`mktemp -d`
-fi
-
-# build statically linked binary with Rust
-$PYTHON -m pip install . --no-deps --no-build-isolation -vvv
diff --git a/recipes/gb-io/build_failure.osx-64.yaml b/recipes/gb-io/build_failure.osx-64.yaml
deleted file mode 100644
index 3d8509b7d299a..0000000000000
--- a/recipes/gb-io/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 7e6e0693a3ac8aa2889ec74d7c05525158f7481f56430408404ac4c5a675b1d8  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gb-io_1717512763030/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol
-  export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gb-io_1717512763030/_build_env
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gb-io_1717512763030/work
-  INFO: activate_clang_osx-64.sh made the following environmental changes:
-      api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-  AR=x86_64-apple-darwin13.4.0-ar
-  AS=x86_64-apple-darwin13.4.0-as
-  CC=x86_64-apple-darwin13.4.0-clang
-  CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-      return build_tree(
-  CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gb-io-0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
-  CLANG=x86_64-apple-darwin13.4.0-clang
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-      utils.check_call_env(
-  CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
-  CMAKE_PREFIX_PATH=:$PREFIX
-  CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
-  CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
-  CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-  DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gb-io-0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  HOST=x86_64-apple-darwin13.4.0
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gb-io_1717512763030/work/conda_build.sh']' returned non-zero exit status 1.
-  LD=x86_64-apple-darwin13.4.0-ld
-  LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
-  LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
-  LIBTOOL=x86_64-apple-darwin13.4.0-libtool
-  LIPO=x86_64-apple-darwin13.4.0-lipo
-  MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
-  NM=x86_64-apple-darwin13.4.0-nm
-  NMEDIT=x86_64-apple-darwin13.4.0-nmedit
-  OBJC=x86_64-apple-darwin13.4.0-clang
-  OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  OTOOL=x86_64-apple-darwin13.4.0-otool
-  PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
-  RANLIB=x86_64-apple-darwin13.4.0-ranlib
-  REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
-  SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
-  SEGEDIT=x86_64-apple-darwin13.4.0-segedit
-  SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
-  SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
-  SIZE=x86_64-apple-darwin13.4.0-size
-  STRINGS=x86_64-apple-darwin13.4.0-strings
-  STRIP=x86_64-apple-darwin13.4.0-strip
-  _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
-  ac_cv_func_malloc_0_nonnull=yes
-  ac_cv_func_realloc_0_nonnull=yes
-  build_alias=x86_64-apple-darwin13.4.0
-  host_alias=x86_64-apple-darwin13.4.0
-  INFO: activate_clangxx_osx-64.sh made the following environmental changes:
-  CLANGXX=x86_64-apple-darwin13.4.0-clang
-  CXX=x86_64-apple-darwin13.4.0-clang
-  CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gb-io-0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gb-io-0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  Using pip 24.0 from $PREFIX/lib/python3.9/site-packages/pip (python 3.9)
-  Non-user install because user site-packages disabled
-  Ignoring indexes: https://pypi.org/simple
-  Created temporary directory: /private/tmp/pip-build-tracker-uolko928
-  Initialized build tracking at /private/tmp/pip-build-tracker-uolko928
-  Created build tracker: /private/tmp/pip-build-tracker-uolko928
-  Entered build tracker: /private/tmp/pip-build-tracker-uolko928
-  Created temporary directory: /private/tmp/pip-install-9z4rp325
-  Created temporary directory: /private/tmp/pip-ephem-wheel-cache-29j_pjg1
-  Processing $SRC_DIR
-    Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-uolko928'
-    Created temporary directory: /private/tmp/pip-modern-metadata-omx74dv9
-    Preparing metadata (pyproject.toml): started
-    Preparing metadata (pyproject.toml): finished with status 'done'
-    Source in $SRC_DIR has version 0.3.2, which satisfies requirement gb-io==0.3.2 from file://$SRC_DIR
-    Removed gb-io==0.3.2 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-uolko928'
-  Created temporary directory: /private/tmp/pip-unpack-3b74mzyh
-  Building wheels for collected packages: gb-io
-    Created temporary directory: /private/tmp/pip-wheel-oz7bnwid
-    Destination directory: /private/tmp/pip-wheel-oz7bnwid
-    Building wheel for gb-io (pyproject.toml): started
-    Building wheel for gb-io (pyproject.toml): finished with status 'error'
-  Failed to build gb-io
-  Exception information:
-  Traceback (most recent call last):
-    File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
-      status = run_func(*args)
-    File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
-      return func(self, options, args)
-    File "$PREFIX/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 429, in run
-      raise InstallationError(
-  pip._internal.exceptions.InstallationError: Could not build wheels for gb-io, which is required to install pyproject.toml-based projects
-  Removed build tracker: '/private/tmp/pip-build-tracker-uolko928'
-# Last 100 lines of the build log.
diff --git a/recipes/gb-io/meta.yaml b/recipes/gb-io/meta.yaml
index 88ef2346b5e42..0905a764c28f6 100644
--- a/recipes/gb-io/meta.yaml
+++ b/recipes/gb-io/meta.yaml
@@ -1,18 +1,19 @@
 {% set name = "gb-io" %}
-{% set version = "0.3.2" %}
+{% set version = "0.3.3" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 build:
-  number: 1
+  number: 0
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir --use-pep517
   run_exports:
     - {{ pin_subpackage('gb-io', max_pin="x.x") }}
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 5bf0a5b2755e5e4aa928184043a44c28e2658158965901abb003ede8c794ad6e
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/gb_io-{{ version }}.tar.gz
+  sha256: 5c628ba04e690b7bdb72cc4fb65230a169e0d1ca029f5b07ae3bba84f65d5c47
 
 requirements:
   build:
@@ -33,5 +34,12 @@ test:
 about:
   home: https://github.com/althonos/gb-io.py
   license: MIT
+  license_family: MIT
   license_file: COPYING
   summary: A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
+  dev_url: https://github.com/althonos/gb-io.py
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/gcnvkernel/meta.yaml b/recipes/gcnvkernel/meta.yaml
index f8c6448ea98bb..d8488006c2f2f 100644
--- a/recipes/gcnvkernel/meta.yaml
+++ b/recipes/gcnvkernel/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "gcnvkernel" %}
-{% set version = "0.8" %}
-{% set gatk_version = "4.5.0.0" %}
-{% set gatk_sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %}
+{% set version = "0.9" %}
+{% set gatk_version = "4.6.1.0" %}
+{% set gatk_sha256 = "ac7015c3f0ef1852745ca0ef647adbf8ddef5db63ab485b00bc1ffe654814155" %}
 
 package:
   name: {{ name|lower }}
@@ -13,47 +13,46 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
+  preserve_egg_dir: true
   run_exports:
      - {{ pin_subpackage('gcnvkernel', max_pin="x") }}
 
 requirements:
   build:
-    - conda-forge::python =3.6.10
+    - conda-forge::python =3.10.13
     - unzip
   run:
     # The following are taken from the GATK python environment:
     #
     # https://github.com/broadinstitute/gatk/blob/master/scripts/gatkcondaenv.yml.template
-    - conda-forge::python =3.6.10
-    - pip =21.3.1
-    - conda-forge::mkl =2019.5
-    - conda-forge::mkl-service =2.3.0
-    - conda-forge::numpy =1.17.5
-    - conda-forge::theano =1.0.4
-    - tensorflow <2
-    - conda-forge::scipy =1.0.0
-    - conda-forge::pymc3 =3.1
-    - conda-forge::h5py =2.10.0 
-    - conda-forge::keras =2.2.4
-    - conda-forge::intel-openmp
-    - conda-forge::scikit-learn =0.23.1
-    - conda-forge::matplotlib =3.2.1
-    - conda-forge::pandas =1.0.3
-    - conda-forge::typing_extensions =4.1.1
-    - conda-forge::dill =0.3.4
-    - r-base =3.6.2
-    - r-data.table =1.12.8
-    - r-dplyr =0.8.5
-    - r-getopt =1.20.3
-    - r-ggplot2 =3.3.0
-    - r-gplots =3.0.3
-    - r-gsalib =2.1
-    - r-optparse =1.6.4
-    - r-backports =1.1.10
-    - biopython =1.76
-    - pyvcf =0.6.8
-    - bioconda::pysam =0.15.3
+    - conda-forge::python =3.10.13
+    - conda-forge::pip =23.3.1
+    - conda-forge:blas =1.0=mkl
+    - conda-forge::numpy =1.26.2
+    - conda-forge::pymc =5.10.1
+    - conda-forge::pytensor =2.18.3
+    - conda-forge::scipy =1.11.4
+    - conda-forge::h5py =3.10.0
+    - conda-forge::pytorch =2.1.0=*mkl*100
+    - conda-forge::pytorch-lightning =2.4.0
+    - conda-forge::scikit-learn =1.3.2
+    - conda-forge::matplotlib =3.8.2
+    - conda-forge::pandas =2.1.3
+    - conda-forge::tqdm =4.66.1
+    - conda-forge::dill =0.3.7
+    - conda-forge::biopython =1.84
+    - r-base =4.3.1
+    - r-data.table =1.14.8
+    - r-dplyr =1.1.3
+    - r-getopt =1.20.4
+    - r-ggplot2 =3.4.4
+    - r-gplots =3.1.3
+    - r-gsalib =2.2.1
+    - r-optparse =1.7.3
+    - r-backports =1.4.1
+    - bioconda::pysam =0.22.0
+    - conda-forge::pyvcf =0.6.8
 
 test:
   imports:
diff --git a/recipes/gempipe/meta.yaml b/recipes/gempipe/meta.yaml
index af1cdf9c4c906..5eef59838acdb 100755
--- a/recipes/gempipe/meta.yaml
+++ b/recipes/gempipe/meta.yaml
@@ -1,32 +1,32 @@
-{% set version = "1.36.0" %}
+{% set name = "gempipe" %}
+{% set version = "1.37.3" %}
 
 package:
-    name: "gempipe"
+    name: {{ name }}
     version: {{ version }}
 
-
 source:
-    url: https://github.com/lazzarigioele/gempipe/archive/v{{ version }}.tar.gz
-    sha256: e7585c905346be95d9018083928d00a5a44e8f6a4c3f8049e5de873bafdf8926
-
+    # with https://github.com/lazzarigioele/{name}/archive/v{version}.tar.gz :
+    url: https://github.com/lazzarigioele/{{ name }}/archive/v{{ version }}.tar.gz
+    # with https://pypi.org/packages/source/{first-letter}/{package-name}/{package-name}-{version}.tar.gz :
+    #url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+    sha256: ac372858f01b995cd9a153ecdc59d1524b652675a9c5aecaaf5c818dd93cd9e4
 
 build:
     number: 0  
     noarch: python
     script: 
-        - {{ PYTHON }} -m pip install . -vv --no-deps  
+        - {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
     entry_points:
         - gempipe = gempipe:main
     run_exports:
         - {{ pin_subpackage('gempipe', max_pin="x") }}
     
-    
 requirements:
     host:
         - python >=3.9
         - pip
-        - poetry >=1.7.1
-        - poetry-core >=1.8.1
+        - poetry-core >=1.0.0
         - ipython >=8.7.0
     run:
         - python >=3.9
@@ -47,8 +47,8 @@ requirements:
         - eggnog-mapper >=2.1.7
         - matplotlib-base >=3.7.0
         - seaborn >=0.13.0
-        
-
+        - scipy >=1.10.0
+        - scikit-learn >=1.3.0
 
 test:
     imports:
@@ -59,17 +59,15 @@ test:
         - gempipe derive --help
         - gempipe autopilot --help
 
-
 about:
     home: "https://github.com/lazzarigioele/gempipe"
     summary: 'gempipe is a tool for the reconstruction of strain-specific genome-scale metabolic models.'
     license: GPL-3.0-only
+    license_family: GPL3
     license_file: LICENSE.txt
     doc_url: "https://gempipe.readthedocs.io/"
     dev_url: "https://github.com/lazzarigioele/gempipe"
 
-
 extra:
     recipe-maintainers:
         - lazzarigioele
-        
diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml
index 113e485ce3f40..536b02f9c1d18 100644
--- a/recipes/gencove/meta.yaml
+++ b/recipes/gencove/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.23.0" %}
-{% set sha256 = "edb1a4855f88d87c41902745d6f823142747005a29932700afcabc0c216f16e9" %}
+{% set version = "2.24.1" %}
+{% set sha256 = "3c6d3c236dcad933fcb8298a394b84882398a577aa5f8c140ddefeabeb167513" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml
index 4bf3f662ad0da..1179d9f7a73bf 100644
--- a/recipes/genmod/meta.yaml
+++ b/recipes/genmod/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "genmod" %}
-{% set version = "3.8.3" %}
+{% set version = "3.9" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 97a411f3f014557cf57aed9cc18e55e097ab7c54b191eb7995c10dd97d4bdeaf
+  sha256: bbe7ad87971b50f4165142481147738882be96e1200d10dcea79a31d614e0cf2
 
 build:
   number: 0
diff --git a/recipes/genodsp/meta.yaml b/recipes/genodsp/meta.yaml
index d8806c20b4d49..74b6df8825a5f 100644
--- a/recipes/genodsp/meta.yaml
+++ b/recipes/genodsp/meta.yaml
@@ -17,8 +17,8 @@ requirements:
     - make
 
 build:
-  number: 0
-  skip: True  # [not linux or not x86_64]
+  number: 1
+  skip: True  # [not linux]
   run_exports:
     - {{ pin_subpackage('genodsp', max_pin="x.x") }}
 
@@ -34,3 +34,7 @@ about:
   license: GPL-3.0-only
   license_file: LICENSE
   license_url: https://github.com/rsharris/genodsp/blob/master/LICENSE
+
+extra:
+  additional-platforms:
+    - linux-aarch64
\ No newline at end of file
diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml
index 4086881aa0d61..dd0c8a0146c90 100644
--- a/recipes/genoflu/meta.yaml
+++ b/recipes/genoflu/meta.yaml
@@ -1,8 +1,8 @@
 {% set user = "USDA-VS" %}
 {% set name = "GenoFLU" %}
 
-{% set version = "1.03" %}
-{% set sha256 = "fe814ff8e256b57e32a3398d4c16d449eb6222cbb02869bd876534484c5b070e" %}
+{% set version = "1.05" %}
+{% set sha256 = "af63053347082cd9fcfeab1ea4bff9ce9340ebbef636e509a72c9e7f4c56be3e" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/geosketch/meta.yaml b/recipes/geosketch/meta.yaml
index aeb1eccd41cf6..19438ca77af46 100644
--- a/recipes/geosketch/meta.yaml
+++ b/recipes/geosketch/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "geosketch" %}
-{% set version = "1.2" %}
+{% set version = "1.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,12 +7,14 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: bbfe97366b91c5927b6076d5a6738d9cfbe094efb5ac1117aab7a30b6081cc4e
+  sha256: 2b2a6056c2134048fa85972ee93b95bdf53555fdf482cc4bfc29c485b78bb5f4
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed -vv ."
+  script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv ."
+  run_exports:
+    - {{ pin_subpackage('geosketch', max_pin="x") }}
 
 requirements:
   host:
@@ -30,9 +32,10 @@ test:
     - geosketch
 
 about:
-  home: https://github.com/brianhie/geosketch/
+  home: https://github.com/brianhie/geosketch
   license: MIT
-  summary: Geometry-preserving random sampling
+  license_family: MIT
+  summary: "Geometry-preserving random sampling."
 
 extra:
   identifiers:
diff --git a/recipes/get_homologues/meta.yaml b/recipes/get_homologues/meta.yaml
index 0528198c7538b..e6dd0fb579d0f 100644
--- a/recipes/get_homologues/meta.yaml
+++ b/recipes/get_homologues/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "3.7.1" %}
-{% set sha256 = "eeb9361695cafc35a1b92b29b647874713f85641218b1de5cddca551d334fe9d" %}
+{% set version = "3.7.2" %}
+{% set sha256 = "01333d82d29047e2dee0f2e4ccc43303ab23831852e9000aee42ffdf3d33b85c" %}
 
 package:
   name: get_homologues
diff --git a/recipes/gfainject/meta.yaml b/recipes/gfainject/meta.yaml
index f3d9aa1891954..22b1d7c8084b7 100644
--- a/recipes/gfainject/meta.yaml
+++ b/recipes/gfainject/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gfainject" %}
-{% set version = "0.1.0" %}
+{% set version = "0.1.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/AndreaGuarracino/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: a4388e524d5942f53d2fa94a93b2e82c926506c27cfdf04c04fbe8669a7ecebf 
+  sha256: a11f41ee94614d8c089454fdb3d0fb96e2f305db46895e2f64d974fa1707e739 
 
 build:
   number: 0
@@ -17,6 +17,11 @@ build:
 requirements:
   build:
     - {{ compiler('rust') }}
+    - cmake
+    - make
+    - pkg-config
+    - {{ compiler('c') }}      # For zlib-ng compilation
+    - {{ compiler('cxx') }}    # For C++ dependencies if any
 
 test:
   commands:
diff --git a/recipes/gfastats/meta.yaml b/recipes/gfastats/meta.yaml
index a08adf7d76b65..606f01e6dd06c 100644
--- a/recipes/gfastats/meta.yaml
+++ b/recipes/gfastats/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gfastats" %}
-{% set version = "1.3.8" %}
+{% set version = "1.3.9" %}
 
 package:
   name: {{ name }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/vgl-hub/gfastats/releases/download/v{{version}}/gfastats.v{{version}}-with_submodules.zip 
-  sha256: e8e2eeef3156628606507d6d50a2be8f546bd1a4734d63ac87c61f84d6834481
+  sha256: d98a14559ad3440ead7e6b04302ecaf1c44cffff40d64725d653b7e885a56a98
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('gfastats', max_pin="x") }}
 
@@ -43,4 +43,4 @@ extra:
     extended-base: true
   skip-lints:
     - uses_vcs_url
-    - missing_hash
\ No newline at end of file
+    - missing_hash
diff --git a/recipes/gfftk/meta.yaml b/recipes/gfftk/meta.yaml
index 60caeb4b3da4a..279ee2df820f0 100644
--- a/recipes/gfftk/meta.yaml
+++ b/recipes/gfftk/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gfftk" %}
-{% set version = "24.2.4" %}
+{% set version = "24.10.30" %}
 
 package:
   name: {{ name|lower }}
@@ -7,14 +7,14 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/gfftk-{{ version }}.tar.gz
-  sha256: 053a95204cfcb24b47e0dc23e5983b57cdc0023a37763a4c80a83d7d92598056
+  sha256: de3ad03d996cf47a910c763e950b7f0889e5b7c483196763d92840fb127b625e
 
 build:
   number: 0
   noarch: python
   entry_points:
     - gfftk = gfftk.__main__:main
-  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   run_exports:
     - {{ pin_subpackage('gfftk', max_pin="x") }}
 
@@ -22,11 +22,14 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - hatchling
   run:
     - python >=3.6
     - natsort
     - numpy
     - table2asn
+    - requests
+    - gb-io >=0.3.2
 
 test:
   imports:
@@ -40,6 +43,7 @@ about:
   license: BSD-2-Clause
   license_family: BSD
   license_file: LICENSE.md
+  dev_url: https://github.com/nextgenusfs/gfftk
 
 extra:
   recipe-maintainers:
diff --git a/recipes/ggcat/build.sh b/recipes/ggcat/build.sh
new file mode 100755
index 0000000000000..0d59a525b3cea
--- /dev/null
+++ b/recipes/ggcat/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash -ex
+
+cargo install --no-track --verbose --root "${PREFIX}" --path crates/cmdline/ --locked
diff --git a/recipes/ggcat/meta.yaml b/recipes/ggcat/meta.yaml
new file mode 100644
index 0000000000000..6410e45bb271f
--- /dev/null
+++ b/recipes/ggcat/meta.yaml
@@ -0,0 +1,44 @@
+{% set name = "ggcat" %}
+{% set version = "1.1.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('ggcat', max_pin="x.x") }}
+
+source:
+  url: https://github.com/algbio/ggcat/archive/v1.1.0.zip
+  sha256: 028021bc47ae58fb0e39ca29b79e0f318f5dc1f8e7d6649f9a446574bff3d0fc
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - {{ compiler('c') }}
+  host:
+    - zlib
+
+test:
+  commands:
+    - ggcat --help
+
+about:
+  home: "https://github.com/algbio/ggcat"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: |
+    Compacted and colored de Bruijn graph construction and querying.
+  dev_url: "https://github.com/algbio/ggcat"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - guilucand
+  identifiers:
+    - doi:10.1101/gr.277615.122
diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml
index 73317212bce16..833d27cffca25 100644
--- a/recipes/gmap/meta.yaml
+++ b/recipes/gmap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "GMAP" %}
-{% set version = "2024.10.10" %}
-{% set sha256 = "634952166008886f6f61bccbd32fd1a258a687aa2d5c65f0bbf58a41d34cb6f6" %}
+{% set version = "2024.10.20" %}
+{% set sha256 = "0983bc956c094af01b3733f02eb8d30849fd9171b68114e9cd3b8e20e0df17fe" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml
index 82ec7ca69faca..3df5f937b3bf1 100644
--- a/recipes/gnparser/meta.yaml
+++ b/recipes/gnparser/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.10.3" %}
-{% set sha256 = "899661ab88b716b7c1e3c4430bfb388997e510b28961e0246c361407f34cf0d2" %}
+{% set version = "1.11.1" %}
+{% set sha256 = "e7a389d1d3d617a94fe10dc6d7c1442758a9506861323b29b8a1fba39938b7ab" %}
 
 package:
   name: "gnparser"
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('gnparser', max_pin="x") }}
 
diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml
index f9a23e06eccd6..8f9f9d54b4ba4 100644
--- a/recipes/goldrush/meta.yaml
+++ b/recipes/goldrush/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "goldrush" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,11 +7,11 @@ package:
 
 source:
   url: https://github.com/bcgsc/goldrush/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz
-  sha256: 3f70860ed92b9313dbab16efed65ea7bc6080d78b4e18afc8cb910e086a7f0f7
+  sha256: 0b8b91b0477510d341af1736539416f30f70f67af9bd84161ea51c4c4a0fcc39
 
 build:
   skip: true  # [py < 38 or win or py > 39]
-  number: 0
+  number: 2
   run_exports: {{ pin_subpackage("goldrush", max_pin="x") }}
 
 requirements:
@@ -37,10 +37,11 @@ requirements:
     - ntlink >=1.3.0
     - btllib >=1.6.2
     - tigmint >=1.2.6
-    - minimap2
+    - minimap2 >=2.17
     - gperftools
     - bc
     - snakemake
+    - numpy >=1.22.4
 
 test:
   commands:
diff --git a/recipes/gottcha2/meta.yaml b/recipes/gottcha2/meta.yaml
index 50a0db70f10d7..29e33a06cc724 100644
--- a/recipes/gottcha2/meta.yaml
+++ b/recipes/gottcha2/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "GOTTCHA2" %}
-{% set version = "2.1.8.6" %}
+{% set version = "2.1.8.7" %}
 
 package:
   name: {{ name|lower }}
@@ -8,7 +8,7 @@ package:
 build:
   noarch: python
   number: 0
-  script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation .
+  script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation --no-cache-dir .
   entry_points:
     - gottcha2 = cmd:gottcha2_command
   run_exports:
@@ -16,12 +16,13 @@ build:
 
 source:
   url: https://github.com/poeli/GOTTCHA2/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 18ae74fa448e837ade605676334c5c37cda07473a6cf0105937d8afe1b017359
+  sha256: 52426b49dff96d5c17ac3f9e496df01846c519a41de0d0f2071a16a486ceefdf
 
 requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - minimap2 >=2.17
diff --git a/recipes/gretl/build.sh b/recipes/gretl/build.sh
new file mode 100644
index 0000000000000..3f9a7281b5eef
--- /dev/null
+++ b/recipes/gretl/build.sh
@@ -0,0 +1,12 @@
+#!/bin/bash -euo
+
+mkdir -p $PREFIX/bin
+
+RUST_BACKTRACE=1 cargo install --no-track --verbose --root "${PREFIX}" --path .
+
+SCRIPTS="block.py core.py multi.auto.py multi.correlate.py multi.heatmap.py multi.histogram.py multi.scatter.py nwindow.py path.py ps.py saturation_plotter.py stats_path.py window.py"
+
+for SCRIPT in ${SCRIPTS} ; do
+    cp scripts/${SCRIPT} ${PREFIX}/bin/${SCRIPT}
+    chmod +x ${PREFIX}/bin/${SCRIPT}
+done
diff --git a/recipes/gretl/meta.yaml b/recipes/gretl/meta.yaml
new file mode 100644
index 0000000000000..d0622bac5a177
--- /dev/null
+++ b/recipes/gretl/meta.yaml
@@ -0,0 +1,35 @@
+{% set version = '0.1.0' %}
+
+package:
+  name: gretl
+  version: {{ version }}
+
+source:
+  url: https://github.com/moinsebi/gretl/archive/8f48a287f7d6fe0a4b44e9318942684a71f8506d.tar.gz
+  sha256: 49e1b48235273629439e4d30848435b84b41976b6e062fc922c9f9236dd57f38
+
+build:
+  number: 0
+  run_exports: '{{ pin_subpackage("gretl", max_pin="x") }}'
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('rust') }}
+    - cmake
+    - make
+  run:
+    - python =3.10
+    - matplotlib-base >=3.9
+    - numpy >=2.1.3
+    - pandas >=2.1.3
+    - seaborn-base >=0.13.2
+test:
+  commands:
+    - gretl --help
+about:
+  home: https://github.com/moinsebi/gretl
+  dev_url: https://github.com/moinsebi/gretl
+  license: MIT
+  summary: gretl is a tool to compute a range of statistics on variation graphs in gfa format.
+  license_family: MIT
diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml
index 57e181ec0d301..666784f6c44ed 100644
--- a/recipes/gseapy/meta.yaml
+++ b/recipes/gseapy/meta.yaml
@@ -1,10 +1,10 @@
 package:
   name: gseapy
-  version: "1.1.3"
+  version: "1.1.4"
 
 source:
-  url: https://files.pythonhosted.org/packages/28/c2/7c03f74682de640b71ba9a9958c5c8a90867b0f4f9ffef2c15702113d47a/gseapy-1.1.3.tar.gz
-  sha256: 7f9218bb4014a862680d4d3e806e59bec8f81601e876a04495922da81da1b395
+  url: https://files.pythonhosted.org/packages/12/92/0a4e24f4a0ac772e8ec652f299a89292eb66d67e329579e1ea48cc006250/gseapy-1.1.4.tar.gz
+  sha256: 7e858752d7684b1abed124c585f3ca2f156ff22985575234232a54c57b88ba66
 
 build:
   entry_points:
@@ -12,7 +12,7 @@ build:
   run_exports:
     - {{ pin_subpackage("gseapy", max_pin="x") }}
   skip: True  # [py2k or py == 36 ]
-  number: 1
+  number: 0
 
 requirements:
   build: 
diff --git a/recipes/gsmap/meta.yaml b/recipes/gsmap/meta.yaml
index 6e49d56bd3d26..97fc02a0dd18f 100644
--- a/recipes/gsmap/meta.yaml
+++ b/recipes/gsmap/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gsmap" %}
-{% set version = "1.70" %}
+{% set version = "1.71.2" %}
 
 package:
   name: {{ name }}
@@ -7,12 +7,12 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/gsMap/{{ name }}-{{ version }}.tar.gz"
-  sha256: 54a8373c79c1ffe71e0b4c1e2cf33aed1a61b742e23efa05b00b8466b3ec3da9
+  sha256: d058fb9c1e346b40cf3e6a1cf27fc6458acf3cdb29eb7d4dd74cb119ab0f88a9
 
 build:
   noarch: python
   number: 0
-  script: {{ PYTHON }} -m pip install . --no-deps -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -20,8 +20,7 @@ requirements:
   host:
     - python >=3.8
     - pip
-    - flit >=3.2,<4
-
+    - flit-core >=3.2,<4
   run:
     - python >=3.8
     - numpy
@@ -29,7 +28,7 @@ requirements:
     - scipy
     - scikit-learn
     - matplotlib-base
-    - seaborn
+    - seaborn-base
     - tqdm
     - progress
     - pyyaml
@@ -51,6 +50,7 @@ test:
 about:
   home: https://github.com/LeonSong1995/gsMap
   license: MIT
+  license_family: MIT
   license_file: LICENSE
   summary: "gsMap (genetically informed spatial mapping of cells for complex traits)"
   description: |
diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml
index 1a94e22d51527..1a4a923150f61 100644
--- a/recipes/gtotree/meta.yaml
+++ b/recipes/gtotree/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 81e5856fa188a5096725605a31a1bf6bf4f8baa1dc2acc83eda29a0ff7a742b5
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_compatible(name, max_pin='x') }}
 
@@ -21,7 +21,7 @@ requirements:
     - python
     - biopython
     - hmmer
-    - muscle =5
+    - muscle =5.1
     - trimal
     - fasttree
     - iqtree >=2.2.2
@@ -38,6 +38,7 @@ requirements:
     - file
     - coreutils =9.1
     - curl
+    - pyarrow
 
 test:
   commands:
diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml
index 2166a683609f3..a2454b35b7e55 100644
--- a/recipes/gubbins/meta.yaml
+++ b/recipes/gubbins/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gubbins" %}
-{% set version = "3.3.5" %}
-{% set sha256 = "4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774" %}
+{% set version = "3.4" %}
+{% set sha256 = "ff134b7c1d06eee548e94f417394fb67229caf1b0d35b097a71309017ac7a91d" %}
 
 package:
   name: {{ name|lower }}
@@ -29,6 +29,7 @@ requirements:
     - perl
     - zlib
     - python >=3.8,<3.10
+    - pip
     - scipy
     - setuptools
     - dendropy
diff --git a/recipes/gzrt/build.sh b/recipes/gzrt/build.sh
new file mode 100644
index 0000000000000..c912bc43c9d6e
--- /dev/null
+++ b/recipes/gzrt/build.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+# Exit on error
+set -e
+
+if [ -z "$PREFIX" ]; then
+    echo "PREFIX environment variable not set"
+    exit 1
+fi
+
+export CFLAGS="${CFLAGS:-} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS:-} -L${PREFIX}/lib"
+export CPATH="${PREFIX}/include"
+
+# If-body reserved to docker build
+if [ ! -f "$(command -v cc)" ]; then
+    # Ensure that the CC environment variable is set (for compiler)
+    if [ -z "$CC" ]; then
+        echo "CC environment variable not set, but it is required."
+        exit 1
+    fi
+
+    # Create a temporary directory
+    mkdir -p "$SRC_DIR/bin"
+
+    # Create a symlink named cc that points to $CC
+    CC_PATH="$(which "${CC}")"  
+    if [ ! -x "${CC_PATH}" ]; then  
+        echo "Could not find compiler at: ${CC_PATH}"  
+        exit 1  
+    fi  
+    ln -sf "${CC_PATH}" "${SRC_DIR}/bin/cc"
+
+    # Prepend the temporary directory to the PATH
+    export PATH="${SRC_DIR}/bin:${PATH}"
+fi
+
+if ! make; then
+    echo "Build failed"
+    exit 1
+fi
+
+if [ ! -f gzrecover ]; then
+    echo "Build did not produce gzrecover binary"
+    exit 1
+fi
+
+chmod 755 gzrecover
+
+if ! mkdir -p "$PREFIX/bin"; then
+    echo "Failed to create bin directory"
+    exit 1
+fi
+
+if ! cp gzrecover "$PREFIX/bin/"; then
+    echo "Failed to install gzrecover"
+    exit 1
+fi
diff --git a/recipes/gzrt/gpl-2.0.txt b/recipes/gzrt/gpl-2.0.txt
new file mode 100644
index 0000000000000..9efa6fbc96283
--- /dev/null
+++ b/recipes/gzrt/gpl-2.0.txt
@@ -0,0 +1,338 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
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+special exception, the source code distributed need not include
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+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Moe Ghoul>, 1 April 1989
+  Moe Ghoul, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
diff --git a/recipes/gzrt/meta.yaml b/recipes/gzrt/meta.yaml
new file mode 100644
index 0000000000000..703c3fd209dcb
--- /dev/null
+++ b/recipes/gzrt/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = "0.8" %}   # latest release on 2013-10-03
+{% set sha256 = "b0b7dc53dadd8309ad9f43d6d6be7ac502c68ef854f1f9a15bd7f543e4571fee" %}
+
+package:
+  name: gzrt
+  version: {{ version }}
+
+source:
+  url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('gzrt', max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("c") }}
+    - make
+    - zlib
+  host:
+    - zlib
+
+test:
+  commands:
+    - gzrecover -h
+    # Create and test with a corrupted gzip file
+    - echo "test" | gzip > test.gz
+    - dd if=/dev/zero of=test.gz bs=1 count=1 seek=5 conv=notrunc
+    - gzrecover test.gz || [[ $? -eq 1 ]]
+
+about:
+  home: https://www.urbanophile.com/arenn/hacking/gzrt
+  summary: "Unofficial build of the gzip Recovery Toolkit aka gzrecover"
+  license: GPL-2.0-only
+  license_family: GPL
+  license_file: gpl-2.0.txt
+  description: |
+    gzrecover is a program that will attempt to extract any readable data
+    out of a gzip file that has been corrupted.
+  dev_url: https://github.com/arenn/gzrt
+
+extra:
+  recipe-maintainers:
+    - mazzalab
diff --git a/recipes/halfdeep/build.sh b/recipes/halfdeep/build.sh
new file mode 100644
index 0000000000000..69df8bfa05cbd
--- /dev/null
+++ b/recipes/halfdeep/build.sh
@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+set -o xtrace
+
+mkdir -vp "${PREFIX}/bin"
+
+# Define installation manifest
+declare -A files=(
+    ["bam_depth.sh"]="0755"
+    ["halfdeep.sh"]="0755"
+    ["halfdeep.r"]="0755"
+    ["scaffold_lengths.py"]="0755"
+)
+
+# Install files
+for file in "${!files[@]}"; do
+    if [[ ! -f "$SRC_DIR/$file" ]]; then
+        echo "Source file $file not found in $SRC_DIR" >&2
+        exit 1
+    fi
+
+    if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then
+        echo "Failed to install $file" >&2
+        exit 1
+    fi
+done
diff --git a/recipes/halfdeep/meta.yaml b/recipes/halfdeep/meta.yaml
new file mode 100644
index 0000000000000..7cc7471ed8165
--- /dev/null
+++ b/recipes/halfdeep/meta.yaml
@@ -0,0 +1,41 @@
+{% set name = "HalfDeep" %}
+{% set version = "0.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/richard-burhans/{{ name }}/archive/refs/tags/{{ version }}.zip
+  sha256: 308341c567298703fb99d4ceac7b34f0718cf6a37b02fc166f68d661a7f44f27
+
+requirements:
+  run:
+    - bash
+    - coreutils
+    - gawk
+    - genodsp
+    - grep
+    - gzip
+    - minimap2
+    - python >={{ python_min | default("3.9") }}
+    - r-base >={{ r_base | default("4.3.*") }}
+    - samtools
+    - sed
+
+build:
+  number: 0
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x.x") }}
+
+test:
+  commands:
+    - ${PREFIX}/bin/genodsp --help
+
+about:
+  home: https://github.com/richard-burhans/{{ name }}
+  summary: Automated detection of intervals covered at half depth by sequenced reads.
+  license: BSD-3-Clause
+  license_file: LICENSE
+  license_url: https://github.com/richard-burhans/{{ name }}/blob/master/LICENSE
diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml
index 7dd9fe1ffeb0c..82f7f13f9ac2d 100644
--- a/recipes/harpy/meta.yaml
+++ b/recipes/harpy/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.9" %}
-{% set sha256 = "9b9b717eea2eff2d35b3096d5867f34813d1d7ca9d8946df10844c0635b98fd8" %}
+{% set version = "1.12" %}
+{% set sha256 = "e6b0ecdd862d154b8c5de6c1414a131e0b5d2f8449edbe85425f9bc9534525db" %}
 
 package:
   name: harpy
@@ -10,7 +10,7 @@ source:
   sha256: '{{ sha256 }}'
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx or py < 39]
   script_env:
     - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
@@ -36,7 +36,6 @@ requirements:
     - apptainer
     - bcftools =1.20
     - conda >24.7
-    - pandas
     - pysam
     - python
     - rich-click
diff --git a/recipes/haystac/meta.yaml b/recipes/haystac/meta.yaml
index 3564d22685597..db609b34bfffc 100644
--- a/recipes/haystac/meta.yaml
+++ b/recipes/haystac/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "haystac" %}
-{% set version = "0.4.11" %}
+{% set version = "0.4.12" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 77727ce69b8df4211c43b424a292cd703987946e889a370337ce4afc7b6f0edd
+  sha256: 65f87603cb278f69003b8eea1f78d255d37b3c8dcb0f0c9ac71f8a85038c50e2
 
 build:
   number: 0
@@ -17,7 +17,7 @@ build:
   script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps"
   run_exports:
     - {{ pin_subpackage("haystac", max_pin="x.x") }}
-
+    
 requirements:
   host:
     - numpy
diff --git a/recipes/hicstuff/LICENSE b/recipes/hicstuff/LICENSE
deleted file mode 100644
index 61d18602bd64e..0000000000000
--- a/recipes/hicstuff/LICENSE
+++ /dev/null
@@ -1,674 +0,0 @@
-GNU GENERAL PUBLIC LICENSE
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-not convey it at all.  For example, if you agree to terms that obligate you
-to collect a royalty for further conveying from those to whom you convey
-the Program, the only way you could satisfy both those terms and this
-License would be to refrain entirely from conveying the Program.
-
-  13. Use with the GNU Affero General Public License.
-
-  Notwithstanding any other provision of this License, you have
-permission to link or combine any covered work with a work licensed
-under version 3 of the GNU Affero General Public License into a single
-combined work, and to convey the resulting work.  The terms of this
-License will continue to apply to the part which is the covered work,
-but the special requirements of the GNU Affero General Public License,
-section 13, concerning interaction through a network will apply to the
-combination as such.
-
-  14. Revised Versions of this License.
-
-  The Free Software Foundation may publish revised and/or new versions of
-the GNU General Public License from time to time.  Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
-  Each version is given a distinguishing version number.  If the
-Program specifies that a certain numbered version of the GNU General
-Public License "or any later version" applies to it, you have the
-option of following the terms and conditions either of that numbered
-version or of any later version published by the Free Software
-Foundation.  If the Program does not specify a version number of the
-GNU General Public License, you may choose any version ever published
-by the Free Software Foundation.
-
-  If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
-
-  Later license versions may give you additional or different
-permissions.  However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
-  15. Disclaimer of Warranty.
-
-  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-  16. Limitation of Liability.
-
-  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
-  17. Interpretation of Sections 15 and 16.
-
-  If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
-  If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
-    <program>  Copyright (C) <year>  <name of author>
-    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
-  You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<https://www.gnu.org/licenses/>.
-
-  The GNU General Public License does not permit incorporating your program
-into proprietary programs.  If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
\ No newline at end of file
diff --git a/recipes/hicstuff/meta.yaml b/recipes/hicstuff/meta.yaml
index dc6a57f61a040..840aceb2aa63c 100644
--- a/recipes/hicstuff/meta.yaml
+++ b/recipes/hicstuff/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.2.3" %}
+{% set version = "3.2.4" %}
 
 package:
   name: hicstuff
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/h/hicstuff/hicstuff-{{ version }}.tar.gz
-  sha256: 11a88844a5a75928c7e48b391829b7e0d73aae86cb7c116a0618560d2a16f283
+  sha256: 7d74bcbddaff40029a07ed18283701110b338617fbbda13b9b6ec6e3cc107d02
 
 build:
   number: 0
@@ -15,14 +15,15 @@ build:
     - hicstuff=hicstuff.main:main
   run_exports:
     - {{ pin_subpackage('hicstuff', max_pin='x') }}
-  script: {{ PYTHON }} -m pip install . --no-deps -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
 
 requirements:
   host:
-    - python >=3.7
+    - python >=3.6
     - pip
+    - setuptools
   run:
-    - python >=3.7
+    - python >=3.6
     - biopython
     - docopt
     - matplotlib-base
@@ -48,11 +49,11 @@ test:
 
 about:
   home: https://github.com/koszullab/hicstuff
-  license: GPL-3.0-only
-  license_family: GPL3
+  license: BSD-3-Clause
+  license_family: BSD
   license_file: LICENSE
   summary: "General purpose stuff to generate and handle Hi-C data in its simplest form."
-  doc_url: https://hicstuff.readthedocs.io/en/latest/
+  doc_url: https://hicstuff.readthedocs.io/en/latest
   dev_url: https://github.com/koszullab/hicstuff
 
 extra:
diff --git a/recipes/hictkpy/CMakeLists.txt.patch b/recipes/hictkpy/CMakeLists.txt.patch
deleted file mode 100644
index a5c3cb5839689..0000000000000
--- a/recipes/hictkpy/CMakeLists.txt.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 01a1413..b0dcdb4 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -17,6 +17,8 @@ set(CMAKE_C_STANDARD 11)
- # -std=gnu++20 for example when compiling with PCH enabled
- set(CMAKE_CXX_EXTENSIONS OFF)
- 
-+set(CMAKE_OSX_DEPLOYMENT_TARGET 10.15)
-+
- project(
-   hictkpy
-   LANGUAGES C CXX
diff --git a/recipes/hictkpy/build.sh b/recipes/hictkpy/build.sh
index a6d756aa71a09..d3d9558f2169c 100755
--- a/recipes/hictkpy/build.sh
+++ b/recipes/hictkpy/build.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
+CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
 
 scratch=$(mktemp -d)
 export CONAN_HOME="$scratch/conan"
@@ -8,33 +8,47 @@ export CONAN_HOME="$scratch/conan"
 # shellcheck disable=SC2064
 trap "rm -rf '$scratch'" EXIT
 
-declare -a CMAKE_PLATFORM_FLAGS
 if [[ ${HOST} =~ .*darwin.* ]]; then
-  export MACOSX_DEPLOYMENT_TARGET=10.15  # Required to use std::filesystem
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
+  if [[ "$OSX_ARCH" == 'x86_64' ]]; then
+    # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
+    CFLAGS+=' -D_LIBCPP_DISABLE_AVAILABILITY'
+    CXXFLAGS+=' -D_LIBCPP_DISABLE_AVAILABILITY'
+  fi
+  CMAKE_ARGS+=" -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT}"
   conan_profile='apple-clang'
 else
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
-  conan_profile='gcc'
+  # Workaround missing LLVMgold.so on Linux
+  CMAKE_ARGS+=' -DCMAKE_LINKER_TYPE=LLD'
+  CMAKE_ARGS+=" -DCMAKE_TOOLCHAIN_FILE=${RECIPE_DIR}/cross-linux.cmake"
+  conan_profile='clang'
 fi
 
 # Remember to update these profiles when bioconda's compiler toolchains are updated
 mkdir -p "$CONAN_HOME/profiles/"
 ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/default"
 
-# explicitly set CMAKE_OSX_DEPLOYMENT_TARGET
-patch CMakeLists.txt < "${RECIPE_DIR}/CMakeLists.txt.patch"
-
-# Remove unnecessary dependencies from conanfile.txt
-patch conanfile.txt < "${RECIPE_DIR}/conanfile.txt.patch"
+# Remove unnecessary dependencies from conanfile.py
+patch conanfile.py < "${RECIPE_DIR}/conanfile.py.patch"
 
 # Build hictkpy as a shared library
 patch pyproject.toml < "${RECIPE_DIR}/pyproject.toml.patch"
 
-CMAKE_ARGS+=" -DPython_EXECUTABLE=$PYTHON"
+# See https://github.com/conda-forge/conda-forge.github.io/pull/2321
+Python_INCLUDE_DIR="$("$PYTHON" -c 'import sysconfig; print(sysconfig.get_path("include"))')"
+Python_NumPy_INCLUDE_DIR="$("$PYTHON" -c 'import numpy; print(numpy.get_include())')"
+
+CMAKE_ARGS+=" -DPython_EXECUTABLE:PATH=${PYTHON}"
+CMAKE_ARGS+=" -DPython_INCLUDE_DIR:PATH=${Python_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython_NumPy_INCLUDE_DIR=${Python_NumPy_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython3_EXECUTABLE:PATH=${PYTHON}"
+CMAKE_ARGS+=" -DPython3_INCLUDE_DIR:PATH=${Python_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython3_NumPy_INCLUDE_DIR=${Python_NumPy_INCLUDE_DIR}"
+
+echo "CFLAGS='$CFLAGS'"
+echo "CXXFLAGS='$CXXFLAGS'"
+echo "CMAKE_ARGS='$CMAKE_ARGS'"
 
-echo "$CMAKE_ARGS"
-export CMAKE_ARGS
+export CMAKE_ARGS CMAKE_BUILD_PARALLEL_LEVEL CFLAGS CXXFLAGS
 
 SETUPTOOLS_SCM_PRETEND_VERSION="$PKG_VERSION" \
 "$PYTHON" -m pip install "$SRC_DIR" -vv
diff --git a/recipes/hictkpy/conan_profiles/gcc b/recipes/hictkpy/conan_profiles/clang
similarity index 73%
rename from recipes/hictkpy/conan_profiles/gcc
rename to recipes/hictkpy/conan_profiles/clang
index ef7e2f6219ff1..9ee58cee260e2 100644
--- a/recipes/hictkpy/conan_profiles/gcc
+++ b/recipes/hictkpy/conan_profiles/clang
@@ -1,8 +1,8 @@
 [settings]
 arch=x86_64
 build_type=Release
-compiler=gcc
+compiler=clang
 compiler.cppstd=17
 compiler.libcxx=libstdc++11
-compiler.version=13
+compiler.version=18
 os=Linux
diff --git a/recipes/hictkpy/conanfile.py.patch b/recipes/hictkpy/conanfile.py.patch
new file mode 100644
index 0000000000000..5aed5d1d3f6e0
--- /dev/null
+++ b/recipes/hictkpy/conanfile.py.patch
@@ -0,0 +1,90 @@
+diff --git a/conanfile.py b/conanfile.py
+index a7d5c74..c08b356 100644
+--- a/conanfile.py
++++ b/conanfile.py
+@@ -35,21 +35,11 @@ class HictkpyConan(ConanFile):
+         return 17
+ 
+     def requirements(self):
+-        self.requires("arrow/17.0.0#81be2aa6c49800df8cc163adf4b99e9f")
+-        self.requires("boost/1.86.0#cd839a2082585255010f9e82eea94c7f", force=True)
+         self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
+         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
+-        self.requires("eigen/3.4.0#2e192482a8acff96fe34766adca2b24c")
+-        self.requires("fast_float/6.1.5#e067b96a6271d1b4c255858ca9805bdd")
+-        self.requires("fmt/11.0.2#5c7438ef4d5d69ab106a41e460ce11f3", force=True)
+-        self.requires("hdf5/1.14.4.3#df1467d7374938c231edbe10e83f2bb4", force=True)
+-        self.requires("highfive/2.10.0#3d1bd25944a57fa1bc30a0a22923d528")
+-        self.requires("libdeflate/1.22#f95aebe763153ccbc4cc76c023e42e5a")
+         self.requires("parallel-hashmap/1.4.0#36ac84df77219748440cdb0f23624d56")
+         self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
+         self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
+-        self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03")
+-        self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b", force=True)
+ 
+     def validate(self):
+         if self.settings.get_safe("compiler.cppstd"):
+@@ -58,63 +48,3 @@ class HictkpyConan(ConanFile):
+     def configure(self):
+         if self.settings.compiler in ["clang", "gcc"]:
+             self.settings.compiler.libcxx = "libstdc++11"
+-
+-        self.options["arrow"].compute = True
+-        self.options["arrow"].parquet = False
+-        self.options["arrow"].with_boost = True
+-        self.options["arrow"].with_re2 = True
+-        self.options["arrow"].with_thrift = False
+-        self.options["boost"].system_no_deprecated = True
+-        self.options["boost"].asio_no_deprecated = True
+-        self.options["boost"].filesystem_no_deprecated = True
+-        self.options["boost"].filesystem_version = 4
+-        self.options["boost"].zlib = False
+-        self.options["boost"].bzip2 = False
+-        self.options["boost"].lzma = False
+-        self.options["boost"].zstd = False
+-        self.options["boost"].without_atomic = False
+-        self.options["boost"].without_charconv = True
+-        self.options["boost"].without_chrono = True
+-        self.options["boost"].without_cobalt = True
+-        self.options["boost"].without_container = True
+-        self.options["boost"].without_context = True
+-        self.options["boost"].without_contract = True
+-        self.options["boost"].without_coroutine = True
+-        self.options["boost"].without_date_time = True
+-        self.options["boost"].without_exception = True
+-        self.options["boost"].without_fiber = True
+-        self.options["boost"].without_filesystem = False
+-        self.options["boost"].without_graph = True
+-        self.options["boost"].without_graph_parallel = True
+-        self.options["boost"].without_iostreams = True
+-        self.options["boost"].without_json = True
+-        self.options["boost"].without_locale = True
+-        self.options["boost"].without_log = True
+-        self.options["boost"].without_math = True
+-        self.options["boost"].without_mpi = True
+-        self.options["boost"].without_nowide = True
+-        self.options["boost"].without_process = False
+-        self.options["boost"].without_program_options = True
+-        self.options["boost"].without_python = True
+-        self.options["boost"].without_random = True
+-        self.options["boost"].without_regex = True
+-        self.options["boost"].without_serialization = True
+-        self.options["boost"].without_stacktrace = True
+-        self.options["boost"].without_system = False
+-        self.options["boost"].without_test = True
+-        self.options["boost"].without_thread = True
+-        self.options["boost"].without_timer = True
+-        self.options["boost"].without_type_erasure = True
+-        self.options["boost"].without_url = True
+-        self.options["boost"].without_wave = True
+-        self.options["fmt"].header_only = True
+-        self.options["hdf5"].enable_cxx = False
+-        self.options["hdf5"].hl = False
+-        self.options["hdf5"].threadsafe = False
+-        self.options["hdf5"].parallel = False
+-        self.options["highfive"].with_boost = False
+-        self.options["highfive"].with_eigen = False
+-        self.options["highfive"].with_opencv = False
+-        self.options["highfive"].with_xtensor = False
+-        self.options["spdlog"].header_only = True
+-        self.options["zstd"].build_programs = False
diff --git a/recipes/hictkpy/conanfile.txt.patch b/recipes/hictkpy/conanfile.txt.patch
deleted file mode 100644
index 038babbd4c0df..0000000000000
--- a/recipes/hictkpy/conanfile.txt.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff --git a/conanfile.txt b/conanfile.txt
-index cffb547..66cf415 100644
---- a/conanfile.txt
-+++ b/conanfile.txt
-@@ -5,30 +5,12 @@
- [requires]
- bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c
- concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502
--fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e
--fmt/10.2.1#9199a7a0611866dea5c8849a77467b25
--hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1
--highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5
--libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602
- parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7
- readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83
- span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422
--spdlog/1.13.0#2775cc949e26b339029a852785b6b276
--zstd/1.5.6#67383dae85d33f43823e7751a6745ea1
- 
- [generators]
- CMakeDeps
- 
- [options]
--fmt*:header_only=True
--hdf5*:enable_cxx=False
--hdf5*:hl=False
--hdf5*:threadsafe=False
--hdf5*:parallel=False
--highfive*:with_boost=False
--highfive*:with_eigen=False
--highfive*:with_opencv=False
--highfive*:with_xtensor=False
--spdlog*:header_only=True
--zstd*:build_programs=False
- 
diff --git a/recipes/hictkpy/conda_build_config.yaml b/recipes/hictkpy/conda_build_config.yaml
new file mode 100644
index 0000000000000..3397464cf13fd
--- /dev/null
+++ b/recipes/hictkpy/conda_build_config.yaml
@@ -0,0 +1,8 @@
+c_compiler:             # [linux]
+  - clang               # [linux]
+c_compiler_version:     # [linux]
+  - 18                  # [linux]
+cxx_compiler:           # [linux]
+  - clangxx             # [linux]
+cxx_compiler_version:   # [linux]
+  - 18                  # [linux]
diff --git a/recipes/hictkpy/meta.yaml b/recipes/hictkpy/meta.yaml
index 084412b76ff50..6f9f527301f06 100644
--- a/recipes/hictkpy/meta.yaml
+++ b/recipes/hictkpy/meta.yaml
@@ -1,61 +1,68 @@
 {% set name = "hictkpy" %}
-{% set version = "0.0.5" %}
-{% set sha256 = "e9576a1a719ce378873da15b76e9f7e699748c0486901607e4d7e87c3f0c6556" %}
+{% set version = "1.0.0" %}
+{% set sha256 = "a12c05cba9395ce39eb742b5d1e1a6e0cc0179a5b6981ae8a828ff9aee2c64ce" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: True  # [py < 39]
   run_exports:
-    - {{ pin_subpackage('hictkpy', max_pin='x.x') }}
+    - {{ pin_subpackage('hictkpy', max_pin='x') }}
 
 source:
-  url: https://github.com/paulsengroup/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  url: https://pypi.python.org/packages/source/h/{{ name }}/{{ name }}-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - cmake >=3.25
+    - cmake >=3.29
     - conan >=2
     - make
-    - fast_float >=5
-    - fmt >=10
-    - highfive >=2.7
-    - spdlog >=1.12
+    - eigen >=3.4
+    - fast_float >=6
+    - fmt >=11
+    - highfive >=2.9
+    - spdlog >=1.14
+
   host:
     - python
     - pip
     - hdf5 >=1.12
-    - libdeflate
-    - scikit-build-core
+    - libarrow >=16
+    - libdeflate >=1
+    - lld  # [linux]
+    - nanobind >=2
+    - numpy
+    - scikit-build-core >=0.10
     - setuptools_scm
     - zstd >=1.5
 
   run:
     - python
-    - hdf5 >=1.12
-    - libdeflate
-    - numpy
-    - pandas
-    - scipy
-    - zstd >=1.5
+    - {{ pin_compatible('hdf5', min_pin='1.12') }}
+    - {{ pin_compatible('libdeflate', min_pin='1') }}
+    - {{ pin_compatible('numpy') }}
+    - {{ pin_compatible('pandas', min_pin='2.1') }}
+    - {{ pin_compatible('pyarrow', min_pin='16') }}
+    - {{ pin_compatible('scipy') }}
+    - {{ pin_compatible('zstd', min_pin='1.5') }}
 
 about:
   home: https://github.com/paulsengroup/{{ name }}
   license: MIT
   license_file: LICENSE
-  summary: Python bindings for hictk
+  summary: "Python bindings for hictk: read and write .cool and .hic files directly from Python"
   dev_url: https://github.com/paulsengroup/{{ name }}
-  doc_url: https://github.com/paulsengroup/{{ name }}#readme
+  doc_url: https://{{ name }}.readthedocs.io/en/stable/
 
 test:
    requires:
-     - pytest>=6
+     - pytest>=8
    source_files:
      - test/*
    imports:
diff --git a/recipes/hictkpy/pyproject.toml.patch b/recipes/hictkpy/pyproject.toml.patch
index 6763068194b11..afa8522558a7f 100644
--- a/recipes/hictkpy/pyproject.toml.patch
+++ b/recipes/hictkpy/pyproject.toml.patch
@@ -1,13 +1,13 @@
 diff --git a/pyproject.toml b/pyproject.toml
-index 1a03623..36102d0 100644
+index 5ded5b9..fe8d305 100644
 --- a/pyproject.toml
 +++ b/pyproject.toml
-@@ -49,7 +49,7 @@ HICTK_BUILD_EXAMPLES = "OFF"
- HICTK_BUILD_BENCHMARKS = "OFF"
- HICTK_BUILD_TOOLS = "OFF"
- HICTK_ENABLE_GIT_VERSION_TRACKING = "OFF"
+@@ -74,7 +74,7 @@ wheel.expand-macos-universal-tags = true
+ cmake.build-type = "Release"
+ 
+ [tool.scikit-build.cmake.define]
 -BUILD_SHARED_LIBS = "OFF"
 +BUILD_SHARED_LIBS = "ON"
- CONAN_INSTALL_ARGS = "--settings=compiler.cppstd=17;--build=missing;--update;--options=*/*:shared=False"
- 
- [tool.setuptools_scm]
+ CMAKE_OSX_DEPLOYMENT_TARGET = "10.15"
+ CMAKE_PROJECT_TOP_LEVEL_INCLUDES = { env="HICTKPY_PROJECT_TOP_LEVEL_INCLUDES", default="cmake/conan_provider.cmake" }
+ CONAN_INSTALL_ARGS = { env="HICTKPY_CONAN_INSTALL_ARGS", default="--settings=compiler.cppstd=17;--settings=build_type=Release;--build=missing;--update;--options=*/*:shared=False" }
diff --git a/recipes/hictkpy/run_test.sh b/recipes/hictkpy/run_test.sh
index a6729f994b26e..57e137c421dc2 100644
--- a/recipes/hictkpy/run_test.sh
+++ b/recipes/hictkpy/run_test.sh
@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 
 "$PYTHON" -c 'import hictkpy; print(hictkpy.__version__)'
-"$PYTHON" -m pytest test
+"$PYTHON" -m pytest test -v
diff --git a/recipes/hisat2-pipeline/meta.yaml b/recipes/hisat2-pipeline/meta.yaml
index dfa4a265057f7..722eaa158bc83 100644
--- a/recipes/hisat2-pipeline/meta.yaml
+++ b/recipes/hisat2-pipeline/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "hisat2-pipeline" %}
-{% set version = "1.0.7" %}
-{% set sha256 = "4c21e62b8cf1e326b398eafb78e09d2b90843c852198bedb164ac5f1cfc7d33f" %}
+{% set version = "1.0.8" %}
+{% set sha256 = "0dfab47f5d95d448250fb9f0b973ee69b6d47b7baa41623141a6a0e11e18adc7" %}
 {% set DOI = "https://doi.org/10.5281/zenodo.10389729" %}
 
 package:
@@ -10,10 +10,9 @@ package:
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   run_exports:
-  - {{ pin_subpackage('hisat2-pipeline', max_pin="x.x") }}
-  
+  - {{ pin_subpackage('hisat2-pipeline', max_pin="x") }}
 
 source:
   url: https://github.com/mcamagna/HISAT2-pipeline/archive/refs/tags/v{{ version }}-bioconda.tar.gz
@@ -23,6 +22,7 @@ requirements:
   host:
   - python >=3
   - pip
+  - setuptools
   run:
   - python >=3
   - hisat2
@@ -49,8 +49,9 @@ about:
   license: GPL-3.0-or-later
   license_family: GPL
   license_file: LICENSE
-  summary: 'A pipeline to automatically run an RNA-seq analysis using HISAT2/Stringtie using default settings'
-  
+  summary: 'A pipeline to automatically run an RNA-seq analysis using HISAT2/Stringtie using default settings.'
+  dev_url: https://github.com/mcamagna/HISAT2-pipeline
+
 extra:
   identifiers:
   - {{ DOI }}
diff --git a/recipes/hlafreq/meta.yaml b/recipes/hlafreq/meta.yaml
index 3dfbdc5e02169..451c90a13fdcf 100644
--- a/recipes/hlafreq/meta.yaml
+++ b/recipes/hlafreq/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "HLAfreq" %}
-{% set version = "0.0.4" %}
+{% set version = "0.0.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,12 +7,12 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0]|lower }}/{{ name|lower }}/{{ name|lower }}-{{ version }}.tar.gz"
-  sha256: 58aa7aaa1d554a3264531f6aaa3bd0a5a29c13b58441dc6564537adf4d096051
+  sha256: 297ae735de85dfdc9f60f94f3fef92d4a1f055b455b282b7171e10d3de358b96
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage('hlafreq', max_pin="x.x") }}
 
@@ -20,6 +20,7 @@ requirements:
   host:
     - python >=3.10
     - pip
+    - setuptools
   run:
     - bs4
     - matplotlib-base >=3.6.0
@@ -41,7 +42,8 @@ about:
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: "Download and combine HLA frequency data from multiple studies"
+  summary: "Download and combine HLA frequency data from multiple studies."
+  dev_url: "https://github.com/Vaccitech/HLAfreq"
 
 extra:
   recipe-maintainers:
diff --git a/recipes/hmftools-chord/build.sh b/recipes/hmftools-chord/build.sh
index a1a96f8a03b8b..4138fe335551c 100644
--- a/recipes/hmftools-chord/build.sh
+++ b/recipes/hmftools-chord/build.sh
@@ -5,9 +5,8 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
 [ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin"
 
 cd "${SRC_DIR}"
-mv jar/chord*.jar $TGT/chord.jar
-${R} CMD INSTALL --build src/chord/src/main/R/mutSigExtractor
-${R} CMD INSTALL --build src/chord/src/main/R/CHORD
+mv chord*.jar $TGT/chord.jar
 
 cp $RECIPE_DIR/chord.sh $TGT/chord
 ln -s $TGT/chord ${PREFIX}/bin/
+chmod 0755 "${PREFIX}/bin/chord"
\ No newline at end of file
diff --git a/recipes/hmftools-chord/meta.yaml b/recipes/hmftools-chord/meta.yaml
index cb5e88a813be6..c529dd49582ae 100644
--- a/recipes/hmftools-chord/meta.yaml
+++ b/recipes/hmftools-chord/meta.yaml
@@ -1,51 +1,33 @@
 {% set version = "2.1.0_beta" %}
-{% set sha256_jar = "26d0a40e20635c4b797d28e0c7819b1653c9f8fa28180b9a556215d22387968c" %}
-{% set sha256_src = "ed039e7b405130a1e52df71c3535c6a5ed8aab0f80724bc83df88ae14aeaa257" %}
+{% set beta_suffix = ".2" %}
+{% set sha256 = "847e0239b7440b70d67957d38afb3ab42bd3acecb931afc49ab8aef4c248a1da" %}
 
 package:
   name: hmftools-chord
   version: '{{ version }}'
 
 source:
-  - folder: jar
-    url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord-{{ version }}.jar
-    sha256: '{{ sha256_jar }}'
-  - folder: src
-    url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/chord-v{{ version }}.tar.gz
-    sha256: '{{ sha256_src }}'
+  url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord_v{{ version }}{{ beta_suffix }}.jar
+  sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 3
   run_exports:
     - {{ pin_subpackage("hmftools-chord", max_pin="x.x") }}
 
 requirements:
-  host:
-    - r-base
-    - r-randomforest
-    - r-stringr
-    - bioconductor-bsgenome
-    - bioconductor-bsgenome.hsapiens.ucsc.hg19
-    - bioconductor-bsgenome.hsapiens.ucsc.hg38
   run:
     - openjdk >=8
     - r-base
     - r-randomforest
-    - r-stringr
-    - bioconductor-bsgenome
-    - bioconductor-bsgenome.hsapiens.ucsc.hg19
-    - bioconductor-bsgenome.hsapiens.ucsc.hg38
 
 test:
   commands:
-    - $R -e "library('CHORD')"
-    - $R -e "library('mutSigExtractor')"
-    - 'chord com.hartwig.hmftools.chord.ChordRunner -version | grep CHORD'
+    - 'chord -version | grep CHORD'
 
 about:
   home: https://github.com/hartwigmedical/hmftools/blob/master/chord/
   license: GPL-3.0-only
   license_family: GPL3
-  license_file: LICENSE
   summary: Predict HRD using somatic mutations contexts
diff --git a/recipes/hmftools-cuppa/build.sh b/recipes/hmftools-cuppa/build.sh
index 0cd12bf1a92f0..b2466610649c4 100644
--- a/recipes/hmftools-cuppa/build.sh
+++ b/recipes/hmftools-cuppa/build.sh
@@ -1,12 +1,17 @@
 #!/bin/bash
 
 TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
-[ -d "$TGT" ] || mkdir -p $TGT/{,chart/}
+[ -d "$TGT" ] || mkdir -p $TGT
 [ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin"
 
 cd "${SRC_DIR}"
-mv jar/cuppa*.jar $TGT/cuppa.jar
-${PYTHON} -m pip install --no-build-isolation --no-deps --no-cache-dir -vvv src/cuppa/src/main/python/pycuppa/
+mv cuppa*.jar $TGT/cuppa.jar
 
 cp $RECIPE_DIR/cuppa.sh $TGT/cuppa
 ln -s $TGT/cuppa ${PREFIX}/bin/
+chmod 0755 "${PREFIX}/bin/cuppa"
+
+mkdir -p /tmp/cuppa_jar/
+unzip -n $TGT/cuppa.jar -d /tmp/cuppa_jar/
+${PYTHON} -m pip install --no-build-isolation --no-deps --no-cache-dir -vvv /tmp/cuppa_jar/pycuppa/
+rm -r /tmp/cuppa_jar/
diff --git a/recipes/hmftools-cuppa/meta.yaml b/recipes/hmftools-cuppa/meta.yaml
index 840622e449152..bb1424cfae91d 100644
--- a/recipes/hmftools-cuppa/meta.yaml
+++ b/recipes/hmftools-cuppa/meta.yaml
@@ -1,22 +1,18 @@
 {% set version = "2.3.0_beta" %}
-{% set sha256_jar = "69f94a54f232a2a22927dce165120d1f166d4931bfb8f299515edaa577607c7c" %}
-{% set sha256_src = "65a2070e78243fed975b8738d2ce79dfead1a5702c2bc91e26488c806e25d158" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "ae3a3d9bc31e45cba52943df01b6f8f190beff904dff392e6413c1396d7db36d" %}
 
 package:
   name: hmftools-cuppa
   version: '{{ version }}'
 
 source:
-  - folder: jar
-    url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa-{{ version|replace(".0", "") }}.jar
-    sha256: '{{ sha256_jar }}'
-  - folder: src
-    url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/cuppa-v{{ version }}.tar.gz
-    sha256: '{{ sha256_src }}'
+  url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa_v{{ version|replace(".0", "") }}{{ beta_suffix }}.jar
+  sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("hmftools-cuppa", max_pin="x.x") }}
 
@@ -24,6 +20,7 @@ requirements:
   host:
     - python ==3.11
     - r-base >=4.2,<4.3.0a0
+    - unzip
   run:
     - openjdk >=8
     - python ==3.11
diff --git a/recipes/hmftools-esvee/meta.yaml b/recipes/hmftools-esvee/meta.yaml
index 9a11455bde79d..2707038fefc1e 100644
--- a/recipes/hmftools-esvee/meta.yaml
+++ b/recipes/hmftools-esvee/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "1.0_beta" %}
-{% set beta_suffix = ".2" %}
-{% set sha256 = "75933500cde12741534580d84bdafc6ad7b3290f382973dbcf540580b9453bd9" %}
+{% set beta_suffix = ".4" %}
+{% set sha256 = "9a833992f4b8c5c01d845ed60c96fc93c43c5955171658255c545413cedb23d5" %}
 
 package:
   name: hmftools-esvee
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 2
+  number: 5
   run_exports:
     - {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }}
 
diff --git a/recipes/hmftools-linx/meta.yaml b/recipes/hmftools-linx/meta.yaml
index 300175a2287dd..aaaa83c83890c 100644
--- a/recipes/hmftools-linx/meta.yaml
+++ b/recipes/hmftools-linx/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "2.0_beta" %}
-{% set beta_suffix = ".1" %}
-{% set sha256 = "34bb84e9563d3847544f5e457211ff9a74473131e5a609ebae960a7a3cfcf8d9" %}
+{% set beta_suffix = ".3" %}
+{% set sha256 = "a23e690b6da95226f20d90a3aade31caaee2e08996d6b05f9c1eaae869d33ba1" %}
 
 package:
   name: hmftools-linx
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('hmftools-linx', max_pin="x") }}
 
diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml
index 6db3361d5da0b..e78d3011cc1ce 100644
--- a/recipes/hmftools-orange/meta.yaml
+++ b/recipes/hmftools-orange/meta.yaml
@@ -1,17 +1,18 @@
 {% set version = "3.7.1_beta" %}
-{% set sha256 = "1592dacf6a75c7d82fbb865b85e17cbb5b04d1acda8cdf5fb61c4a5cf9868929" %}
+{% set beta_suffix = ".3" %}
+{% set sha256 = "b729b440aa0361f52e31b446234b98234cde768ec75e97044dca952909e120c1" %}
 
 package:
   name: hmftools-orange
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/orange-v{{ version }}/orange_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/orange-v{{ version }}/orange_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 2
   run_exports:
     - {{ pin_subpackage('hmftools-orange', max_pin="x") }}
 
diff --git a/recipes/hmftools-pave/meta.yaml b/recipes/hmftools-pave/meta.yaml
index 8d3d58bc78dd7..f75fa9630ac7b 100644
--- a/recipes/hmftools-pave/meta.yaml
+++ b/recipes/hmftools-pave/meta.yaml
@@ -1,17 +1,18 @@
 {% set version = "1.7_beta" %}
-{% set sha256 = "b6e67aa0bb96db3b50429afe4a6c6fad168660bf220f61b638e06b0c643969ab" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "adfc0bbbf3a8b35faa7a5ce2d1fb0a5c016ae71fcd80cfa2dd28caa4e1b5826a" %}
 
 package:
   name: hmftools-pave
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('hmftools-pave', max_pin="x.x") }}
 
diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml
index d979ebdf55c18..e112c5fe0bdfe 100644
--- a/recipes/hmftools-purple/meta.yaml
+++ b/recipes/hmftools-purple/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "4.1_beta" %}
-{% set beta_suffix = ".1" %}
-{% set sha256 = "aa5b1ec3c0e67027750fce6ac71bc31d55c37405c8e00571594d58c837e74a51" %}
+{% set beta_suffix = ".5" %}
+{% set sha256 = "92c97c12db08383187ed467d2574540672e36df7b5594c202777e1b3f05e8868" %}
 
 package:
   name: hmftools-purple
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 2
   run_exports:
     - {{ pin_subpackage('hmftools-purple', max_pin="x") }}
 
diff --git a/recipes/hmftools-redux/meta.yaml b/recipes/hmftools-redux/meta.yaml
index 7abd6496a2637..8d940a51d025b 100644
--- a/recipes/hmftools-redux/meta.yaml
+++ b/recipes/hmftools-redux/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "1.0_beta" %}
-{% set beta_suffix = ".1" %}
-{% set sha256 = "0789230f3f7c8fe65c26709fbe4bc95a70e8b7465526dac8c1613d632c43a1e8" %}
+{% set beta_suffix = ".4" %}
+{% set sha256 = "e3398c8fba7f9e572ac06def6d957ceed1598f0c6b9b06563814ccfec5c3158f" %}
 
 package:
   name: hmftools-redux
@@ -12,13 +12,13 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 6
   run_exports:
     - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}
 
 requirements:
   run:
-    - openjdk >=8
+    - openjdk >=8,<=21
     - sambamba >=1.0.1
 
 test:
diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml
index 14d85d65a3c30..13d88d9de1259 100644
--- a/recipes/hmftools-sage/meta.yaml
+++ b/recipes/hmftools-sage/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "4.0_beta" %}
-{% set beta_suffix = ".1" %}
-{% set sha256 = "22a3495f4ebe425114af4b9ba472860b3e2fe16395e3223827d0b6eccba27eb3" %}
+{% set beta_suffix = ".3" %}
+{% set sha256 = "6675b28bd271ab12cd6881abccc3b0b309f5faa1544f31d3c3ec762f219ead7f" %}
 
 package:
   name: hmftools-sage
@@ -12,14 +12,14 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 3
   run_exports:
     - {{ pin_subpackage('hmftools-sage', max_pin="x") }}
 
 requirements:
   run:
     - zlib
-    - openjdk >=8
+    - openjdk >=9
     - bioconductor-variantannotation
     - bioconductor-genomicranges
     - r-dplyr
diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml
index 069d3780b89be..df405b33da02d 100644
--- a/recipes/hybpiper/meta.yaml
+++ b/recipes/hybpiper/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "hybpiper" %}
-{% set version = "2.3.0" %}
+{% set version = "2.3.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://github.com/mossmatters/HybPiper/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 7b9d0af243dbdd24cb299cf8e05e65dafa873afc2c7605e3fae74b455457b491
+  sha256: 0f341fb26dffd39c13b3bfc5c1d568936bcd0edbe9064399e4aa947d5882d220
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.7
     - pip
+    - setuptools
   run:
     - bbmap >=38.44
     - biopython >=1.80
@@ -38,8 +39,7 @@ requirements:
     - psutil >=5.9.0
     - samtools >=1.14
     - seaborn-base >=0.11.1
-    - spades >=3.15.2  # [osx]
-    - spades >=3.15.4  # [linux]
+    - spades >=4.0.0
     - trimmomatic
 
 test:
diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml
index 2084feff2576c..748dac08e3c7b 100644
--- a/recipes/hybracter/meta.yaml
+++ b/recipes/hybracter/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "hybracter" %}
-{% set version = "0.10.0" %}
+{% set version = "0.10.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz
-  sha256: 6640aacea33671c2bf1714693ecdd48c87a708d8bbf0ad1f964ddd6fc34e0224
+  sha256: 4e8e3454d18a33727156dfea274e83fbb9f2e3b9cc6cd5d5a7a8e53a5c5223ce
 
 build:
   number: 0
diff --git a/recipes/icfree-ml/meta.yaml b/recipes/icfree-ml/meta.yaml
index d0e9659d2aa05..09c13b468f85f 100644
--- a/recipes/icfree-ml/meta.yaml
+++ b/recipes/icfree-ml/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "icfree-ml" %}
-{% set version = "2.5.0" %}
+{% set version = "2.5.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/brsynth/icfree-ml/archive/refs/tags/2.5.0.tar.gz
-  sha256: 9720880aba7613b582cd519749c5908195679e228a196cbc6ae941814410aef3
+  url: https://github.com/brsynth/icfree-ml/archive/refs/tags/2.5.1.tar.gz
+  sha256: 4c62b4ee55d77a8af8d277ae1b58b0df2c977ca39aead9188ede7ae061a8f18d
 
 build:
   number: 0
diff --git a/recipes/im2deep/meta.yaml b/recipes/im2deep/meta.yaml
index 8d186c0704c2b..041fae8628975 100644
--- a/recipes/im2deep/meta.yaml
+++ b/recipes/im2deep/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "im2deep" %}
-{% set version = "0.2.0" %}
-{% set sha256 = "51678cfa2af905af196176e37e694c8629d9d8f2c4a1848185b5794697e0544b" %}
+{% set version = "0.3.1" %}
+{% set sha256 = "6a07bd8d161b1b89dfe5fa6f2b882876715f647066708a92cff9401561628846" %}
 
 package:
   name: {{ name|lower }}
@@ -24,6 +24,7 @@ requirements:
   host:
     - pip
     - python >=3.8
+    - setuptools
   run:
     - python >=3.8
     - click
@@ -49,4 +50,3 @@ about:
 extra:
   recipe-maintainers:
     - compomics
-
diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml
new file mode 100644
index 0000000000000..a81bac3f6af7b
--- /dev/null
+++ b/recipes/instanovo/meta.yaml
@@ -0,0 +1,65 @@
+{% set name = "instanovo" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/instanovo-{{ version }}.tar.gz
+  sha256: fd9cfc377d9f8da5272f96b2eb4c14c08b579d7a65466aa402601ec6c4b42672
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name | lower, max_pin="x.x") }}
+
+
+requirements:
+  host:
+    - python >=3.10,<3.12
+    - setuptools >=69.1.1
+    - pip
+  run:
+    - click
+    - datasets
+    - hydra-core
+    - jaxtyping
+    - jiwer
+    - matchms
+    - neptune
+    - numpy
+    - omegaconf
+    - pandas
+    - polars
+    - pyopenms
+    - python-dotenv
+    - pytorch-lightning
+    - s3fs
+    - scikit-learn
+    - spectrum_utils
+    - tensorboard
+    - pytorch
+    - tqdm
+
+test:
+  imports:
+    - instanovo
+  commands:
+    - python -c "import instanovo; print(instanovo.__version__)"
+  requires:
+    - pip
+
+about:
+  home: https://github.com/instadeepai/instanovo
+  summary: De novo peptide sequencing with InstaNovo
+  license: Apache-2.0
+  license_file: LICENSE.md
+
+extra:
+  recipe-maintainers:
+    - BioGeek
+  identifiers:
+    - doi:10.1101/2023.08.30.555055 
diff --git a/recipes/iseq/meta.yaml b/recipes/iseq/meta.yaml
index 193270e7e7cef..478271bd01ce4 100644
--- a/recipes/iseq/meta.yaml
+++ b/recipes/iseq/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "iSeq" %}
-{% set version = "1.1.0" %}
+{% set version = "1.2.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,23 +7,23 @@ package:
 
 source:
   url: https://github.com/BioOmics/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: de0b9f1e06842a14f0a112023b989a38f6d422d860d44b19d3ec717d3c00bc34
+  sha256: 9ddac60c63f774aac274de5a2abb1917774499c56f3c233aa19abe22f053fef3
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
 requirements:
-  build:
+  host:
     - bash
   run:
     - pigz
     - wget
     - axel
     - aspera-cli
-    - sra-tools =2.11.0
+    - sra-tools >=2.11.0
 
 test:
   commands:
@@ -32,8 +32,10 @@ test:
 about:
   home: https://github.com/BioOmics/iSeq
   license: MIT
-  summary: "iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases"
+  license_family: MIT
+  summary: "iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases."
+  dev_url: https://github.com/BioOmics/iSeq
 
 extra:
   recipe-maintainers:
-    - Haoyu Chao <haoyuchao@zju.edu.cn>
+    - BioOmics
diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml
index ee3930be3b942..b6b2fd3056ed7 100644
--- a/recipes/isoquant/meta.yaml
+++ b/recipes/isoquant/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "IsoQuant" %}
-{% set version = "3.6.1" %}
-{% set sha256 = "6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d" %}
+{% set version = "3.6.2" %}
+{% set sha256 = "b742fe460b44d0d9feb967938176e707cfe4f281c53bf4fe04af2440c31e7862" %}
 
 package:
   name: {{ name | lower }}
diff --git a/recipes/isoseq/meta.yaml b/recipes/isoseq/meta.yaml
index 20546dac0f1e4..69cb18789c425 100644
--- a/recipes/isoseq/meta.yaml
+++ b/recipes/isoseq/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "isoseq" %}
-{% set version = "4.0.0" %}
-{% set sha256 = "5766001507cf2a351b260cf38b717351dd676a7c87eb7c285c3c43a4a458f4b2" %}
+{% set version = "4.2.0" %}
+{% set sha256 = "e22ee0cd508129455486d1d54aeef3df53cabf8cc419fd4c2bd5a1fc4ea514c0" %}
 
 package:
   name: {{ name }}
@@ -13,6 +13,9 @@ source:
 build:
   number: 0
   skip: True  # [osx]
+  binary_relocation: False
+  run_exports:
+    - {{ pin_subpackage('isoseq', max_pin='x.x') }}
 
 test:
   commands:
diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml
index cbef171ed668d..0f3c1b5b93e26 100644
--- a/recipes/itsxpress/meta.yaml
+++ b/recipes/itsxpress/meta.yaml
@@ -1,8 +1,8 @@
 {% set name = "itsxpress" %}
-{% set version = "2.1.2" %}
+{% set version = "2.1.3" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "5a19ef9333ac4acacfa1da9c27ff3f713d7521661fbfe7541c58221c2ce2d08f" %}
+{% set hash_value = "a911701cbcf86ca6fc59b606d20fbee7015577477cfd4aa41d97420f23ad87c0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -17,7 +17,7 @@ build:
   number: 0
   entry_points:
     - itsxpress=itsxpress.main:main
-  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   run_exports:
     - {{ pin_subpackage('itsxpress', max_pin="x") }}
 
@@ -25,8 +25,8 @@ requirements:
   host:
     - pip
     - python >=3.8
+    - setuptools
   run:
-    - pip
     - python >=3.8
     - biopython >=1.79
     - hmmer =3.1b2
@@ -44,7 +44,7 @@ about:
   license: CC0-1.0
   license_family: 'PUBLIC-DOMAIN'
   summary: 'ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files'
-
+  dev_url: http://github.com/usda-ars-gbru/itsxpress
 
 extra:
   recipe-maintainers:
diff --git a/recipes/jaeger-bio/meta.yaml b/recipes/jaeger-bio/meta.yaml
index 388ff7957b63e..0e7aa7a4d9a46 100644
--- a/recipes/jaeger-bio/meta.yaml
+++ b/recipes/jaeger-bio/meta.yaml
@@ -1,50 +1,48 @@
 {% set name = "jaeger-bio" %}
-{% set version = "1.1.26" %}
+{% set version = "1.1.30" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 7f7d8794cd04185f7787d92a6ccc89fa59bb58acbe0fe929c6bffbee39a90fe4
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/jaeger_bio-{{ version }}.tar.gz"
+  sha256: ffc54d7257201310ff137dd61dcb1d8afe6c7f95bf2fdf578fec79a16145aeae
 
 build:
   number: 0
-  script: "{{ PYTHON }} -m pip install . --no-cache-dir -vvv"
-  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
-    - {{ pin_subpackage('jaeger-bio', max_pin="x.x.x") }}
+    - {{ pin_subpackage('jaeger-bio', max_pin="x") }}
+  noarch: python
 
 requirements:
   host:
-    - python =3
+    - python >=3.9,<3.12
     - pip
   run:
-    - python =3
-    - pip
     - h5py >=3.8
-    - biopython >=1.78
     - kneed >=0.8.5
     - matplotlib-base >=3.7
     - numpy >=1.24
     - pandas >=1.5
+    - progressbar2 >=4.4.2
     - psutil >=5
+    - pycirclize
+    - pyfastx >=2
+    - python >=3.9,<3.12
     - ruptures >=1.1.9
     - scikit-learn ==1.3.2
-    - seaborn >=0.12.2
-    - tqdm >=4.64.0
-    - tensorflow >=2.15,<2.16
     - parasail-python >=1.3.4
+    - tensorflow >=2.15,<2.16
 
 test:
   imports:
     - jaegeraa
     - jaegeraa.data
     - jaegeraa.nnlib
-
   commands:
-    - Jaeger --help
+    - jaeger --help
 
 about:
   home: "https://github.com/Yasas1994/Jaeger"
@@ -56,7 +54,5 @@ about:
   doc_url: https://readthedocs.org/projects/jaeger-docs/
 
 extra:
-  identifiers:
-    - biotools:jaeger
   recipe-maintainers:
     - Yasas1994
diff --git a/recipes/jarvis3/build.sh b/recipes/jarvis3/build.sh
new file mode 100644
index 0000000000000..47e19355f4a79
--- /dev/null
+++ b/recipes/jarvis3/build.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include
+export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib
+
+cd src 
+make CC=$CC CFLAGS="$CFLAGS -fcommon"
+mkdir -p ${PREFIX}/bin
+make
+
+mv extra/ ${PREFIX}/bin
+mv JARVIS3.sh ${PREFIX}/bin
+mv JARVIS3 ${PREFIX}/bin
+
+cd ${PREFIX}/bin
+sed -i.bak 's/ \.\// /g; s/\"\.\//"/g; s/make/make CC=$CC CFLAGS="$CFLAGS -fcommon"/g' JARVIS3.sh
+chmod +x JARVIS3.sh
+JARVIS3.sh --install
diff --git a/recipes/jarvis3/meta.yaml b/recipes/jarvis3/meta.yaml
new file mode 100644
index 0000000000000..ef7376be780c4
--- /dev/null
+++ b/recipes/jarvis3/meta.yaml
@@ -0,0 +1,34 @@
+{% set version = "3.7" %}
+
+package:
+  name: jarvis3
+  version: {{ version }}
+
+build:
+  # Passes some invalid flags for clang
+  skip: True  # [osx]
+  number: 2
+  run_exports:
+    - {{ pin_subpackage("jarvis3", max_pin="x") }}
+
+source:
+  url: https://github.com/cobilab/jarvis3/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 7600b4da05d27150e96f3481ca5e8cbc1dc75ee1b537727abf717224ed42c613
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+
+test:
+  commands:
+    - JARVIS3 --version 2>&1 | grep "Version 3, Release 7"
+    - printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa; JARVIS3.sh -i test.fa | grep "test.fa.tar"
+
+about:
+  home: https://github.com/cobilab/jarvis3
+  license: GPL3
+  license_file: LICENSE
+  license_family: GPL3
+  summary: Improved encoder for genomic sequences.
+  dev_url: https://github.com/cobilab/jarvis3
diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml
index 821dfee562371..99e94882dfff8 100644
--- a/recipes/jbrowse2/meta.yaml
+++ b/recipes/jbrowse2/meta.yaml
@@ -1,12 +1,12 @@
 # When updating, check the @jbrowse/cli version in build.sh too
-{% set version = "2.15.4" %}
+{% set version = "2.17.0" %}
 
 package:
   name: jbrowse2
   version: {{ version }}
 
 source:
-  sha256: fa0a6163dab65d1705c1968cc41adc0f6b035a8fbc572b7ddff12721b5b58642
+  sha256: cf863b95ad3c21d2ceceb05761ae5824b26191e9421ddc0cd2c5073afce22dbe
   url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip
 
 build:
diff --git a/recipes/k8/build_failure.linux-aarch64.yaml b/recipes/k8/build_failure.linux-aarch64.yaml
deleted file mode 100644
index 0f24706a1a3cb..0000000000000
--- a/recipes/k8/build_failure.linux-aarch64.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-recipe_sha: 751a182044682904040e221315daeec2db6609dd34a65b46fd328abc6bd46c37  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: CI unresponsive
-reason: CPU at 100% for most of the build and timing out. Try in a separate PR.
\ No newline at end of file
diff --git a/recipes/k8/build_failure.osx-64.yaml b/recipes/k8/build_failure.osx-64.yaml
deleted file mode 100644
index 29e18e3dfa6d2..0000000000000
--- a/recipes/k8/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,106 +0,0 @@
-recipe_sha: 751a182044682904040e221315daeec2db6609dd34a65b46fd328abc6bd46c37  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tzfmt.o ../deps/icu-small/source/i18n/tzfmt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tzfmt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uregexc.o ../deps/icu-small/source/i18n/uregexc.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uregexc.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/measfmt.o ../deps/icu-small/source/i18n/measfmt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/measfmt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/brktrans.o ../deps/icu-small/source/i18n/brktrans.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/brktrans.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
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-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbt_data.o ../deps/icu-small/source/i18n/rbt_data.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbt_data.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/units_complexconverter.o ../deps/icu-small/source/i18n/units_complexconverter.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/units_complexconverter.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/csrecog.o ../deps/icu-small/source/i18n/csrecog.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/csrecog.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_patternstring.o ../deps/icu-small/source/i18n/number_patternstring.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_patternstring.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/udat.o ../deps/icu-small/source/i18n/udat.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/udat.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tolowtrn.o ../deps/icu-small/source/i18n/tolowtrn.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tolowtrn.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/numparse_impl.o ../deps/icu-small/source/i18n/numparse_impl.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/numparse_impl.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/unum.o ../deps/icu-small/source/i18n/unum.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/unum.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbtz.o ../deps/icu-small/source/i18n/rbtz.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbtz.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uni2name.o ../deps/icu-small/source/i18n/uni2name.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common  -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uni2name.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/v8_bigint.stamp
-    touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/v8_heap_base.stamp
-    touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/cppgc_base.stamp
-    touch 7c3e22e70fd7ad60278a99f71782417440fb78d1.intermediate
-    LD_LIBRARY_PATH=$SRC_DIR/node-v18.19.1/out/Release/lib.host:$SRC_DIR/node-v18.19.1/out/Release/lib.target:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH; cd ../tools/v8_gypfiles; mkdir -p $SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/src/inspector/protocol $SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/include/inspector; /usr/local/bin/python3.11 ../../deps/v8/third_party/inspector_protocol/code_generator.py --jinja_dir ../../deps/v8/third_party --output_base "$SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/src/inspector" --config ../../deps/v8/src/inspector/inspector_protocol_config.json --config_value "protocol.path=../../deps/v8/include/js_protocol.pdl" --inspector_protocol_dir ../../deps/v8/third_party/inspector_protocol
-  In file included from ../deps/v8/src/libplatform/tracing/trace-writer.cc:14:
-  ../deps/v8/src/libplatform/tracing/recorder.h:17:10: fatal error: 'os/signpost.h' file not found
-  #include <os/signpost.h>
-           ^~~~~~~~~~~~~~~
-  1 error generated.
-  make[1]: *** [tools/v8_gypfiles/v8_libplatform.target.mk:175: /opt/mambaforge/envs/bioconda/conda-bld/k8_1717953792721/work/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o] Error 1
-  make[1]: *** Waiting for unfinished jobs....
-  make: *** [Makefile:134: node] Error 2
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-foreground-task-runner.o ../deps/v8/src/libplatform/default-foreground-task-runner.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-foreground-task-runner.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-job.o ../deps/v8/src/libplatform/default-job.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-job.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-      utils.check_call_env(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-platform.o ../deps/v8/src/libplatform/default-platform.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-platform.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/k8_1717953792721/work/conda_build.sh']' returned non-zero exit status 2.
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-worker-threads-task-runner.o ../deps/v8/src/libplatform/default-worker-threads-task-runner.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-worker-threads-task-runner.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/delayed-task-queue.o ../deps/v8/src/libplatform/delayed-task-queue.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/delayed-task-queue.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/task-queue.o ../deps/v8/src/libplatform/task-queue.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/task-queue.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-buffer.o ../deps/v8/src/libplatform/tracing/trace-buffer.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-buffer.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-config.o ../deps/v8/src/libplatform/tracing/trace-config.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-config.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-object.o ../deps/v8/src/libplatform/tracing/trace-object.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-object.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o ../deps/v8/src/libplatform/tracing/trace-writer.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/tracing-controller.o ../deps/v8/src/libplatform/tracing/tracing-controller.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/tracing-controller.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-    x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/worker-thread.o ../deps/v8/src/libplatform/worker-thread.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include  -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/worker-thread.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c
-  rm 7c3e22e70fd7ad60278a99f71782417440fb78d1.intermediate
-# Last 100 lines of the build log.
-category: |-
-  compiler error
diff --git a/recipes/kalamari/meta.yaml b/recipes/kalamari/meta.yaml
index 86fd246313eeb..8d4a7dbd29474 100644
--- a/recipes/kalamari/meta.yaml
+++ b/recipes/kalamari/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "Kalamari" %}
-{% set version = "5.7.1" %}
+{% set version = "5.7.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/lskatz/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 41a70037424da3658e6c92e3faca335d4cf02301fc74a5b5b27cd2611aef5681
+  sha256: 9f206e8bb949961d2b0f4788dae0deb2941632237391ae04891ea77ef8f02d89
 
 build:
   number: 0
diff --git a/recipes/kaptive/meta.yaml b/recipes/kaptive/meta.yaml
index 8d9a87e3e7b3c..fe9d11b65adb2 100644
--- a/recipes/kaptive/meta.yaml
+++ b/recipes/kaptive/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "kaptive" %}
-{% set version = "3.0.0b5" %}
+{% set version = "3.0.0b6" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kaptive-{{ version }}.tar.gz
-  sha256: d1462db66b22b6c9f42922df6ba05526cb08a453e311e6da2704603e60cb84c3
+  sha256: 7144b5bea531a5c5e8022a5898e16d24b0705ebedefedb4470bf5a5864225ae8
 
 build:
   entry_points:
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
     - biopython >=1.83
diff --git a/recipes/kestrel/build.sh b/recipes/kestrel/build.sh
new file mode 100644
index 0000000000000..6069aed727d79
--- /dev/null
+++ b/recipes/kestrel/build.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -euo pipefail
+
+kestrel="${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION}"
+
+mkdir -p "${kestrel}"
+cp -r ./* "${kestrel}"
+chmod +x "${kestrel}/kestrel"
+mkdir -p "${PREFIX}/bin"
+
+if [[ -L "${PREFIX}/bin/kestrel" ]]; then
+    echo "Error: File ${PREFIX}/bin/kestrel already exists"
+    exit 1
+fi
+
+if [[ ! -f "${kestrel}/kestrel" ]]; then
+    echo "Error: Target file ${kestrel}/kestrel does not exist"
+    exit 1
+fi
+ln -s "${kestrel}/kestrel" "${PREFIX}/bin/kestrel" || exit 1
diff --git a/recipes/kestrel/meta.yaml b/recipes/kestrel/meta.yaml
new file mode 100644
index 0000000000000..0bf3d2202ceb8
--- /dev/null
+++ b/recipes/kestrel/meta.yaml
@@ -0,0 +1,38 @@
+{% set name = "kestrel" %}
+{% set version = "1.0.3" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/paudano/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}-linux.tar.gz
+  sha256: 992c579fc52dce7b9d80e6232914da02663a2480d28b672277d80fdfcdda33e3
+
+build:
+  noarch: generic
+  detect_binary_files_with_prefix: true
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('kestrel', max_pin="x") }}
+
+requirements:
+  run:
+    # Enforce a version requirement on openjdk to ensure
+    # it comes from the conda-forge channel and not default.
+    # Many yaks were shaved to bring us this information.
+    # Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906
+    - openjdk >=8.0.144
+
+test:
+  commands:
+    - kestrel
+    - kestrel -h 
+
+about:
+  home: 'https://github.com/paudano/kestrel'
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: COPYING
+  summary: 'Mapping-free variant caller for short-read Illumina data'
+
diff --git a/recipes/kinex/meta.yaml b/recipes/kinex/meta.yaml
index 80ebad9c3037b..8e2f49ea40b45 100644
--- a/recipes/kinex/meta.yaml
+++ b/recipes/kinex/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "kinex" %}
-{% set version = "1.0.2" %}
+{% set version = "1.1.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,22 +7,23 @@ package:
 
 source:
   url: "https://github.com/bedapub/{{ name }}/archive/v{{ version }}.tar.gz"
-  sha256: ec9809bf7f401a064824d4883ef2877d945e65b7eb1e6f10b160590b515f4553
+  sha256: 43dbcabe85fa5c4a593949ffd02887722b94d9285fa01e8bd0ed0a8e7998fa02
 
 build:
   number: 0
   noarch: python
   script:
-    - {{ PYTHON }} -m pip install . --no-deps -vv
+    - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   run_exports:
     - {{ pin_subpackage("kinex", max_pin="x") }}
 
 requirements:
   host:
     - pip
-    - python >=3.8,<=3.11
+    - python >=3.8
+    - setuptools
   run:
-    - python >=3.8,<=3.11
+    - python >=3.8
     - scipy >=1.10.0
     - numpy >=1.19.5
     - nbformat >=4.2.0
@@ -40,8 +41,9 @@ test:
 about:
   home: "https://github.com/bedapub/kinex"
   license: GPL-3.0-only
+  license_family: GPL3
   license_file: LICENSE
-  summary: "Kinex infers causal kinases from phosphoproteomics data"
+  summary: "Kinex infers causal kinases from phosphoproteomics data."
   doc_url: "https://kinex.readthedocs.io/en/latest/"
   dev_url: "https://github.com/bedapub/kinex"
 
diff --git a/recipes/kleborate/meta.yaml b/recipes/kleborate/meta.yaml
index b1c2fad6fee70..371b9dae8b3b4 100644
--- a/recipes/kleborate/meta.yaml
+++ b/recipes/kleborate/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "kleborate" %}
-{% set version = "3.1.0" %}
+{% set version = "3.1.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kleborate-{{ version }}.tar.gz"
-  sha256: efb249d5b402502ae325d9b189c425464de930a0e455c5060d8aeea35dbbc920
+  sha256: c0a69dbb95bbf64f099cd98eb8ff853025e20f4718b75a4496426c8d0ac57760
 
 build:
   number: 0
@@ -23,6 +23,7 @@ requirements:
   host:
     - pip
     - python >=3.9
+    - setuptools
   run:
     - python >=3.9
     - biopython >=1.83
diff --git a/recipes/kmer-jellyfish/build.sh b/recipes/kmer-jellyfish/build.sh
index d80b1f2cbe9b7..d64bbe1f11fdd 100644
--- a/recipes/kmer-jellyfish/build.sh
+++ b/recipes/kmer-jellyfish/build.sh
@@ -1,11 +1,16 @@
 #!/bin/bash -euo
 
-./configure --prefix=${PREFIX} --enable-python-binding --with-sse CXX="${CXX}" \
-	CXXFLAGS="${CXXFLAGS} -O3" CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
-	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
-make -j ${CPU_COUNT}
+./configure --prefix="${PREFIX}" --enable-python-binding --with-sse CXX="${CXX}" \
+	CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
+
+make -j"${CPU_COUNT}"
 make install
-make check -j ${CPU_COUNT}
+#make check -j"${CPU_COUNT}"
 cd swig/python
-pip install . --prefix=$PREFIX
+${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/kmer-jellyfish/meta.yaml b/recipes/kmer-jellyfish/meta.yaml
index 3c7f76dafe597..d349363ebfb1d 100644
--- a/recipes/kmer-jellyfish/meta.yaml
+++ b/recipes/kmer-jellyfish/meta.yaml
@@ -10,7 +10,8 @@ source:
   sha256: ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd
 
 build:
-  number: 3
+  number: 4
+  skip: True  # [py < 38]
   run_exports:
     - {{ pin_subpackage("kmer-jellyfish", max_pin="x") }}
 
@@ -18,10 +19,13 @@ requirements:
   build:
     - {{ compiler('cxx') }}
     - make
+    - pkg-config
   host:
-    - python >=3.8
+    - python
+    - pip
+    - yaggo
   run:
-    - python >=3.8
+    - python
 
 test:
   commands:
@@ -33,11 +37,14 @@ about:
   home: "https://genome.umd.edu/jellyfish.html"
   license: "GPL-3.0-or-later"
   license_family: GPL3
+  license_file: "LICENSE-GPL-3.0"
   summary: "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence."
   dev_url: "https://github.com/gmarcais/Jellyfish"
   doc_url: "https://genome.umd.edu/docs/JellyfishUserGuide.pdf"
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:jellyfish
     - doi:10.1093/bioinformatics/btr011
diff --git a/recipes/konezumiaid/meta.yaml b/recipes/konezumiaid/meta.yaml
index 5ead433a9586c..91121c8a30c31 100644
--- a/recipes/konezumiaid/meta.yaml
+++ b/recipes/konezumiaid/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "KOnezumiAID" %}
-{% set version = "0.3.1" %}
+{% set version = "0.3.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/konezumiaid-{{ version }}.tar.gz
-  sha256: 78379cd1c923c5e6ae81fe0c0e84f6624b05ecca0cb87a73381431756e8a3489
+  sha256: 7bc66fa4daa3fbe8d0c9f02fe1f594eeb8eb3fc722a788c2d31e290279218777
 
 build:
   entry_points:
diff --git a/recipes/krakentools/meta.yaml b/recipes/krakentools/meta.yaml
index 55c5462baa269..0993897f425fe 100644
--- a/recipes/krakentools/meta.yaml
+++ b/recipes/krakentools/meta.yaml
@@ -12,8 +12,9 @@ source:
 
 build:
   noarch: python
-  number: 0
-
+  number: 1
+  run_exports:
+      - {{ pin_subpackage("krakentools", max_pin="x.x") }}
 requirements:
   host:
     - python 
@@ -21,6 +22,7 @@ requirements:
     - python 
     - biopython
     - numpy 
+    - scipy
 
 test:
   commands:
@@ -40,9 +42,8 @@ about:
   home: https://github.com/jenniferlu717/KrakenTools
   license: GPL-3.0
   license_family: GPL
-  summary: {{ name }} is a suite of scripts to be used for post-analysis of
-    Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using
-    {{ name }} with any of the listed programs.
+  license_file: LICENSE
+  summary: {{ name }} scripts for analysis of Kraken/KrakenUniq/Kraken2/Bracken results
 
 extra:
   identifiers:
diff --git a/recipes/lamps/meta.yaml b/recipes/lamps/meta.yaml
new file mode 100644
index 0000000000000..928e649120589
--- /dev/null
+++ b/recipes/lamps/meta.yaml
@@ -0,0 +1,55 @@
+{% set name = "lamps" %}
+{% set version = "1.0.3" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/lamps-{{ version }}.tar.gz
+  sha256: c85de92edcb4cd450aeebcb829729f163a02b3905146ef5208f911f38f2abe63
+
+build:
+  entry_points:
+    - lamp = lamp.__main__:main
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('lamps', max_pin="x") }}   
+
+requirements:
+  host:
+    - python >=3.8
+    - setuptools >=61.0
+    - wheel
+    - pip
+  run:
+    - python >=3.8
+    - numpy
+    - scipy
+    - pandas
+    - pyside6
+    - pyteomics
+    - openpyxl
+    - pyjanitor
+
+test:
+  imports:
+    - lamp
+  commands:
+    - pip check
+    - lamp --help
+  requires:
+    - pip
+
+about:
+  home: https://pypi.org/project/lamps/
+  summary: Liverpool Annotation of metabolites using Mass Spectrometry
+  dev_url: https://github.com/wanchanglin/lamp
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - harryln-1
diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml
index e4ced42950a1a..1421ee6fad184 100644
--- a/recipes/last/meta.yaml
+++ b/recipes/last/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "LAST" %}
-{% set version = "1584" %}
+{% set version = "1595" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.tar.gz"
-  sha256: 5ed143d7311a1e2ea1fe2be87a2484612689a1498420e2a454762a6b3ab38ba3
+  sha256: dedc8dbcecd7f134d5c0f64e97c500c1588303235528022a42c3ca74bb22995f
 
 build:
   number: 0
diff --git a/recipes/liana/meta.yaml b/recipes/liana/meta.yaml
new file mode 100644
index 0000000000000..0b735c8ee063e
--- /dev/null
+++ b/recipes/liana/meta.yaml
@@ -0,0 +1,62 @@
+{% set name = "liana" %}
+{% set version = "1.4.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/liana-{{ version }}.tar.gz
+  sha256: 1172a9bef67ee22d5eb3f27144c61dddec3122bd515b131c9ed5b0529fcbf2d1
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("liana", max_pin="x.x.x") }}
+    
+requirements:
+  host:
+    - python >=3.8,<3.12
+    - poetry-core >=1.0.0
+    - pip
+  run:
+    - python >=3.8,<3.12
+    - anndata >=0.7.4
+    - mudata
+    - scanpy >=1.8.0
+    - numba >=0.54.0
+    - plotnine >=0.10.0
+    - tqdm >=4.0.0,<5.0.0
+    - docrep >=0.3.1
+    - pre-commit >=3.0.0
+    - omnipath >=1.0.6
+    - decoupler >=1.4.0
+    - pydeseq2 >=0.3.5
+    - cell2cell
+    - muon
+    - mofax
+    - mofapy2 >=0.7.0
+    - corneto
+    - cvxpy >=1.4,<2
+    - cylp >=0.91.5,<0.92.0
+    - requests >=2.25.1,<3.0.0
+
+test:
+  imports:
+    - liana
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://liana-py.readthedocs.io
+  summary: 'LIANA+: a one-stop-shop framework for cell-cell communication'
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - nilchia
diff --git a/recipes/libcifpp/meta.yaml b/recipes/libcifpp/meta.yaml
index e81459934f2a9..c1e89d66c0293 100644
--- a/recipes/libcifpp/meta.yaml
+++ b/recipes/libcifpp/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "libcifpp" %}
-{% set version = "7.0.7" %}
-{% set sha256 = "0e88805b4704d4a899aeee6df5aaace1d6b47d8ccb3a3f39b35bc5a3997c09ac" %}
+{% set version = "7.0.8" %}
+{% set sha256 = "2297e6649a4f71caf9da5f1d97f59512e7324bb62083bb5b08eb00c1c0385cb3" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/libgff/build.sh b/recipes/libgff/build.sh
new file mode 100644
index 0000000000000..5a9ce48866885
--- /dev/null
+++ b/recipes/libgff/build.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+export M4="${BUILD_PREFIX}/bin/m4"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+
+cmake --build build --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/libgff/meta.yaml b/recipes/libgff/meta.yaml
new file mode 100644
index 0000000000000..aeca79f5a22da
--- /dev/null
+++ b/recipes/libgff/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "libgff" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/COMBINE-lab/libgff/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 1
+  run_exports:
+    - {{ pin_subpackage('libgff', max_pin='x') }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+
+test:
+  commands:
+    - "ls ${PREFIX}/lib/libgff.a"
+
+about:
+  home: https://github.com/COMBINE-lab/libgff
+  license: MIT
+  license_family: MIT
+  summary: 'A simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase.'
+  dev_url: https://github.com/COMBINE-lab/libgff
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/libmaus2/build.sh b/recipes/libmaus2/build.sh
index cdd58fb79e892..7d73807646dd1 100644
--- a/recipes/libmaus2/build.sh
+++ b/recipes/libmaus2/build.sh
@@ -1,10 +1,14 @@
 #!/bin/bash
 set -eu
-export LIBS="-lstdc++fs -lcurl"
+export LIBS="-lstdc++fs -lcurl -lz -ldeflate"
 
-./configure --prefix $PREFIX --with-snappy --with-io_lib
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" CC="${CC}" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	--with-snappy --with-io_lib --with-libdeflate \
+	--with-libsecrecy --with-nettle \
+	--with-lzma --with-gmp
 
-cat config.log
-
-make -j${CPU_COUNT}
+make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/libmaus2/meta.yaml b/recipes/libmaus2/meta.yaml
index 3d8c6738d991c..7a7a7f2f344b6 100644
--- a/recipes/libmaus2/meta.yaml
+++ b/recipes/libmaus2/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "libmaus2" %}
-{% set version = "2.0.810" %}
-{% set datestamp = "20220216151520" %}
-{% set sha256hash = "6639289aba6bbece3057ab7d1782a1b94b80a9ae22fc3d136a78ba8f7b9edaee" %}
+{% set version = "2.0.813" %}
+{% set datestamp = "20221210220409" %}
+{% set sha256 = "4125f8daefd6900185675026498369457088e25e81029597659249be49cd5261" %}
 
 package:
   name: {{ name }}
@@ -10,47 +10,61 @@ package:
 build:
   # There's some issue with clang
   skip: True  # [osx]
-  number: 6
+  number: 0
   run_exports:
-    - {{ pin_subpackage('libmaus2', max_pin='x.x') }}
+    - {{ pin_subpackage('libmaus2', max_pin='x') }}
 
 source:
   url: https://gitlab.com/german.tischler/libmaus2/-/archive/{{ version }}-release-{{ datestamp }}/libmaus2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
-  patches:
+  sha256: {{ sha256 }}
+  #patches:
     # Until gcc >=8 is being used
-    - patch
+    #- patch
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
     - boost-cpp
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - libcurl
     # snappy 1.1.9 introduced a binary incompatible build change (https://github.com/mhx/dwarfs/issues/56#issuecomment-896857211)
     # enabling -fno-rtti. libmaus needs typeid, which is only available with activated rtti.
     # Hence, we stick with snappy 1.1.8
-    - snappy =1.1.8 
+    - snappy =1.1.8
     - staden_io_lib >=1.14.14
+    - libdeflate
+    - gmp
+    - nettle
+    - zlib
   run:
     - boost-cpp
-    - libcurl
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - snappy =1.1.8
     - staden_io_lib >=1.14.14
-  ignore_run_exports:
-    - snappy
-
-about:
-  home: https://gitlab.com/german.tischler/libmaus2
-  license: GPL3
-  summary: collection of data structures and algorithms for NGS data
 
 test:
   commands:
     - echo
 
+about:
+  home: https://gitlab.com/german.tischler/libmaus2
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: GPLv3
+  summary: "Collection of data structures and algorithms for NGS data."
+  dev_url: https://gitlab.com/german.tischler/libmaus2
+
 extra:
   additional-platforms:
     - linux-aarch64
+  identifiers:
+    - biotools:libmaus
diff --git a/recipes/libmaus2/patch b/recipes/libmaus2/patch
index f66efbfe6c761..1d8376b29a4a1 100644
--- a/recipes/libmaus2/patch
+++ b/recipes/libmaus2/patch
@@ -127,36 +127,6 @@ index 134ff0f4..b8fcfe88 100644
  
  				setHWTReq  (p_hwt_req.string());
  				setHWT     (p_hwt.string());
-diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-index 1e8e53b9..a91d1916 100644
---- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-+++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-@@ -111,11 +111,11 @@ namespace libmaus2
- 				// base tmp directory name
- 				std::string tmpdirname;
- 				// tmpdirname as path object
--				std::filesystem::path tmppath;
--				std::filesystem::path base_tmp_path;
--				std::filesystem::path ds_tmp_path_base_ds_tmp;
--				std::filesystem::path merge_tmp_path;
--				std::filesystem::path ds_tmp_path_merge_ds_tmp;
-+				std::experimental::filesystem::path tmppath;
-+				std::experimental::filesystem::path base_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
-+				std::experimental::filesystem::path merge_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
- 
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
-@@ -333,7 +333,7 @@ namespace libmaus2
- 					return C;
- 				}
- 
--				static std::filesystem::path ensureDirectory(std::filesystem::path path)
-+				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
- 				{
- 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
- 					return path;
 diff --git a/src/libmaus2/util/ArgInfo.cpp b/src/libmaus2/util/ArgInfo.cpp
 index 3802cbb7..8ecd441c 100644
 --- a/src/libmaus2/util/ArgInfo.cpp
@@ -267,6 +237,42 @@ index 2ff71e4a..0714e612 100644
  				dictpath /= digest;
  
  				std::cerr << "[V] writing " << dictpath << " for " << pat.sid << " in " << ref << std::endl;
--- 
-2.33.0
-
+diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+index 180f466..0b69f74 100644
+--- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
++++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+@@ -111,11 +111,11 @@ namespace libmaus2
+ 				// base tmp directory name
+ 				std::string tmpdirname;
+ 				// tmpdirname as path object
+-				std::filesystem::path tmppath;
+-				std::filesystem::path base_tmp_path;
+-				std::filesystem::path ds_tmp_path_base_ds_tmp;
+-				std::filesystem::path merge_tmp_path;
+-				std::filesystem::path ds_tmp_path_merge_ds_tmp;
++				std::experimental::filesystem::path tmppath;
++				std::experimental::filesystem::path base_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
++				std::experimental::filesystem::path merge_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
+ 
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
+@@ -333,7 +333,7 @@ namespace libmaus2
+ 					return C;
+ 				}
+ 
+-				static std::filesystem::path ensureDirectory(std::filesystem::path path)
++				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
+ 				{
+ 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
+ 					return path;
+@@ -358,7 +358,7 @@ namespace libmaus2
+ 					preisasamplingrate(std::min(options.maxpreisasamplingrate,blocksizeprevtwo)),
+ 					V_boundedlcpblockvalues(new libmaus2::util::AtomicArray<uint64_t>(numblocks,0)),
+ 					// tmp directory name
+-					tmpdirname(ensureDirectory(std::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
++					tmpdirname(ensureDirectory(std::experimental::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
+ 					// path object for tmp directory name
+ 					tmppath(tmpdirname),
+ 					base_tmp_path(ensureDirectory(tmppath / "base_tmp")),
diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml
index 53d51fabd39ef..f0bf8cdd59581 100644
--- a/recipes/lima/meta.yaml
+++ b/recipes/lima/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "lima" %}
-{% set version = "2.9.0" %}
+{% set version = "2.12.0" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/PacificBiosciences/barcoding/releases/download/v{{ version }}/lima.tar.gz
-  sha256: a13437bc7a90ab5df3c19eac44384de2a14370d0391586b5aa63a6478f9c2c53
+  sha256: 7e6ac701b8625867bf7486583e741cc86a58e8c91384826613067364229e5627
 
 build:
   number: 1
diff --git a/recipes/locityper/build.sh b/recipes/locityper/build.sh
index 0698575530e7c..d1c7c01febf6a 100644
--- a/recipes/locityper/build.sh
+++ b/recipes/locityper/build.sh
@@ -8,6 +8,10 @@ fi
 export C_INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 
+if [[ `uname` == 'Darwin' ]]; then
+    export MACOSX_DEPLOYMENT_TARGET=10.11
+fi
+
 git clone https://github.com/smarco/WFA2-lib WFA2
 
 # build statically linked binary with Rust
diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml
index c9c450090f4ed..393549ad8f4ce 100644
--- a/recipes/locityper/meta.yaml
+++ b/recipes/locityper/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "locityper" %}
-{% set version = "0.16.12" %}
+{% set version = "0.17.3" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0bd3a82c1df6de921ed477edfca4ffb5017cf194807e358e482b49afba867dd7
+  sha256: d9ecc464a4394a0523afd6ba4c5f7bf80fe44ca15926cca1075ac70cd14b9255
 
 build:
   number: 0
diff --git a/recipes/lofreq/meta.yaml b/recipes/lofreq/meta.yaml
index 0d1ccfe2d7006..a4e8fbd6e32c5 100644
--- a/recipes/lofreq/meta.yaml
+++ b/recipes/lofreq/meta.yaml
@@ -11,7 +11,7 @@ source:
     - 0001-patches
 
 build:
-  number: 13
+  number: 14
   run_exports:
     - {{ pin_subpackage('lofreq', max_pin='x') }}
 
@@ -32,12 +32,14 @@ requirements:
   run:
     - python
     - samtools
+    - bcftools
     - gsl
 
 test:
   commands:
     - lofreq version
     - samtools --help
+    - bcftools --help
 
 about:
   home: "https://csb5.github.io/lofreq"
diff --git a/recipes/longcallr_nn/meta.yaml b/recipes/longcallr_nn/meta.yaml
index 387e4451d9830..a76c1551439cf 100644
--- a/recipes/longcallr_nn/meta.yaml
+++ b/recipes/longcallr_nn/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ hash }}
  
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - longcallR_nn=longcallR_nn.longcallR_nn:main
@@ -23,16 +23,17 @@ build:
 requirements:
   host:
     - pip
-    - python 3.9.*
+    - python >=3.9,<3.11
   run:
-    - python 3.9.*
-    - numpy 1.21.0
-    - pyyaml
-    - pysam
-    - tensorboardX
-    - pytorch 1.13.*
-    - torchvision
-    - torchmetrics
+    - python >=3.9,<3.11
+    - requests
+    - numpy >=1.21.0
+    - pyyaml >=5.3
+    - pysam >=0.16
+    - tensorboardX >=2.2
+    - pytorch >=1.13
+    - torchvision >=0.14
+    - torchmetrics >=0.9
 
 test:
   commands:
diff --git a/recipes/lotus2/build.sh b/recipes/lotus2/build.sh
index 5b4edbec842fd..79c1bbc3500d4 100644
--- a/recipes/lotus2/build.sh
+++ b/recipes/lotus2/build.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 SHARE_DIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 
-rm -rf bin/installs/ bin/LCA bin/rtk bin/sdm bin/vsearch configs/sdm_src/
+rm -rf bin/installs/ bin/lambda3* bin/LCA bin/rtk bin/sdm bin/vsearch
 # Configure LotuS2
 cp configs/LotuS.cfg.def lOTUs.cfg
-for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm vsearch; do
+for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm usearch vsearch; do
     sed -i.bak -e "s|^$binary[[:space:]].*|$binary $PREFIX/bin/$binary|" lOTUs.cfg
 done
 for binary in cd-hit fasttree hmmsearch iqtree itsx makeBlastDB RDPjar; do
diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml
index bc46dd5be022e..2da7f320f44bf 100644
--- a/recipes/lotus2/meta.yaml
+++ b/recipes/lotus2/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
diff --git a/recipes/lsabgc/meta.yaml b/recipes/lsabgc/meta.yaml
index 2f794a8713fad..566c66d3b4984 100644
--- a/recipes/lsabgc/meta.yaml
+++ b/recipes/lsabgc/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 04eadeadd7887883d48112624dd23496c19e2a038605e29fb0102c79badab5f4 
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv"
   run_exports:
@@ -25,7 +25,7 @@ requirements:
     - python >=3.10
     - r-base
     - axel
-    - zol >=1.4.12
+    - zol =1.4.12
     - orthofinder =2.5.5
     - pyseer >=1.3
     - gecco =0.9.6
diff --git a/recipes/macsyfinder/meta.yaml b/recipes/macsyfinder/meta.yaml
index e8304f673014b..e60f30f1d0927 100644
--- a/recipes/macsyfinder/meta.yaml
+++ b/recipes/macsyfinder/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
   entry_points:
     - macsyfinder=macsypy.scripts.macsyfinder:main
@@ -27,16 +27,18 @@ requirements:
   host:
     - pip
     - python >=3.10
+    - setuptools
+
   run:
     - python >=3.10
     - colorlog
     - PyYAML >=5.1.1
     - packaging >=18.0
     - networkx >=2.4
-    - pandas >=1.1.5,<=1.5.1
+    - pandas >=1.1.5,<=2.2.3
     - colorama >=0.4.4
     - certifi
-    - hmmer >=3.1b2,<=3.3.2
+    - hmmer >=3.1b2,<=3.4
     - git >1.7.0
     - gitpython >=3.1.30 
 
diff --git a/recipes/marti/meta.yaml b/recipes/marti/meta.yaml
index e86203beedb7e..d9eafb176f1f1 100644
--- a/recipes/marti/meta.yaml
+++ b/recipes/marti/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "MARTi" %}
-{% set version = "0.9.16" %}
+{% set version = "0.9.18" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/richardmleggett/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 85b06a61df8860d17c6de5282a820a8bd1b66bbb3d1f2351dbf5b54522aa1cb6
+  sha256: 7983a39b9d597fbe40850f8d88dd8078aec064fa7053ff029119a5b85806232e
 
 build:
   noarch: generic
diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml
index 09f269a84b383..6b139f28cf273 100644
--- a/recipes/massdash/meta.yaml
+++ b/recipes/massdash/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "massdash" %}
-{% set version = "0.0.9" %}
+{% set version = "0.1.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,37 +7,36 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 68d90f668312d94ec44f744376c0dad0b671fe78f01906d2e36ce43cc9c85ffa
+  sha256: dd62b62368ba6457d74b0b07bc0b3ba1df095f4788800a79a9cec6e4cbaf564d
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  entry_points:
+    - massdash = massdash.main:cli
   run_exports:  
     - {{ pin_subpackage('massdash', max_pin='x.x') }}
 
 requirements:
   host:
     - pip
-    - python
-    - flake8
-    - flit
+    - python >=3.10,<=3.12
     - flit-core
-    - pylint
-    - snapshottest
   run:
-    - bokeh ==2.4.3
-    - click
+    - python >=3.10,<=3.12
+    - bokeh >3.0
+    - click >=8.1
     - joblib
     - matplotlib-base
-    - matplotlib-venn
     - upsetplot
     - numpy >=1.9.0
     - pandas >=0.17
-    - plotly
+    - plotly ==5.24.1
     - psutil
-    - pyopenms
-    - scipy
+    - pyopenms >=3.2.0
+    - requests
+    - scipy >=1.12.0
     - streamlit
     - tqdm
 
@@ -47,9 +46,10 @@ test:
 
 about:
   home: https://github.com/Roestlab/massdash
-  license: BSD
+  license: BSD-3-Clause
   license_family: BSD
-  summary: MassDash is a streamlined DIA mass spec visualization, analysis, optimization, and rapid prototyping.
+  summary: "MassDash is a streamlined DIA mass spec visualization, analysis, optimization, and rapid prototyping."
+  dev_url: https://github.com/Roestlab/massdash
 
 extra:
   recipe-maintainers:
diff --git a/recipes/masurca/0001-install.sh.patch b/recipes/masurca/0001-install.sh.patch
new file mode 100644
index 0000000000000..79eebbf7f7be1
--- /dev/null
+++ b/recipes/masurca/0001-install.sh.patch
@@ -0,0 +1,14 @@
+diff --git a/install.sh b/install.sh
+index c30290e..0bce5d1 100755
+--- a/install.sh
++++ b/install.sh
+@@ -17,7 +17,7 @@ export NUM_THREADS=`grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl -n
+ BINDIR=$DEST/bin
+ LIBDIR=$DEST/lib
+ export PKG_CONFIG_PATH=$LIBDIR/pkgconfig:$PKG_CONFIG_PATH
+-(cd global-1 && ./configure --prefix=$DEST --bindir=$BINDIR --libdir=$LIBDIR && make -j $NUM_THREADS install-special)
++(cd global-1 && autoreconf -if && ./configure --prefix=$DEST --bindir=$BINDIR --libdir=$LIBDIR && make -j $NUM_THREADS install-special)
+ echo "creating example config file masurca_config_example.txt"
+ $BINDIR/masurca -g masurca_config_example.txt
+-(cd Flye && make && cp -a ../Flye $DEST);
++(cd Flye && make && cp -arf ../Flye $DEST);
diff --git a/recipes/masurca/build.sh b/recipes/masurca/build.sh
index 4ef46c2e1234b..afeeeebe96e46 100755
--- a/recipes/masurca/build.sh
+++ b/recipes/masurca/build.sh
@@ -1,13 +1,14 @@
 #!/usr/bin/env bash
 
 set -x -e
-BOOST_ROOT=${PREFIX}
-export DEST=${PREFIX}
+BOOST_ROOT="${PREFIX}"
+export DEST="${PREFIX}"
 export PERL_EXT_CPPFLAGS="-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector"
-export PERL_EXT_LDFLAGS="-shared -O2 -fstack-protector"
-export LDFLAGS="-L${PREFIX}/lib"
-export LIBRARY_PATH="$PREFIX/lib"
-export CPATH=${PREFIX}/include
-export CFLAGS="${CFLAGS} -std=gnu90 ${LDFLAGS}"
-export CXXFLAGS="$CXXFLAGS -std=gnu++14 ${LDFLAGS}"
+export PERL_EXT_LDFLAGS="-shared -O3 -fstack-protector"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export LIBRARY_PATH="${PREFIX}/lib"
+export INCLUDE_PATH="${PREFIX}/include"
+export CPATH="${PREFIX}/include"
+export CFLAGS="${CFLAGS} -O3 -std=gnu90 ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include ${LDFLAGS}"
 ./install.sh
diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml
index 589e24b633076..3f00ac29f5fe2 100644
--- a/recipes/masurca/meta.yaml
+++ b/recipes/masurca/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "masurca" %}
-{% set version = "4.1.1" %}
+{% set version = "4.1.2" %}
 
 package:
   name: {{ name }}
@@ -7,27 +7,31 @@ package:
 
 source:
   url: https://github.com/alekseyzimin/masurca/releases/download/v{{ version }}/MaSuRCA-{{ version }}.tar.gz
-  sha256: 8758f6196bf7f57e24e08bda84abddfff08feb4cea204c0eb5e1cb9fe8198573
+  sha256: 68d17e80295a242733bd875ef918f1af4fb3bb8ade29112e1a76cedc92dd619a
+  patches:
+    - 0001-install.sh.patch
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx]
   run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
+    - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - make
+    - automake
+    - autoconf
+    - libtool
+    - pkg-config
   host:
     - zlib
     - bzip2
     - boost-cpp
-    - perl
     - yaggo
   run:
-    - zlib
     - boost-cpp
     - perl
     - grep
@@ -40,10 +44,12 @@ test:
     - masurca --help
 
 about:
-  home: http://masurca.blogspot.co.uk/
-  license: GPL-3.0-only
-  license_family: GPL
-  license_file: LICENSE.txt
+  home: "https://masurca.blogspot.co.uk"
+  license: "GPL-3.0-only"
+  license_family: GPL3
+  license_file: "LICENSE.txt"
+  dev_url: "https://github.com/alekseyzimin/masurca"
+  doc_url: "https://github.com/alekseyzimin/masurca/blob/v{{ version }}/README.md"
   summary:
     MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software.
     MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore
diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml
index 6485c985ee7c8..5d730e31b4a31 100644
--- a/recipes/matchms/meta.yaml
+++ b/recipes/matchms/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "matchms" %}
-{% set version = "0.27.0" %}
+{% set version = "0.28.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 96d15fbc006c90ac306e91b9fc609255108c48536094d2a55502f6a2e65fbce8
+  sha256: 63b0c3af5cbdc6367a50ecae002e832f96c96d5a7073774b608984ce2b515d46
 
 build:
-  number: 1
+  number: 0
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   run_exports:
@@ -19,26 +19,26 @@ build:
 requirements:
   host:
     - pip
-    - python >=3.9,<3.13
+    - python >=3.10,<3.13
     - poetry-core
   run:
     - deprecated >=1.2.14
     - lxml >=4.9.3,<5
     - matplotlib-base >=3.7
-    - networkx >=3.0
-    - numba >=0.57.1,<0.60
-    - numpy >1.22,<1.27
+    - networkx >=3.4.2
+    - numba >=0.60.0
+    - numpy >=2.0.0
     - pickydict >=0.4.0
     - pyteomics >=4.6
-    - python >=3.9,<3.13
+    - python >=3.10,<3.13
     - pyyaml >=6.0.1
-    - rdkit >=2023.9.6
+    - rdkit >=2024.3.5
     - requests >=2.31.0
-    - scipy >=1.11
-    - sparsestack >=0.4.1
+    - scipy >=1.14.1
+    - sparsestack >=0.6.0
     - tqdm >=4.65.0
     - pillow !=9.4.0
-    - pandas >=2.0.3
+    - pandas >=2.2.3
     - pubchempy
 
 test:
diff --git a/recipes/maxit/data-binary_linux-x86_64.tar.xz b/recipes/maxit/data-binary_linux-x86_64.tar.xz
deleted file mode 100644
index 02fdced44170c..0000000000000
Binary files a/recipes/maxit/data-binary_linux-x86_64.tar.xz and /dev/null differ
diff --git a/recipes/maxit/meta.yaml b/recipes/maxit/meta.yaml
index 69b9d593ddd0d..02ddd83cbf6c9 100644
--- a/recipes/maxit/meta.yaml
+++ b/recipes/maxit/meta.yaml
@@ -17,11 +17,11 @@ source:
       - binary.csh.patch  # [linux]
       - system-util.C.patch  # [linux]
       - Makefile.patch  # [linux]
-  - path: ./data-binary_linux-x86_64.tar.xz  # [linux and x86_64]
-    sha256: 44a626b2f082a91c8dcdf110a0a0779dbb0e9aaa72b128a7dbd523f1456bb0be  # [linux and x86_64]
+  - url: https://github.com/eunos-1128/maxit-data-binaries/archive/refs/tags/v11.200.tar.gz  # [linux and x86_64]
+    sha256: b28f04dedc5fe46052a160b8124e92e94b8194ce57a463af76b37a0ca1d6f4ec  # [linux and x86_64]
 
 build:
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml
index bb85221963f0a..f8d22b73e9bfe 100644
--- a/recipes/melon/meta.yaml
+++ b/recipes/melon/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "melon" %}
-{% set version = "0.2.0" %}
+{% set version = "0.2.1" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 3020c20f8619aeeb254a52eb8822dab3689956b3e218450cd8506a42f263f7f4
+  sha256: 3b3d09801212282b5ebb8030976d49361484031460c53f6440c61706af90cd63
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ build:
 requirements:
   host:
     - pip
+    - setuptools
     - python >=3.7
   run:
     - python >=3.7
@@ -40,7 +41,7 @@ about:
   home: https://github.com/xinehc/melon
   license: MIT
   license_family: MIT
-  summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification'
+  summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes'
 
 extra:
   recipe-maintainers:
diff --git a/recipes/merqury/meta.yaml b/recipes/merqury/meta.yaml
index 583ae7429b8e1..d903c7837069f 100644
--- a/recipes/merqury/meta.yaml
+++ b/recipes/merqury/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 3
   noarch: generic
   run_exports:
     - {{ pin_subpackage("merqury", max_pin='x.x') }}  
@@ -22,7 +22,7 @@ requirements:
     - openjdk  >=11.0.1
     - r-base  >=4
     - r-argparse  >=2.0.1
-    - r-ggplot2  >=3.3.2
+    - r-ggplot2  >=3.3.2,<=3.3.6
     - r-scales  >=1.1.1
     - bedtools  >=2.29.2
     - samtools  >=1.10
diff --git a/recipes/merquryfk/meta.yaml b/recipes/merquryfk/meta.yaml
index 97923a411e0ae..a6825bf9b88ef 100644
--- a/recipes/merquryfk/meta.yaml
+++ b/recipes/merquryfk/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "MERQURYFK" %}
-{% set version = "1.1.0" %}
-{% set sha256 = "2af9dd265d10d79dceba495f8ef2469e5f832783b5824ab554e1efcb6ffe660c" %}
+{% set version = "1.1.1" %}
+{% set sha256 = "c530eaba0b6f46e57dcba421434027776629651ac9f9630d4470063f17ffe663" %}
 
 package:
   name: {{ name|lower }}
@@ -13,7 +13,7 @@ source:
     - patch
 
 build:
-  number: 1
+  number: 0
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage("merquryfk", max_pin="x") }}
@@ -53,4 +53,4 @@ about:
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64
diff --git a/recipes/mess/meta.yaml b/recipes/mess/meta.yaml
index 01c9ddfd0baad..950a2567dc22d 100644
--- a/recipes/mess/meta.yaml
+++ b/recipes/mess/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: a0bb9d8dc81548cfad1cc45d43c82d41b28a399dd8f6bad4c5588a8201196f1a
 
 build:
-  number: 1
+  number: 2
   noarch: python
   entry_points:
     - mess=mess.__main__:main
@@ -28,10 +28,9 @@ requirements:
   run:
     - python >=3.11
     - apptainer >=1.3.2
-    - snakemake-minimal >=8.0.0
+    - snakemake-minimal >=8.0.0,<=8.24.1
     - snaketool-utils >=0.0.5
     - attrmap >=0.0.7
-    - pyyaml >=6.0.1
     - pandas >=2.2.3
     - biopython >=1.83
     - rich-click >=1.8.3
diff --git a/recipes/meta-neuro/build.sh b/recipes/meta-neuro/build.sh
new file mode 100644
index 0000000000000..b30b786bedb79
--- /dev/null
+++ b/recipes/meta-neuro/build.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+set -ex
+
+unset LD LINK ARCH
+export CMAKE_INSTALL_RPATH='$ORIGIN/../lib'
+export CMAKE_BUILD_WITH_INSTALL_RPATH=ON
+
+mkdir -p "$PREFIX/bin"
+mkdir -p "$PREFIX/lib"
+mkdir -p "$PREFIX/share"
+mkdir -p $SRC_DIR/build
+
+## copy small test data:
+mkdir -p $PREFIX/share/meta-neuro/example
+cp $SRC_DIR/resources/test.nii.gz $PREFIX/share/meta-neuro/example/
+
+cd $SRC_DIR/build
+cmake -S $SRC_DIR -B $SRC_DIR/build  \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=$PREFIX \
+    -DCMAKE_CXX_STANDARD=17 \
+    -DCMAKE_MODULE_PATH=$PREFIX/share/cmake \
+    -DCMAKE_PREFIX_PATH=$PREFIX \
+    -DCMAKE_INSTALL_RPATH=$CMAKE_INSTALL_RPATH \
+    -DCMAKE_BUILD_WITH_INSTALL_RPATH=$CMAKE_BUILD_WITH_INSTALL_RPATH
+
+cmake --build . --config Release --parallel ${CPU_COUNT} --verbose
+cmake --install .
+
+# Clean up build directory
+rm -rf $SRC_DIR/build
+
+# Install MeTA package
+cd ${SRC_DIR}
+${PYTHON} -m pip install . --no-deps -vv
diff --git a/recipes/meta-neuro/conda_build_config.yaml b/recipes/meta-neuro/conda_build_config.yaml
new file mode 100644
index 0000000000000..09a4e9197bc16
--- /dev/null
+++ b/recipes/meta-neuro/conda_build_config.yaml
@@ -0,0 +1,18 @@
+build_variant:
+  - "osmesa"  # [linux]
+  - "qt"      # [osx]
+
+python:
+  - 3.11.*  *_cpython
+  - 3.10.*  *_cpython
+  - 3.9.*  *_cpython
+
+python_impl:
+  - cpython
+  - cpython
+  - cpython
+
+numpy:
+  - 1.23.*
+  - 1.22.*
+  - 1.22.*
diff --git a/recipes/meta-neuro/meta.yaml b/recipes/meta-neuro/meta.yaml
new file mode 100644
index 0000000000000..dfcd922cb0f7c
--- /dev/null
+++ b/recipes/meta-neuro/meta.yaml
@@ -0,0 +1,74 @@
+{% set name = "meta-neuro" %}
+{% set version = "1.0.0" %}
+{% set sha256 = "c67bcad0899fc3f9c890ee26e9c1c2ab1a892430ce00a9ac090e36697efc9434" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/bagari/meta/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: true  # [win ]
+  run_exports:
+    - {{ pin_subpackage('meta-neuro', max_pin="x.x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - make  # [not win]
+
+  host:
+    - vtk >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libitk-devel ==5.3.0
+    - hdf5 >=1.14.2,<1.14.3.0a0
+    - libboost-python-devel >=1.82.0,<1.83.0
+    - python
+    - pip
+    - setuptools
+
+  run:
+    - vtk >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libitk-devel ==5.3.0
+    - hdf5 >=1.14.2,<1.14.3.0a0
+    - libboost-python-devel >=1.82.0,<1.83.0
+    - qhull
+    - python
+    - pip
+    - setuptools
+    - numpy
+    - tqdm
+    - dipy
+    - scipy
+    - pandas
+    - nibabel
+    - tslearn
+    - pyvista
+
+test:
+  imports:
+    - meta
+  commands:
+    - vtklevelset $PREFIX/share/meta-neuro/example/test.nii.gz test.vtk 0.1
+    - cmrep_vskel -c 3 -p 1.5 -g test.vtk test_skeleton.vtk
+
+about:
+  home: https://github.com/bagari/meta
+  license: BSD-3-Clause
+  license_file: LICENSE.txt
+  summary: 'Medial Tractography Analysis (MeTA)'
+  description: |
+    MeTA is a workflow implemented to minimize microstructural heterogeneity in diffusion MRI (dMRI) metrics by extracting and parcellating the core volume along the bundle length in the voxel-space directly while effectively preserving bundle shape and efficiently capturing the regional variation within and along white matter (WM) bundles.
+  dev_url: https://github.com/bagari/meta
+  doc_url: https://github.com/bagari/meta/wiki
+
+extra:
+  bulk: true
+  additional-platforms:
+    - osx-arm64
+  recipe-maintainers:
+    - bagari
diff --git a/recipes/metabolabpy/meta.yaml b/recipes/metabolabpy/meta.yaml
index 73a6b1bf7d748..625f33cf1005e 100644
--- a/recipes/metabolabpy/meta.yaml
+++ b/recipes/metabolabpy/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "metabolabpy" %}
-{% set version = "0.9.59" %}
-{% set sha256 = "b1d84db29e59998186c46b76f8a6a08abef0b424254660a472dde96ab97dbd6c" %}
+{% set version = "0.9.63" %}
+{% set sha256 = "a9ae288f518b8a1a8c614032c1c0511fc932389dd656dbca52896f5598af9d95" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml
index b235bec50bcfe..7984177eb2af4 100644
--- a/recipes/metabolights-utils/meta.yaml
+++ b/recipes/metabolights-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "metabolights-utils" %}
-{% set version = "1.2.1" %}
+{% set version = "1.3.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
-  sha256: 2db0e90df0540f87820955de31f8ec7bf9cbc6a0f669632c252c1f5908b31c9d
+  sha256: 84cf47a421ef77fa3b14e90290396eec96cd6440128b239de211543b29b59818
 
 build:
   entry_points:
diff --git a/recipes/metaphor/meta.yaml b/recipes/metaphor/meta.yaml
index 71a95ce8a10f9..a73669ed4ed8d 100644
--- a/recipes/metaphor/meta.yaml
+++ b/recipes/metaphor/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "metaphor" %}
-{% set version = "1.7.13" %}
+{% set version = "1.7.14" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,20 +7,22 @@ package:
 
 source:
   url: https://github.com/vinisalazar/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 88f959b4eb30cb7794d361015b386220cc5a0e1c0e09d710a575890febed57d9
+  sha256: 86025b04ffa49d0f6430c02bba06533ce30e4ea5e45daeac3564d4be3a98bb84
 
 build:
   number: 0
   noarch: python
+  entry_points:
+    - metaphor = metaphor.cli.cli:main
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
   script:
-    - "{{ PYTHON }} -m pip install . -vv"
+    - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
 
 requirements:
   host:
     - pip
-    - python >=3.9
+    - python >=3.9,<3.12
   run:
     - jinja2
     - networkx
@@ -28,7 +30,7 @@ requirements:
     - python >=3.9,<3.12
     - pyyaml
     - requests
-    - snakemake >=7.5
+    - snakemake-minimal >=7.5,<8.0
     - snakemake-wrapper-utils
     - tqdm
     - zstandard
diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml
index eae9441d91acc..313c062578cfc 100644
--- a/recipes/mgnify-pipelines-toolkit/meta.yaml
+++ b/recipes/mgnify-pipelines-toolkit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mgnify-pipelines-toolkit" %}
-{% set version = "0.1.7" %}
+{% set version = "0.1.8" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz
-  sha256: 506eb725d226ff33ceaf8001502a0ab97bcaf41ac84ce011f98a2ccb892389ed
+  sha256: 57c299db9d80ab66c343d53a12382871eb166cf5e55470197ff4447fb7f93e78
 
 build:
   entry_points:
diff --git a/recipes/mikrokondo-tools/meta.yaml b/recipes/mikrokondo-tools/meta.yaml
new file mode 100644
index 0000000000000..1c96c8b6e9a71
--- /dev/null
+++ b/recipes/mikrokondo-tools/meta.yaml
@@ -0,0 +1,50 @@
+{% set name = "mikrokondo-tools" %}
+{% set version = "0.0.1rc0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://files.pythonhosted.org/packages/source/{{ name[0] }}/{{ name }}/mikrokondo_tools-{{ version }}.tar.gz
+  sha256: 97a6805c4de8acf568ea1be22a91b442a7c780f66d54520e1c9c8af9ef08d7ef
+
+build:
+  entry_points:
+    - mikrokondo-tools = mikrokondo_tools.cli:safe_entry_point
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.8
+    - hatchling
+    - pip
+  run:
+    - python >=3.8
+    - click
+    - requests
+    - jsonschema
+
+test:
+  imports:
+    - mikrokondo_tools
+  commands:
+    - pip check
+    - mikrokondo-tools --help
+  requires:
+    - pip
+
+about:
+  home: https://pypi.org/project/mikrokondo-tools
+  summary: A collection of utilities to make using the mikrokondo pipeline easier
+  dev_url: https://github.com/DOED-DAAD/mikrokondo-tools
+  license: Apache-2.0
+  license_file: LICENSE.txt
+
+extra:
+  recipe-maintainers:
+    - mattheww95
diff --git a/recipes/mimeo/meta.yaml b/recipes/mimeo/meta.yaml
index 12bc24ed38e28..0d5bc68a083c8 100644
--- a/recipes/mimeo/meta.yaml
+++ b/recipes/mimeo/meta.yaml
@@ -1,29 +1,34 @@
 package:
   name: mimeo
-  version: "1.1.1"
+  version: "1.1.2"
 
 source:
-  url: https://pypi.python.org/packages/c2/06/2d02f67ab0869090dbb669c67e070b9450191be302745446b0290295123a/mimeo-1.1.1.tar.gz
-  md5: 45d523f694829cf0d081ec8bc0a62729
+  url: https://files.pythonhosted.org/packages/4e/7c/e2f51b7f98a35a8af8627db183aa8013a34ac153385993a20b0d2a537fb2/mimeo-1.1.2.tar.gz
+  sha256: 29a08af948affc0b9cbac214f9a27aa84fc5b53e33f99282bb7865b3e0c4b8f6
 
 build:
   noarch: python
-  number: 2
-  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  number: 0
+  script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv
   entry_points:
     - mimeo-self=mimeo.run_self:main
     - mimeo-x=mimeo.run_interspecies:main
     - mimeo-map=mimeo.run_map:main
     - mimeo-filter=mimeo.run_filter:main
+  run_exports:
+    - {{ pin_subpackage('mimeo', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3
+    - python >=3.8
     - pip
+    - hatchling
+    - hatch-vcs
   run:
-    - python >=3
+    - python >=3.8
     - pandas >=0.20.3
     - biopython >=1.70
+    #- argparse-tui
 
 test:
   imports:
@@ -37,6 +42,7 @@ test:
 
 about:
   home: https://github.com/Adamtaranto/mimeo
-  license: MIT License
+  license: MIT
   summary: 'Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.'
   license_family: MIT
+  dev_url: https://github.com/Adamtaranto/mimeo
diff --git a/recipes/minimac4/build.sh b/recipes/minimac4/build.sh
new file mode 100644
index 0000000000000..d3b62199c6ca3
--- /dev/null
+++ b/recipes/minimac4/build.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+set -euo pipefail
+
+echo "Building Minimac4 version ${PKG_VERSION}"
+
+# Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzma
+export CXXFLAGS="-I${PREFIX}/include -I${PREFIX}/lib"
+export LDFLAGS="-L${PREFIX}/lib -llzma"
+CMAKE_MAKE_PROGRAM="$(which make)"
+CMAKE_C_COMPILER="${CC}"
+CMAKE_CXX_COMPILER="${CXX}"
+
+export CMAKE_MAKE_PROGRAM
+export CMAKE_C_COMPILER
+export CMAKE_CXX_COMPILER
+
+# Set up dependencies and directories
+if [ ! -f ./requirements.txt ]; then
+    echo "Error: requirements.txt not found"
+    exit 1
+fi
+cget ignore xz || exit 1
+cget install -f ./requirements.txt || exit 1
+
+cmake --version
+mkdir -p build || exit 1
+cd build || exit 1
+
+cmake \
+    -DBUILD_TESTS=1 \
+    -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+    -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} \
+    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} \
+    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \
+    -DCPACK_GENERATOR="STGZ" \
+    -DCPACK_PACKAGE_CONTACT="csg-devel@umich.edu" \
+    ..
+
+make || exit 1
+make install || exit 1
+make CTEST_OUTPUT_ON_FAILURE=1 test || exit 1
+echo "Minimac4 installation completed successfully"
+
+cd .. || exit 1
diff --git a/recipes/minimac4/meta.yaml b/recipes/minimac4/meta.yaml
new file mode 100644
index 0000000000000..889e9cbc3f5d8
--- /dev/null
+++ b/recipes/minimac4/meta.yaml
@@ -0,0 +1,41 @@
+{% set version = "4.1.6" %}
+
+package:
+  name: minimac4
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('minimac4', max_pin='x.x.x') }}
+
+source:
+  url: https://github.com/statgen/Minimac4/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333
+
+requirements:
+  build:
+    - make
+    - cmake >=3.24
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - cget
+  host:
+    - bcftools >=1.20
+    - zlib
+    - savvy ==2.1.0
+    - xz
+  run:
+    - cget
+
+test:
+  commands:
+    - minimac4 --help
+    - minimac4 --version
+
+about:
+  home: https://github.com/statgen/Minimac4
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: "Computationally efficient genotype imputation"
+  description: "Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3."
diff --git a/recipes/miniprot/build.sh b/recipes/miniprot/build.sh
index 538daeacc98c7..65a03d01d4c0f 100644
--- a/recipes/miniprot/build.sh
+++ b/recipes/miniprot/build.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 
-make CC=$CC CFLAGS="$CFLAGS -I$PREFIX/include" LIBS="$LDFLAGS -L$PREFIX/lib -lpthread -lz -lm"
+set -xe
+
+make -j"${CPU_COUNT}" CC=$CC CFLAGS="$CFLAGS -I$PREFIX/include" LIBS="$LDFLAGS -L$PREFIX/lib -lpthread -lz -lm"
 
 if [ ! -d $PREFIX/bin ] ; then
 	mkdir -p $PREFIX/bin
diff --git a/recipes/miniprot/meta.yaml b/recipes/miniprot/meta.yaml
index d3ee72d13b2c3..203fcc669f373 100644
--- a/recipes/miniprot/meta.yaml
+++ b/recipes/miniprot/meta.yaml
@@ -7,7 +7,7 @@ package:
   version: "{{ version }}"
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -35,3 +35,8 @@ about:
   summary: |
     Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
     It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
\ No newline at end of file
diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml
index 8ce2b630e521a..ca14a1a16b2ab 100644
--- a/recipes/minute/meta.yaml
+++ b/recipes/minute/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.9.0" %}
+{% set version = "0.10.1" %}
 
 package:
   name: minute
@@ -6,21 +6,22 @@ package:
 
 source:
   url: https://github.com/elsasserlab/minute/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: bac0252f635ff015d80abd35375407ccf48b12babd947f900889d6475f2cac13
+  sha256: 666204aa5ba17fe1c77a156b0987d036ecf7a8792f860745e0741e3ad33b0976
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage('minute', max_pin='x.x') }}
 
 requirements:
   host:
     - pip
-    - python >=3.8
+    - python >=3.7
+    - setuptools
   run:
-    - python >=3.8
+    - python >=3.7
     - ruamel.yaml
     - snakemake-minimal >=7.22.0
     - samtools >=1.13
@@ -50,8 +51,11 @@ test:
 about:
   home: https://github.com/elsasserlab/minute/
   license: MIT
+  license_family: MIT
+  license_file: LICENSE
   summary: MINUTE-ChIP data analysis workflow
-
+  dev_url: https://github.com/elsasserlab/minute
+  doc_url: https://minute.readthedocs.io/en/latest
 extra:
   recipe-maintainers:
     - marcelm
diff --git a/recipes/mkdesigner/meta.yaml b/recipes/mkdesigner/meta.yaml
index 7c89662a1d4a4..92a931f5b02ac 100644
--- a/recipes/mkdesigner/meta.yaml
+++ b/recipes/mkdesigner/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mkdesigner" %}
-{% set version = "0.4.4" %}
+{% set version = "0.5.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mkdesigner-{{ version }}.tar.gz
-  sha256: 29513140681b1f667764081bf981c1a548be3cf877bab4ffe551df96b1efbd9d
+  sha256: 532609a307abcabe2a090ea64a73d29092fafcd543d62d0d10fbadcee0ba9df5
 
 build:
   entry_points:
@@ -18,12 +18,13 @@ build:
   script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
   run_exports:
-    - {{ pin_subpackage('mkdesigner', max_pin="x") }}
+    - {{ pin_subpackage('mkdesigner', max_pin="x.x") }}
 
 requirements:
   host:
     - python >=3.8,<4.0
     - pip
+    - setuptools
   run:
     - python >=3.8,<4.0
     - pandas >=2.0.2,<3.0.0
@@ -34,6 +35,7 @@ requirements:
     - samtools >=1.6,<2.0
     - bcftools >=1.5,<2.0
     - matplotlib-base
+    - timeout-decorator
 
 test:
   imports:
@@ -44,11 +46,12 @@ test:
     - mkselect --help
 
 about:
-  home: https://github.com/KChigira/mkdesigner/
+  home: https://github.com/KChigira/mkdesigner
   summary: Genome-wide design of markers for PCR-based genotyping from NGS data.
   license: MIT
   license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/KChigira/mkdesigner
 
 extra:
   recipe-maintainers:
diff --git a/recipes/ms-entropy/meta.yaml b/recipes/ms-entropy/meta.yaml
index d8692e0b3c899..ec4f112fedc41 100644
--- a/recipes/ms-entropy/meta.yaml
+++ b/recipes/ms-entropy/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ms-entropy" %}
-{% set version = "1.2.0" %}
+{% set version = "1.3.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,22 +7,23 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms_entropy-{{ version }}.tar.gz
-  sha256: 428b43006b75824d80bd494dea0f80fa2e3c3366b7b31d556055ea6500a568cd
+  sha256: 08fe799e237af12f7e5a3bcea8ae83e8940dc46f75c46fe2a4c717db4a75215c
 
 build:
-  script: {{ PYTHON }} -m pip install . -vv
-  number: 1
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  number: 0
+  skip: True  # [py < 310]
   run_exports:
-    - {{ pin_subpackage('ms-entropy', max_pin='x.x') }}
+    - {{ pin_subpackage('ms-entropy', max_pin='x') }}
 
 requirements:
   build:
     - {{ compiler('c') }}
+    - libclang  # [osx]
   host:
     - python
-    - setuptools >=61.0
-    - cython >=0.26.1
-    - numpy >=1.9.3
+    - cython
+    - {{ pin_compatible('numpy') }}
     - pip
   run:
     - python
@@ -31,17 +32,19 @@ requirements:
 test:
   imports:
     - ms_entropy
-  commands:
-    - pip check
-  requires:
-    - pip
 
 about:
-  home: https://github.com/YuanyueLi/MSEntropy
-  summary: This package provides a Python implementation of calculating spectral entropy, entropy similarity, and Flash entropy search for mass spectrometry data.
+  home: "https://github.com/YuanyueLi/MSEntropy"
+  summary: "This package provides a Python implementation of calculating spectral entropy, entropy similarity, and Flash entropy search for mass spectrometry data."
   license: Apache-2.0
+  license_family: APACHE
   license_file: LICENSE
+  dev_url: "https://github.com/YuanyueLi/MSEntropy"
+  doc_url: "https://msentropy.readthedocs.io/en/latest"
 
 extra:
   recipe-maintainers:
     - hechth
+  identifiers:
+    - doi:10.1038/s41592-023-02012-9
+    - doi:10.1038/s41592-021-01331-z
diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml
index 4aebeeddd48cc..2dd1a9aedceb0 100644
--- a/recipes/ms2deepscore/meta.yaml
+++ b/recipes/ms2deepscore/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2deepscore" %}
-{% set version = "2.2.0" %}
-{% set sha256 = "c4f6458b88cf8ea95e4ec4b7b7872d0f4dc9c9f7e8c5538c8ff2e59c78b8bb15" %}
+{% set version = "2.4.0" %}
+{% set sha256 = "50c5827b0e6a40a29be270bcd9dd3873f0ef1094d8d9c06b354f09f67110fd56" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/msa4u/meta.yaml b/recipes/msa4u/meta.yaml
new file mode 100644
index 0000000000000..a932f8d7df7a1
--- /dev/null
+++ b/recipes/msa4u/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "msa4u" %}
+{% set version = "0.4.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/msa4u-{{ version }}.tar.gz
+  sha256: 0471f334bbc1fbb8ea6c0974c39f9aed59030b32d3d790caf814c8f53c393c17
+
+build:
+  run_exports:    
+    - {{ pin_subpackage("msa4u", max_pin="x.x") }}
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  noarch: python
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - biopython
+    - pandas
+    - reportlab
+    - configs
+
+test:
+  imports:
+    - msa4u
+  commands:
+    - msa4u --help
+
+about:
+  home: https://github.com/GCA-VH-lab/msa4u
+  summary: "A simple visualisation tool for Multiple Sequence Alignment."
+  license: WTFPL
+  license_file: LICENSE
diff --git a/recipes/muscle/build.sh b/recipes/muscle/build.sh
index 6e358f5e2b44b..a6fb04c9c3860 100644
--- a/recipes/muscle/build.sh
+++ b/recipes/muscle/build.sh
@@ -1,9 +1,18 @@
 #!/bin/bash
+set -e
 
-cd src/
-sed -i.bak -e 's/ -static//' Makefile
+mkdir -p ${PREFIX}/bin
+cd src || exit 1
+echo "0" > gitver.txt
 
-make CXX=$CXX
+cp ${RECIPE_DIR}/vcxproj_make.py .
+chmod +x vcxproj_make.py
+./vcxproj_make.py --openmp --cppcompiler ${CXX}
 
-mkdir -p "$PREFIX"/bin
-cp "$(uname)"/muscle "$PREFIX"/bin/muscle
+# Verify binary exists and is executable
+if [ ! -x ../bin/muscle ]; then
+    echo "Error: muscle binary not found"
+    exit 1
+fi
+
+cp ../bin/muscle ${PREFIX}/bin/muscle
diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml
index 9953f38bd5c3e..1bd528fba686b 100644
--- a/recipes/muscle/meta.yaml
+++ b/recipes/muscle/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "muscle" %}
-{% set version = "5.1.0" %}
+{% set version = "5.3" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/rcedgar/muscle/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d
+  url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 74b22a94e630b16015c2bd9ae83aa2be2c2048d3e41f560b2d4a954725c81968
   patches:
     - support-linux-aarch64.patch
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -21,16 +21,21 @@ requirements:
   build:
     - {{ compiler('cxx') }}
     - llvm-openmp  # [osx]
+    - macports-legacy-support  # [osx]
     - make
 
 test:
+  files:
+    - test_data.fna
   commands:
-    - muscle -version
+    - muscle --version
+    - muscle --help
+
 about:
   home: https://github.com/rcedgar/muscle
   license: GPL-3.0-only
   license_file: LICENSE
-  summary: "MUSCLE: multiple sequence alignment with high accuracy and high throughput"
+  summary: Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences
 
 extra:
   additional-platforms:
diff --git a/recipes/muscle/run_test.sh b/recipes/muscle/run_test.sh
new file mode 100644
index 0000000000000..3fad89ae2e7cd
--- /dev/null
+++ b/recipes/muscle/run_test.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+muscle -msastats test_data.fna
+muscle -super5 test_data.fna -output test_output.fna
+cat test_output.fna
diff --git a/recipes/muscle/support-linux-aarch64.patch b/recipes/muscle/support-linux-aarch64.patch
index 9308bf3333e2b..f9c8e2081e8b8 100644
--- a/recipes/muscle/support-linux-aarch64.patch
+++ b/recipes/muscle/support-linux-aarch64.patch
@@ -1,10 +1,10 @@
-diff --git i/src/myutils.h w/src/myutils.h
-index 49d28ef..8e8167e 100644
---- i/src/myutils.h
-+++ w/src/myutils.h
-@@ -11,7 +11,7 @@
- #define TRACK_ALLOC		0
- #define ALLOC_TOTALS	0
+diff --git a/src/myutils.h b/src/myutils.h
+index a5d8a58..fbf6f9f 100644
+--- a/src/myutils.h
++++ b/src/myutils.h
+@@ -10,7 +10,7 @@
+ #include <cstddef>
+ #include "myalloc.h"
  
 -#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__)
 +#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__aarch64__)
diff --git a/recipes/muscle/test_data.fna b/recipes/muscle/test_data.fna
new file mode 100644
index 0000000000000..864b3f67398da
--- /dev/null
+++ b/recipes/muscle/test_data.fna
@@ -0,0 +1,6 @@
+>1
+GKGDP
+>2
+MQDRVK
+>3
+IKKPL
diff --git a/recipes/muscle/vcxproj_make.py b/recipes/muscle/vcxproj_make.py
new file mode 100644
index 0000000000000..739663b29c933
--- /dev/null
+++ b/recipes/muscle/vcxproj_make.py
@@ -0,0 +1,225 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+Usage = (
+    "Convert Visual Studio .vcxproj file in current directory to Makefile and run make."
+)
+
+AP = argparse.ArgumentParser(description=Usage)
+
+# Value opts
+AP.add_argument(
+    "--std",
+    required=False,
+    help="C++ standard option for GCC, e.g. c++11 or c++17 (default none)",
+)
+AP.add_argument(
+    "--cppcompiler",
+    required=False,
+    default="g++",
+    help="C++ compiler command name default g++)",
+)
+AP.add_argument(
+    "--ccompiler",
+    required=False,
+    default="gcc",
+    help="C++ compiler command name default gcc)",
+)
+
+# Flag opts
+AP.add_argument("--debug", required=False, action="store_true", help="Debug build")
+AP.add_argument("--openmp", required=False, action="store_true", help="Requires OMP")
+AP.add_argument(
+    "--pthread", required=False, action="store_true", help="Requires pthread"
+)
+AP.add_argument("--lrt", required=False, action="store_true", help="Requires lrt")
+AP.add_argument(
+    "--symbols",
+    required=False,
+    action="store_true",
+    help="Debug symbols (default if --debug)",
+)
+AP.add_argument(
+    "--nostrip",
+    required=False,
+    action="store_true",
+    help="Don't strip symbols (default if --debug or --symbols)",
+)
+
+Args = AP.parse_args()
+debug = Args.debug
+std = Args.std
+cppcompiler = Args.cppcompiler
+ccompiler = Args.ccompiler
+nostrip = debug or Args.symbols
+symbols = debug or Args.symbols
+
+ProjFileName = None
+HdrNames = []
+for FileName in os.listdir("."):
+    if FileName.endswith(".vcxproj"):
+        ProjFileName = FileName
+    elif FileName.endswith(".h"):
+        HdrNames.append(FileName)
+if ProjFileName is None:
+    sys.stderr.write("\nProject file not found in current directory\n")
+    sys.exit(1)
+
+binary = ProjFileName.replace(".vcxproj", "")
+sys.stderr.write("binary=" + binary + "\n")
+
+compiler_opts = " -ffast-math -march=native"
+linker_opts = " -ffast-math -march=native"
+
+if std:
+    compiler_opts += " --std=" + std
+
+if debug:
+    compiler_opts += " -O0 -DDEBUG"
+    linker_opts += " -O0"
+else:
+    compiler_opts += " -O3 -DNDEBUG"
+    linker_opts += " -O3"
+
+if symbols:
+    compiler_opts += " -g3"
+    linker_opts += " -g3"
+
+if Args.openmp:
+    compiler_opts += " -fopenmp"
+    linker_opts += " -fopenmp"
+
+if Args.pthread:
+    compiler_opts += " -pthread"
+    linker_opts += " -lpthread"
+
+rc = os.system(r"rm -rf o/ ../bin/%s*" % binary)
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- failed to clean\n\n")
+    sys.exit(1)
+sys.stderr.write("clean done.\n")
+
+OBJDIR = "o"
+BINDIR = "../bin"
+
+Fields = ProjFileName.split("/")
+n = len(Fields)
+Name = Fields[n - 1]
+Fields = Name.split(".")
+binary = Fields[0]
+
+CXXNames = []
+CNames = []
+with open(ProjFileName) as File:
+    for Line in File:
+        Line = Line.strip()
+        Line = Line.replace('"', "")
+        Line = Line.replace(" ", "")
+        # <ClCompile Include="betadiv.cpp" />
+        if Line.startswith("<ClCompileInclude"):
+            Fields = Line.split("=")
+            if len(Fields) != 2:
+                continue
+            FileName = Fields[1]
+            FileName = FileName.replace("/>", "")
+            if FileName.endswith(".cpp"):
+                FileName = FileName.replace(".cpp", "")
+                CXXNames.append(FileName)
+            elif FileName.endswith(".c"):
+                FileName = FileName.replace(".c", "")
+                CNames.append(FileName)
+
+assert len(CXXNames) > 0 or len(CNames) > 0
+
+with open("Makefile", "w") as f:
+
+    def Out(s):
+        print(s, file=f)
+
+    BINPATH = "$(BINDIR)/%s" % (binary)
+
+    Out("######################################################")
+    Out("# Makefile is generated by " + sys.argv[0])
+    Out("# Don't edit the Makefile -- update the python script")
+    Out("######################################################")
+    Out("")
+    Out("BINDIR := %s" % BINDIR)
+    Out("OBJDIR := %s" % OBJDIR)
+    Out("BINPATH := %s" % BINPATH)
+
+    if CNames:
+        Out("")
+        Out("CC = " + ccompiler)
+        Out("CFLAGS := $(CFLAGS) " + compiler_opts)
+
+    if CXXNames:
+        Out("")
+        Out("CXX = " + cppcompiler)
+        Out("CXXFLAGS := $(CFLAGS) " + compiler_opts)
+
+    Out("")
+    Out("UNAME_S := $(shell uname -s)")
+    Out("LDFLAGS := $(LDFLAGS) " + linker_opts)
+    Out("ifeq ($(UNAME_S),Linux)")
+    Out("    LDFLAGS += -static")
+    Out("endif")
+
+    Out("")
+    Out("HDRS = \\")
+    for Name in sorted(HdrNames):
+        Out("  %s \\" % Name)
+
+    Out("")
+    Out("OBJS = \\")
+    for Name in CXXNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    for Name in CNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    Out("")
+    Out(".PHONY: clean")
+
+    Out("")
+    Out("$(BINPATH) : $(BINDIR)/ $(OBJDIR)/ $(OBJS)")
+
+    if len(CXXNames) > 0:
+        Cmd = "\t$(CXX) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+    else:
+        Cmd = "\t%(CC) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+
+    if Args.lrt:
+        Cmd += " -lrt"
+    Out(Cmd)
+
+    if not nostrip:
+        Out("	strip $(BINPATH)")
+
+    Out("")
+    Out("$(OBJDIR)/ :")
+    Out("	mkdir -p $(OBJDIR)/")
+
+    Out("")
+    Out("$(BINDIR)/ :")
+    Out("	mkdir -p $(BINDIR)/")
+
+    if CNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.c $(HDRS)")
+        Out("	$(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<")
+
+    if CXXNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.cpp $(HDRS)")
+        Out("	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<")
+
+sys.stderr.write("Makefile done.\n")
+
+rc = os.system("make")
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- make failed\n\n")
+    sys.exit(1)
+sys.stderr.write("make done.\n")
diff --git a/recipes/muse/0001-Makefile.patch b/recipes/muse/0001-Makefile.patch
new file mode 100644
index 0000000000000..f74a0587e8375
--- /dev/null
+++ b/recipes/muse/0001-Makefile.patch
@@ -0,0 +1,51 @@
+diff --git a/Makefile b/Makefile
+index 5edd6e1..78d946c 100755
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,6 @@
+-CPP := g++
+-CC := gcc
+-LINK := g++
++CPP := ${CXX}
++CC := ${CC}
++LINK := ${CXX}
+ mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+ 
+ CSOURCES= $(wildcard src/*.c)  
+@@ -11,12 +11,12 @@ COMMONOBJS= lib/libhts.a lib/libboost_iostreams.a lib/libtcmalloc_minimal.a
+ Warnings=-Wreturn-type -Warray-bounds -Wmaybe-uninitialized -Waddress
+ WarningsAsErrors=$(Warnings) -Werror=return-type -Werror=array-bounds -Werror=address
+ CFLAGS=  $(WarningsAsErrors) -Wno-unused-function
+-CPPFLAGS=  $(WarningsAsErrors) -Wno-unused-function -std=c++11
++CPPFLAGS=  $(WarningsAsErrors) -Wno-unused-function -std=c++14
+ 
+ RELEASE_FLAGS= -O3 -g
+ 
+ # Includes
+-INCLUDES = -Iinc/
++INCLUDES += -Iinc/ -Iinc/htslib -I$(PREFIX)/include
+ #
+ # Common flags
+ COMMONFLAGS += $(INCLUDES)
+@@ -24,7 +24,7 @@ COMMONFLAGS += $(INCLUDES)
+ CXXFLAGS += $(COMMONFLAGS)
+ CFLAGS += $(COMMONFLAGS)
+ CPPFLAGS += $(COMMONFLAGS)
+-COMMONLIBS= -Llib/ -lz -lm -lpthread -lbz2 -lcurl -lcrypto -llzma -fopenmp
++COMMONLIBS += -Llib/ -lz -lm -lpthread -lbz2 -lcurl -lcrypto -llzma -lhts -ldl -fopenmp -L${PREFIX}/lib
+ 
+ #LIBS += $(COMMONLIBS) -ltcmalloc
+ LIBS += $(COMMONLIBS)
+@@ -38,10 +38,10 @@ all: $(TARGET)
+ .SUFFIXES: .c .cpp .o
+ 
+ %.c.o: %.c
+-	$(CC) $(CFLAGS) $(RELEASE_FLAGS) -c $< -o $@
++	$(CC) $(CFLAGS) $(RELEASE_FLAGS) $(INCLUDES) $(LIBS) -c $< -o $@
+ 
+ %.cpp.o: %.cpp
+-	$(CPP) $(CPPFLAGS) $(RELEASE_FLAGS) $(OPENMP) -c $< -o $@
++	$(CPP) $(CPPFLAGS) $(RELEASE_FLAGS) $(OPENMP) $(INCLUDES) $(LIBS) -c $< -o $@
+ 
+ $(TARGET): $(OBJS) Makefile
+ 	$(LINKLINE)
diff --git a/recipes/muse/0001-add-LDFLAGS.patch b/recipes/muse/0001-add-LDFLAGS.patch
deleted file mode 100644
index f28ec42a45648..0000000000000
--- a/recipes/muse/0001-add-LDFLAGS.patch
+++ /dev/null
@@ -1,7 +0,0 @@
---- Makefile
-+++ Makefile
-@@ -9,3 +9,3 @@
- $(BIN): $(C_OBJ) $(CPP_OBJ)
--	$(CPP) $(C_OBJ) $(CPP_OBJ) -o $(BIN) -lm -lz
-+	$(CPP) $(C_OBJ) $(CPP_OBJ) -o $(BIN) $(LDFLAGS) -lm -lz
- 	
diff --git a/recipes/muse/build.sh b/recipes/muse/build.sh
index f29124b5ed79f..dc0bf210dc652 100644
--- a/recipes/muse/build.sh
+++ b/recipes/muse/build.sh
@@ -1,6 +1,29 @@
-#!/usr/bin/env bash
+#!/bin/bash
+set -euo pipefail
 
-make CPP="${CXX}" CPPFLAGS="${CXXFLAGS}"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
 
-mkdir -p "${PREFIX}/bin"
-cp MuSE "${PREFIX}/bin/"
+rm -rf boost_1_70_0/
+
+if [[ `uname` == "Darwin" ]]; then
+	ln -sf ${CC} ${PREFIX}/bin/clang
+	ln -sf ${CXX} ${PREFIX}/bin/clang++
+else
+	ln -sf ${CC} ${PREFIX}/bin/gcc
+	ln -sf ${CXX} ${PREFIX}/bin/g++
+fi
+
+./install_muse.sh
+
+if [[ `uname` == "Darwin" ]]; then
+	rm -rf ${PREFIX}/bin/clang
+	rm -rf ${PREFIX}/bin/clang++
+else
+	rm -rf ${PREFIX}/bin/gcc
+	rm -rf ${PREFIX}/bin/g++
+fi
+
+install -d "${PREFIX}/bin"
+install -v -m 0755 MuSE "${PREFIX}/bin"
diff --git a/recipes/muse/fix-install_muse.sh.patch b/recipes/muse/fix-install_muse.sh.patch
new file mode 100644
index 0000000000000..22d3f5f457f2f
--- /dev/null
+++ b/recipes/muse/fix-install_muse.sh.patch
@@ -0,0 +1,99 @@
+diff --git a/install_muse.sh b/install_muse.sh
+index 7bc2153..8a57cf7 100755
+--- a/install_muse.sh
++++ b/install_muse.sh
+@@ -4,13 +4,20 @@ make clean
+ 
+ mkdir -p lib
+ 
++if [[ `uname` == "Darwin" ]]; then
++	export TOOL=clang
++else
++	export TOOL=gcc
++fi
++
+ # compile boost library
+-cd boost_1_70_0/
+-./bootstrap.sh
+-./b2 --clean
+-./b2
++cd boost-1.87.0.beta1/
++./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
++./b2 toolset="${TOOL}" --layout=system link=static \
++	threading=multi strip=on \
++	variant=release address-model=64 install
+ 
+-cp stage/lib/libboost_iostreams.a ../lib/
++cp -f lib/libboost_iostreams.a ../lib/
+ cd ..
+ 
+ # compile libtcmalloc
+@@ -22,12 +29,21 @@ fi
+ 
+ git clone https://github.com/gperftools/gperftools.git
+ cd gperftools
+-git checkout gperftools-2.9.1
++git checkout gperftools-2.10
+ ./autogen.sh
+-./configure --libdir="$PWD"
+-make -j4
+-make install
+-cp libtcmalloc_minimal.a ../lib/
++if [[ $(uname) == 'Darwin' ]]; then
++	export CFLAGS="$CFLAGS -D_XOPEN_SOURCE"
++	./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++	--disable-debugalloc --disable-libunwind
++	make -j"${CPU_COUNT}"
++	make install
++else
++	./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++	--enable-libunwind --enable-frame-pointers
++	make -j"${CPU_COUNT}"
++	make install
++fi
++cp -f libtcmalloc_minimal.a ../lib/
+ cd ..
+ 
+ # combine htslib
+@@ -41,28 +57,20 @@ git clone https://github.com/samtools/htslib.git
+ cd htslib
+ git checkout 1.9
+ #git submodule update --init --recursive
+-autoreconf -i
+-./configure
+-make -j4
+-cp libhts.a ../lib/
++autoreconf -if
++./configure --enable-libcurl --enable-plugins \
++	LDFLAGS="-L${PREFIX}/lib -Wl,-R${PREFIX}/lib" \
++	CPPFLAGS="-I${PREFIX}/include"
++make -j${CPU_COUNT}
++cp -f libhts.a ../lib/
+ 
+ cd ..
+ 
+-make
+-
+-#clean htslib and gperftools and boost libraries
+-rm -r boost_1_70_0/stage
+-
+-chmod -R 755 gperftools
+-rm -r gperftools
+-
+-chmod -R 755 htslib
+-rm -r htslib
+-
+-
+-
+-
+-
+-
+-
++CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" \
++    CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
++    LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
++    make -j"${CPU_COUNT}"
+ 
++rm -rf htslib
++rm -rf gperftools
++rm -rf boost-1.87.0.beta1
diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml
index 690bc876e5203..2ebcef1e3f1a7 100644
--- a/recipes/muse/meta.yaml
+++ b/recipes/muse/meta.yaml
@@ -1,31 +1,63 @@
+{% set name = "MuSE" %}
+{% set version = "2.1.2" %}
+{% set sha256 = "48df7ec3f64244400243163b48eb658105854b7b0d6287af98242dd89f396f59" %}
+
 package:
-  name: muse
-  version: 1.0.rc
+  name: {{ name|lower }}
+  version: {{ version }}
 
 source:
-  md5: c63fdb48c041f6f9545879f1a7e4da58
-  url: https://github.com/danielfan/MuSE/archive/v1.0-rc.tar.gz
+- url: https://github.com/wwylab/MuSE/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
   patches:
-    - 0001-add-LDFLAGS.patch
+    - 0001-Makefile.patch
+    - fix-install_muse.sh.patch
+    - version.patch
+- url: https://github.com/boostorg/boost/releases/download/boost-1.87.0.beta1/boost-1.87.0.beta1-b2-nodocs.tar.gz
+  sha256: f12e906fde4c9d04d88c3aa821f00501817a37503441cbca8ce7852a2194aeb0
+  folder: boost-1.87.0.beta1
 
 build:
-  number: 8
+  number: 2
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('muse', max_pin="x") }}
 
 requirements:
   build:
-    - make
     - {{ compiler('cxx') }}
-    - {{ compiler('c') }}
+    - make
+    - autoconf
+    - automake
+    - libtool
   host:
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
+    - libcurl
+    - icu
+    - bzip2
+    - xz
     - zlib
   run:
-    - zlib
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
 
 test:
   commands:
-    - MuSE 2>&1 | grep Version > /dev/null
+    - 'MuSE 2>&1 | grep "Version"'
 
 about:
-  home: "http://bioinformatics.mdanderson.org/main/MuSE"
-  license: "https://github.com/danielfan/MuSE/blob/master/LICENSE"
-  summary: Somatic point mutation caller
+  home: "https://bioinformatics.mdanderson.org/public-software/muse"
+  license: "GPL-2.0-or-later"
+  license_family: GPL
+  license_file: "LICENSE"
+  summary: "An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples."
+  doc_url: "https://github.com/wwylab/MuSE/blob/v{{ version }}/README.md"
+  dev_url: "https://github.com/wwylab/MuSE"
+
+extra:
+  identifiers:
+    - doi:10.1101/gr.278456.123
+    - doi:10.1186/s13059-016-1029-6
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/muse/version.patch b/recipes/muse/version.patch
new file mode 100644
index 0000000000000..0b826335c5820
--- /dev/null
+++ b/recipes/muse/version.patch
@@ -0,0 +1,32 @@
+diff --git a/src/main_muse.cpp b/src/main_muse.cpp
+old mode 100755
+new mode 100644
+index c2b7ef6..d8ac21d
+--- a/src/main_muse.cpp
++++ b/src/main_muse.cpp
+@@ -362,15 +362,19 @@ int main(int argc, char* argv[]){
+     if(argc < 2)
+         return usage();
+ 
+-	if(strcmp(argv[1], "call") == 0){
++    if(strcmp(argv[1], "call") == 0){
+         get_MuseCallOpts(argc, argv);
+-	}
+-	else if(strcmp(argv[1], "sump") == 0) {
+-		get_MuseSumpOpts(argc-1, argv+1);
+-	}
++    }
++    else if(strcmp(argv[1], "sump") == 0) {
++        get_MuseSumpOpts(argc-1, argv+1);
++    }
++    else if (strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "--v") == 0) {
++        fprintf(stdout, "MuSE %s\n", Version.c_str());
++        return 0; // Successfully printed version
++    } 
+     else {
+         fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+         return 1;
+     }
+-	return 0;
++    return 0;
+ }
diff --git a/recipes/mutyper/meta.yaml b/recipes/mutyper/meta.yaml
new file mode 100644
index 0000000000000..0dd97d2454a96
--- /dev/null
+++ b/recipes/mutyper/meta.yaml
@@ -0,0 +1,60 @@
+{% set name = "mutyper" %}
+{% set version = "1.0.2" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: 28712852efd635440698ea632ecc4252a0023966d2e428953f08498e889f04e3
+
+build:
+  run_exports:
+    - {{ pin_subpackage('mutyper', max_pin="x") }}
+  number: 1
+  skip: True  # [py < 38 or py > 311]
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
+  entry_points:
+    - mutyper=mutyper.cli:main
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - make
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - pandas
+    - cyvcf2 >=0.30.15
+    - pyfaidx
+    - biopython
+    - pyliftover
+
+test:
+  imports:
+    - mutyper
+  commands:
+    - mutyper --help
+    - mutyper ancestor --help
+    - mutyper variants --help
+    - mutyper targets --help
+    - mutyper spectra --help
+    - mutyper ksfs --help
+
+about:
+  home: "https://github.com/harrispopgen/mutyper"
+  license: "MIT"
+  license_family: "MIT"
+  license_file: "LICENSE"
+  summary: "A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs."
+  doc_url: "https://harrispopgen.github.io/mutyper"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
\ No newline at end of file
diff --git a/recipes/mvip/meta.yaml b/recipes/mvip/meta.yaml
index 613e0bbbd9bb8..ca8a853d773e4 100644
--- a/recipes/mvip/meta.yaml
+++ b/recipes/mvip/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mvip" %}
-{% set version = "1.1.4" %}
+{% set version = "1.1.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,12 +7,14 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: ca056513e45714c5988aba02572aa179055b17100a0c4192a274324a02e8cc46
+  sha256: 61f1c5de4bd74b8453eaad5bdd8c95ad46c6b7e10a13977e3734696696785b42
 
 build:
-  number: 0
+  number: 1
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps -vv"
+  entry_points:
+    - mvip = mvip.cli:cli
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage("mvip", max_pin="x") }}
 
@@ -20,7 +22,7 @@ requirements:
   host:
     - python >=3.7
     - pip
-    - flit
+    - flit-core
   run:
     - python >=3.7
     - tqdm
diff --git a/recipes/mycotools/meta.yaml b/recipes/mycotools/meta.yaml
index e67804eb73353..caf0051fa4a26 100644
--- a/recipes/mycotools/meta.yaml
+++ b/recipes/mycotools/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mycotools" %}
-{% set version = "0.32.3" %}
+{% set version = "0.32.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mycotools-{{ version }}.tar.gz
-  sha256: 598caafca226eeb485759c88ff9ab3c05c0d9803e900c2cea7c191cb4df7c77e 
+  sha256: e886c43b5faffb4d788a23f6016d146724c85ec8c9fc57ab3e0fcc24840c30b7 
 
 build:
   number: 0
diff --git a/recipes/mzpaf/LICENSE b/recipes/mzpaf/LICENSE
new file mode 100644
index 0000000000000..0e259d42c9967
--- /dev/null
+++ b/recipes/mzpaf/LICENSE
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
+
+CC0 1.0 Universal
+
+    CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+    LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
+    ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS
+    INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES
+    REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
+    PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
+    THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
+    HEREUNDER.
+
+Statement of Purpose
+
+The laws of most jurisdictions throughout the world automatically confer
+exclusive Copyright and Related Rights (defined below) upon the creator
+and subsequent owner(s) (each and all, an "owner") of an original work of
+authorship and/or a database (each, a "Work").
+
+Certain owners wish to permanently relinquish those rights to a Work for
+the purpose of contributing to a commons of creative, cultural and
+scientific works ("Commons") that the public can reliably and without fear
+of later claims of infringement build upon, modify, incorporate in other
+works, reuse and redistribute as freely as possible in any form whatsoever
+and for any purposes, including without limitation commercial purposes.
+These owners may contribute to the Commons to promote the ideal of a free
+culture and the further production of creative, cultural and scientific
+works, or to gain reputation or greater distribution for their Work in
+part through the use and efforts of others.
+
+For these and/or other purposes and motivations, and without any
+expectation of additional consideration or compensation, the person
+associating CC0 with a Work (the "Affirmer"), to the extent that he or she
+is an owner of Copyright and Related Rights in the Work, voluntarily
+elects to apply CC0 to the Work and publicly distribute the Work under its
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+Work and the meaning and intended legal effect of CC0 on those rights.
+
+1. Copyright and Related Rights. A Work made available under CC0 may be
+protected by copyright and related or neighboring rights ("Copyright and
+Related Rights"). Copyright and Related Rights include, but are not
+limited to, the following:
+
+  i. the right to reproduce, adapt, distribute, perform, display,
+     communicate, and translate a Work;
+ ii. moral rights retained by the original author(s) and/or performer(s);
+iii. publicity and privacy rights pertaining to a person's image or
+     likeness depicted in a Work;
+ iv. rights protecting against unfair competition in regards to a Work,
+     subject to the limitations in paragraph 4(a), below;
+  v. rights protecting the extraction, dissemination, use and reuse of data
+     in a Work;
+ vi. database rights (such as those arising under Directive 96/9/EC of the
+     European Parliament and of the Council of 11 March 1996 on the legal
+     protection of databases, and under any national implementation
+     thereof, including any amended or successor version of such
+     directive); and
+vii. other similar, equivalent or corresponding rights throughout the
+     world based on applicable law or treaty, and any national
+     implementations thereof.
+
+2. Waiver. To the greatest extent permitted by, but not in contravention
+of, applicable law, Affirmer hereby overtly, fully, permanently,
+irrevocably and unconditionally waives, abandons, and surrenders all of
+Affirmer's Copyright and Related Rights and associated claims and causes
+of action, whether now known or unknown (including existing as well as
+future claims and causes of action), in the Work (i) in all territories
+worldwide, (ii) for the maximum duration provided by applicable law or
+treaty (including future time extensions), (iii) in any current or future
+medium and for any number of copies, and (iv) for any purpose whatsoever,
+including without limitation commercial, advertising or promotional
+purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each
+member of the public at large and to the detriment of Affirmer's heirs and
+successors, fully intending that such Waiver shall not be subject to
+revocation, rescission, cancellation, termination, or any other legal or
+equitable action to disrupt the quiet enjoyment of the Work by the public
+as contemplated by Affirmer's express Statement of Purpose.
+
+3. Public License Fallback. Should any part of the Waiver for any reason
+be judged legally invalid or ineffective under applicable law, then the
+Waiver shall be preserved to the maximum extent permitted taking into
+account Affirmer's express Statement of Purpose. In addition, to the
+extent the Waiver is so judged Affirmer hereby grants to each affected
+person a royalty-free, non transferable, non sublicensable, non exclusive,
+irrevocable and unconditional license to exercise Affirmer's Copyright and
+Related Rights in the Work (i) in all territories worldwide, (ii) for the
+maximum duration provided by applicable law or treaty (including future
+time extensions), (iii) in any current or future medium and for any number
+of copies, and (iv) for any purpose whatsoever, including without
+limitation commercial, advertising or promotional purposes (the
+"License"). The License shall be deemed effective as of the date CC0 was
+applied by Affirmer to the Work. Should any part of the License for any
+reason be judged legally invalid or ineffective under applicable law, such
+partial invalidity or ineffectiveness shall not invalidate the remainder
+of the License, and in such case Affirmer hereby affirms that he or she
+will not (i) exercise any of his or her remaining Copyright and Related
+Rights in the Work or (ii) assert any associated claims and causes of
+action with respect to the Work, in either case contrary to Affirmer's
+express Statement of Purpose.
+
+4. Limitations and Disclaimers.
+
+ a. No trademark or patent rights held by Affirmer are waived, abandoned,
+    surrendered, licensed or otherwise affected by this document.
+ b. Affirmer offers the Work as-is and makes no representations or
+    warranties of any kind concerning the Work, express, implied,
+    statutory or otherwise, including without limitation warranties of
+    title, merchantability, fitness for a particular purpose, non
+    infringement, or the absence of latent or other defects, accuracy, or
+    the present or absence of errors, whether or not discoverable, all to
+    the greatest extent permissible under applicable law.
+ c. Affirmer disclaims responsibility for clearing rights of other persons
+    that may apply to the Work or any use thereof, including without
+    limitation any person's Copyright and Related Rights in the Work.
+    Further, Affirmer disclaims responsibility for obtaining any necessary
+    consents, permissions or other rights required for any use of the
+    Work.
+ d. Affirmer understands and acknowledges that Creative Commons is not a
+    party to this document and has no duty or obligation with respect to
+    this CC0 or use of the Work.
diff --git a/recipes/mzpaf/meta.yaml b/recipes/mzpaf/meta.yaml
new file mode 100644
index 0000000000000..a9af7c4e44c90
--- /dev/null
+++ b/recipes/mzpaf/meta.yaml
@@ -0,0 +1,46 @@
+{% set name = "mzpaf" %}
+{% set version = "0.2.0a0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mzpaf-{{ version }}.tar.gz
+  sha256: dbabb1fe8234a5587b451407c44a3c6bb60e1cfbec48978952708b231b45f6d5
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('mzpaf', max_pin="x") }}
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - pyteomics
+
+test:
+  imports:
+    - mzpaf
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://github.com/HUPO-PSI/mzPAF
+  summary: HUPO-PSI Peptide peak annotation format
+  license: CC-BY-1.0
+  license_family: CC
+  license_file: LICENSE
+  dev_url: https://github.com/HUPO-PSI/mzPAF/implementations/python
+  doc_url: https://mzpaf.readthedocs.io/en/latest/
+
+extra:
+  recipe-maintainers:
+    - hechth
diff --git a/recipes/nanoqc/build.sh b/recipes/nanoqc/build.sh
deleted file mode 100644
index 3786386a73c83..0000000000000
--- a/recipes/nanoqc/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt
diff --git a/recipes/nanoqc/meta.yaml b/recipes/nanoqc/meta.yaml
index cdeb02d430944..b46e08dd930b5 100644
--- a/recipes/nanoqc/meta.yaml
+++ b/recipes/nanoqc/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.9.4" %}
+{% set version = "0.10.0" %}
 
 package:
   name: nanoqc
@@ -6,33 +6,42 @@ package:
 
 source:
   url: https://pypi.io/packages/source/n/nanoqc/nanoQC-{{ version }}.tar.gz
-  sha256: 05685656138cbaf099b18831d1ceeaca93faf3399881cc2efda44c04d3b316e3
+  sha256: 5e55b8b244ce7cfb0673fc804f5a0c16dcfc4a03f9aaf84c75b8117d3c3817a6
 
 build:
   entry_points:
     - nanoQC=nanoQC.nanoQC:main
   number: 0
   noarch: python
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  run_exports:
+    - {{ pin_subpackage('nanoqc', max_pin="x.x") }}
 
 requirements:
   host:
     - python >=3
+    - pip
     - setuptools
   run:
     - python >=3
-    - bokeh
+    - plotly >=5.4.0
     - numpy
     - biopython
 
 test:
   imports:
     - nanoQC
-
   commands:
     - nanoQC --help
 
 about:
   home: https://github.com/wdecoster/nanoQC
-  license: MIT License
-  summary: 'Create fastQC-like plots for Oxford Nanopore sequencing data'
-  license_family: MIT
+  license: GPL-3.0-or-later
+  summary: 'Create fastQC-like plots for Oxford Nanopore sequencing data.'
+  license_family: GPL3
+  dev_url: https://github.com/wdecoster/nanoQC
+  license_file: LICENSE
+
+extra:
+  identifiers:
+    - doi:10.1093/bioinformatics/bty149
diff --git a/recipes/ncbi-amrfinderplus/build.sh b/recipes/ncbi-amrfinderplus/build.sh
index 67becc82bc7d9..417e5c7226118 100755
--- a/recipes/ncbi-amrfinderplus/build.sh
+++ b/recipes/ncbi-amrfinderplus/build.sh
@@ -1,21 +1,27 @@
 #!/bin/bash
 
 echo "DEBUGGING environment info because PREFIX did not appear to be set"
-echo "PREFIX=$PREFIX    CONDA_PREFIX=$CONDA_PREFIX"
+echo "PREFIX=$PREFIX CONDA_PREFIX=$CONDA_PREFIX"
 echo "PREFIX =" $PREFIX CONDA_PREFIX = $CONDA_PREFIX BUILD_PREFIX = $BUILD_PREFIX
 echo $PREFIX
 
-# test fix for version 3.9.8
-# move patch to meta.yaml
-# patch < patch.3.9.8
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 
 # fix error because of gnu++17 features. Suggested by https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
-CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY"
 
-# note that for version 3.7 the make command should be:
-make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX="$PREFIX" CONDA_DB_DIR="$CONDA_PREFIX/share/amrfinderplus/data"
+# Get StxTyper source as well
+git submodule update --init
 
-#echo "make CXX=\"$CXX $LDFLAGS\" CPPFLAGS=\"$CXXFLAGS\" PREFIX=\"$PREFIX\" DEFAULT_DB_DIR=\"$PREFIX/share/amrfinderplus/data\""
+make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS -I${PREFIX}/include" PREFIX="$PREFIX" DEFAULT_DB_DIR="${PREFIX}/share/amrfinderplus/data" -j"${CPU_COUNT}"
 
-#make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX=$PREFIX DEFAULT_DB_DIR="$PREFIX/share/amrfinderplus/data"
-make install bindir=$PREFIX/bin
+make install INSTALL_DIR="$PREFIX/bin"
+
+### Temporary bug fix for issue with Makefile. These lines have been added to the makefile
+# for future releases, so remove after version 4.0.3
+if [ ! -e "$PREFIX/bin/stx/stxtyper" ]
+then
+    mkdir "$PREFIX/bin/stx"
+    ln -s ../stxtyper "$PREFIX/bin/stx/stxtyper"
+fi
+# end bug fix
diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml
index 1e8066c9c665a..3ee0696cc7bec 100644
--- a/recipes/ncbi-amrfinderplus/meta.yaml
+++ b/recipes/ncbi-amrfinderplus/meta.yaml
@@ -1,12 +1,13 @@
-{% set version = "3.12.8" %}
-{% set sha256 = "a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0" %}
+{% set version = "4.0.3" %}
+{% set sha256 = "e3007c074ac77e410914691b38d7eaaaaf2cda6c" %}
 
 package:
   name: ncbi-amrfinderplus
   version: {{ version }}
 
 source:
-  url: https://github.com/ncbi/amr/archive/amrfinder_v{{ version }}.tar.gz
+  git_url: https://github.com/ncbi/amr.git
+  git_rev: amrfinder_v{{ version }}
   sha256: {{ sha256 }}
 
 build:
@@ -16,15 +17,15 @@ build:
 
 requirements:
   build:
+    - git
     - make
     - {{ compiler('cxx') }}
-  host:
     - coreutils
+  host:
     - libcurl
   run:
     - blast >=2.9
     - hmmer >=3.2
-    - libcurl
     - curl
 
 test:
@@ -47,10 +48,10 @@ test:
         diff test_both.expected test_both.got
 
 about:
-  home: https://github.com/ncbi/amr/wiki
+  home: https://github.com/ncbi/amr
   license: Public Domain
   license_file: LICENSE
-  summary: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
+  summary: "AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences."
   description: |
       This software and the accompanying database are designed to
       find acquired antimicrobial resistance genes in bacterial protein or
@@ -58,9 +59,13 @@ about:
       AMRFinderPlus we have added select members of additional classes of genes
       such as virulence factors, biocide, heat, acid, and metal resistance genes.
   doc_url: https://github.com/ncbi/amr/wiki
+  dev_url: https://github.com/ncbi/amr
 
 extra:
   recipe-maintainers:
     - evolarjun
   identifiers:
     - doi:10.1038/s41598-021-91456-0
+  skip-lints:
+    - uses_vcs_url
+    - missing_hash
diff --git a/recipes/ncbi-stxtyper/meta.yaml b/recipes/ncbi-stxtyper/meta.yaml
index df64553ebb334..875aafe2edabe 100644
--- a/recipes/ncbi-stxtyper/meta.yaml
+++ b/recipes/ncbi-stxtyper/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.25" %}
-{% set sha256 = "adc734340c6a10f1bfc34ca637197e93e1515d0231bd023b33ce4c07aab9578e" %}
+{% set version = "1.0.27" %}
+{% set sha256 = "07966b8c6aa909bb1201c098d3c72eaf067e7b11de1a2ab0f89fb2cf52820382" %}
 
 package:
   name: ncbi-stxtyper
diff --git a/recipes/neat/meta.yaml b/recipes/neat/meta.yaml
index 575258cfa9ae2..8bcce42c93dd2 100644
--- a/recipes/neat/meta.yaml
+++ b/recipes/neat/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "NEAT" %}
-{% set version = "4.2.6" %}
+{% set version = "4.2.7" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/ncsa/{{ name }}/archive/{{ version }}.tar.gz
-  sha256: 04348e0539b6259ebd4a48a2c60325f04ee0b49323243ceedd675655ba9f94d6
+  sha256: e53149690d9d9996c3d287d496d63aff926f60244d7237dd103da06435ef7001
   
 
 build:
diff --git a/recipes/neptune-signature/meta.yaml b/recipes/neptune-signature/meta.yaml
new file mode 100644
index 0000000000000..f8ff10af29a38
--- /dev/null
+++ b/recipes/neptune-signature/meta.yaml
@@ -0,0 +1,43 @@
+{% set name = "neptune-signature" %}
+{% set version = "2.0.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/phac-nml/neptune/archive/refs/tags/v{{ version }}.tar.gz
+  md5: 3fcce144d67c74c7921d3b9e36aedacb
+
+build:
+  noarch: python
+  number: 0
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  entry_points:
+    - neptune = neptune.Neptune:main
+  run_exports:
+    - {{ pin_subpackage('neptune-signature', max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - setuptools
+  run:
+    - python >=3.10
+    - numpy
+    - scipy
+    - biopython
+    - blast
+
+test:
+  commands:
+    - neptune -h 2>&1 | grep 'usage' > /dev/null
+
+about:
+  home: https://github.com/phac-nml/neptune
+  license: Apache-2.0
+  license_family: APACHE
+  license_file: LICENSE.txt
+  summary: 'Neptune: Genomic Signature Discovery'
+  dev_url: https://github.com/phac-nml/neptune
diff --git a/recipes/neptune/post-link.sh b/recipes/neptune-signature/post-link.sh
similarity index 100%
rename from recipes/neptune/post-link.sh
rename to recipes/neptune-signature/post-link.sh
diff --git a/recipes/neptune/meta.yaml b/recipes/neptune/meta.yaml
deleted file mode 100644
index 79a33a356bda2..0000000000000
--- a/recipes/neptune/meta.yaml
+++ /dev/null
@@ -1,33 +0,0 @@
-package:
-  name: neptune
-  version: 1.2.5
-
-source:
-  url: https://github.com/phac-nml/neptune/archive/v1.2.5.tar.gz
-  md5: ed48846deffefe25784c9f8b7db2de6e
-
-build:
-  noarch: python
-  number: 3
-  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
-
-requirements:
-  host:
-    - python <3
-    - pip
-  run:
-    - python <3
-    - drmaa
-    - numpy
-    - scipy
-    - biopython
-    - blast
-
-test:
-  commands:
-    - neptune -h 2>&1 | grep 'usage' > /dev/null
-
-about:
-  home: https://github.com/phac-nml/neptune
-  license: Apache 2.0
-  summary: 'Neptune: Genomic Signature Discovery'
diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml
index aca422e6b7be0..f2c61476732ef 100644
--- a/recipes/nextclade/meta.yaml
+++ b/recipes/nextclade/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "nextclade" %}
-{% set version = "3.9.0" %}
+{% set version = "3.9.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,13 +7,13 @@ package:
 
 source:
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu   # [linux64]
-    sha256: e42aaed0854ecdc5b8e8523c65e2388c57817a43e2725e0d98f959dd9c820111                                           # [linux64]
+    sha256: 3a9d20c8ac8f6c91902a58fa1d0a49f8d37b6590571a72675d5120bf5895cd3a                                           # [linux64]
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-unknown-linux-gnu  # [aarch64]
-    sha256: f5a08e8bf33a9a6d68407a90fca6cbc77928027b247a1648155b51ab3fd7d680                                           # [aarch64]
+    sha256: ed78dc9a5e328b1ee4837ee9cf140c86128624cfa8546fab949dd3457ed5a624                                           # [aarch64]
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin        # [osx and x86_64]
-    sha256: 5570cf7b59876bb62bd4444112e304cbe60c28ce5e5a3d168a62f401953b9149                                           # [osx and x86_64]
+    sha256: 038130b888684c1941eb784bc63865a2287f723ed427c227cbd55c9118ac12f1                                           # [osx and x86_64]
   - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin       # [osx and arm64]
-    sha256: e328400872efe15a761bc012f6c8144d7b50f0775bff95b77ce4ed816ed239c3                                           # [osx and arm64]
+    sha256: 67c36e657a228357f230274f7deb9bccdde45285ac289ded9e300b575fd33023                                           # [osx and arm64]
 
 build:
   number: 0
diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml
index 923a54a387c81..e6c8bb30f6e99 100644
--- a/recipes/nextflow/meta.yaml
+++ b/recipes/nextflow/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.04.4" %}
-{% set sha256 = "03bf3ad5018ce2eac7bf7836140475a1fda529d800503aa39565fc6c77a40bfd" %}
+{% set version = "24.10.1" %}
+{% set sha256 = "fd034b2d854010c7dfb7ae1b54d29209f45a2735504fa9c34becac44201f9e75" %}
 
 package:
   name: nextflow
diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml
index 88f19b53e3497..0dffea387c08a 100644
--- a/recipes/nextstrain-cli/meta.yaml
+++ b/recipes/nextstrain-cli/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "8.5.3" %}
+{% set version = "8.5.4" %}
 
 package:
   name: nextstrain-cli
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain_cli-{{ version }}.tar.gz
-  sha256: 5401fd3f1b60479cb3b8c0519917fa5df43fdaddd6007e158888283a5c872428
+  sha256: 3aa6c66d038d82de0c3bff2eb1b358599a9efc3f5f446eb523d3c9696aa72854
 
 build:
   number: 0
@@ -21,7 +21,7 @@ requirements:
   host:
     - python >=3.8
     - pip
-
+    - setuptools
   run:
     - python >=3.8
     - docutils
diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml
index b546fdafe2ee0..c518daa0d9876 100644
--- a/recipes/nf-core/meta.yaml
+++ b/recipes/nf-core/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   script: "touch requirements.txt && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - nf-core=nf_core.__main__:run_nf_core
@@ -50,6 +50,7 @@ requirements:
     - ruamel.yaml
     - tabulate
     - textual ==0.71.0
+    - linkify-it-py >=1,<3
     - trogon
     - nextflow >=24.04.4
     - nf-test
diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml
index 13b0e97045e44..77029807c9246 100644
--- a/recipes/nf-test/meta.yaml
+++ b/recipes/nf-test/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.9.0" %}
+{% set version = "0.9.2" %}
 
 
 package:
@@ -13,7 +13,7 @@ build:
 
 source:
   url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz
-  sha256: 3e123ceba36b6e890cb12ad4e98792bf4dd2d7e55c36a549b28708df13df0dc7
+  sha256: bfb2e06df29d4ef41b31cb356a374a99242bef8d98434b8be3037bf6b3d5d4da
 
 requirements:
   host:
diff --git a/recipes/nordic/LICENSE b/recipes/nordic/LICENSE
index 08f13e3f57263..4eb2c55867eb9 100644
--- a/recipes/nordic/LICENSE
+++ b/recipes/nordic/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright © 2023 Clémence Réda
+Copyright © 2023-2024 Clémence Réda
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
\ No newline at end of file
+SOFTWARE.
diff --git a/recipes/nordic/build.sh b/recipes/nordic/build.sh
index 887d0d743b9ae..bb4fb76f5572d 100644
--- a/recipes/nordic/build.sh
+++ b/recipes/nordic/build.sh
@@ -18,6 +18,6 @@ cd ${SRC_DIR}"/bonesis-0.5.7/"
 
 "${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv
 
-cd ${SRC_DIR}"/NORDic-2.4.4/"
+cd ${SRC_DIR}"/NORDic-2.5.0/"
 
-"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv
\ No newline at end of file
+"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv
diff --git a/recipes/nordic/meta.yaml b/recipes/nordic/meta.yaml
index 92b2c630cb9fb..9055506163792 100644
--- a/recipes/nordic/meta.yaml
+++ b/recipes/nordic/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "nordic" %}
 {% set ucname = "NORDic" %}
-{% set version = "2.4.4" %}
+{% set version = "2.5.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -8,7 +8,7 @@ package:
 
 source:
   - url: "https://github.com/sysbio-curie/MaBoSS-env-2.0/archive/refs/heads/master.tar.gz"
-    sha256: 5952813f3c38e10bbc2f0d4bbb91936bc738c47bcf9941da298cea3bfb753d19
+    sha256: 0dfad5312384af15dc02a04944f966b8a303d6e2e35a795298265872fb1b4b06
     folder: "MaBoSS-2.0"
   - url: "https://files.pythonhosted.org/packages/f8/ff/4b5fd3c1968c99d59972da395c926be65e601d7306602ec6cc39c418e24f/mpbn-3.3.tar.gz"
     sha256: 8831531216d94616e7303925c4571bfc40f5d750b33b69d0155edc8404223831
@@ -16,12 +16,12 @@ source:
   - url: "https://files.pythonhosted.org/packages/fb/c9/8fa247a95e6d6b7c650f2d4f879e6027fbb9eeca2aaba8d97f999bfadcfd/bonesis-0.5.7.tar.gz"
     sha256: 0ccef4daa089347f7fd4ac8355f7ab3a8eecf63757e6bf000cc66b7c54bfdb0a
     folder: "bonesis-0.5.7"
-  - url: "https://files.pythonhosted.org/packages/f3/9b/817e2004a1e7f798b5f361dc04d28d7b99657cc469f26abde2d9095fd1e4/{{ ucname }}-{{ version }}.tar.gz"
-    sha256: 01a5d9fbc95c603e46e916a734dd6eecdc20dff914d36c91009337d62488d525
+  - url: "https://files.pythonhosted.org/packages/57/f6/fa7e85548a167889343cedc75c3fc1359f9483ce199f9662d5b563953d9c/{{ name }}-{{ version }}.tar.gz"
+    sha256: a8791602c35a7cf8424458d532ef7096900d25e2b2e1fec1afea7cdd1a218148
     folder: "{{ ucname }}-{{ version }}"
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 38]
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
@@ -41,8 +41,8 @@ requirements:
     - scikit-learn
     - graphviz
     - matplotlib-base
-    - numpy >=1.22.4
-    - omnipath >=1.0.6
+    - numpy >=1.22.4,<2.0.0
+    - omnipath
     - openpyxl >=3.0.10
     - pandas >=1.5.1
     - qnorm >=0.5.1
@@ -57,8 +57,8 @@ requirements:
     - scikit-learn
     - graphviz
     - matplotlib-base
-    - numpy >=1.22.4
-    - omnipath >=1.0.6
+    - numpy >=1.22.4,<2.0.0
+    - omnipath
     - openpyxl >=3.0.10
     - pandas >=1.5.1
     - qnorm >=0.5.1
diff --git a/recipes/notramp/meta.yaml b/recipes/notramp/meta.yaml
index ac4aeed99c8ad..7525c96c6621b 100644
--- a/recipes/notramp/meta.yaml
+++ b/recipes/notramp/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "notramp" %}
-{% set version = "1.0.5" %}
+{% set version = "1.1.7" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: de54fae8cc4c66dcd8abc94ae88957aa533cb8e2e6764e847afa26fbe4b36ec9
+  sha256: 1f6dd890d43943ef934f206ea9fe873b334eef1706fa8eee0fdb609eb8b5bb71
 
 build:
   number: 0
@@ -15,6 +15,8 @@ build:
     - notramp = notramp.notramp_main:run_notramp
   script: "{{ PYTHON }} -m pip install . -vv"
   noarch: python
+  run_exports:
+    - {{ pin_subpackage("notramp", max_pin="x") }}
 
 requirements:
   host:
@@ -36,9 +38,14 @@ about:
   license: BSD-2
   license_family: BSD
   license_file: LICENSE
-  summary: "Normalization and Trimming of long-read (ONT, PB) amplicon sequencing data"
+  summary: "Super-fast Normalization and Trimming for Amplicon Sequencing Data (Long- and Short-read)"
+  description: "NoTrAmp is a Tool for super fast trimming and read-depth normalization of amplicon reads. It is designed to be used in amplicon-tiling panels\
+    \ (or similar multiplexed amplicon sequencing approaches) to cap coverage of each amplicon (if desired) and to trim amplicons to their appropriate length\
+    \ removing barcodes, adpaters and primers (if desired) in a single clipping step.\n\nNoTrAmp is suitable for use with both long (e.g. ONT/PacBio) and short\
+    \ reads (e.g Illumina). When using reads that are significantly shorter than amplicon sizes, you should adjust the minimum required alignment length\
+    \ using the --set_min_len argument.\n\nSee the projects [home](https://github.com/simakro/NoTrAmp) for usage and additional documentation."
   doc_url: "https://github.com/simakro/NoTrAmp/blob/main/README.md"
 
 extra:
   recipe-maintainers:
-    - 74452164
+    - simakro (simon.magin)
diff --git a/recipes/ntstat/build.sh b/recipes/ntstat/build.sh
new file mode 100644
index 0000000000000..4fa9d5a8b56ec
--- /dev/null
+++ b/recipes/ntstat/build.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+
+meson setup --buildtype release --prefix=$PREFIX build
+meson install -C build
diff --git a/recipes/ntstat/meta.yaml b/recipes/ntstat/meta.yaml
new file mode 100644
index 0000000000000..1a00b3d7d9d77
--- /dev/null
+++ b/recipes/ntstat/meta.yaml
@@ -0,0 +1,50 @@
+{% set version = "1.0.1" %}
+
+package:
+  name: ntstat
+  version: {{ version }}
+
+source:
+  url: https://github.com/bcgsc/ntStat/releases/download/v{{ version }}/ntStat-{{ version }}.tar.gz
+  sha256: 4cf215c15c2b1035c40a453372e39c3a87c37c4b09b5716ef5a07bba96f9cb99
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('ntstat', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - meson
+    - meson-python
+    - cmake
+    - python
+  host:
+    - python
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
+    - btllib >=1.7.2
+    - cpp-argparse
+    - cpp-tabulate
+    - indicators
+    - pybind11
+  run:
+    - python
+    - ntcard
+    - btllib >=1.7.2
+    - matplotlib-base
+    - numpy
+    - scipy
+    - tabulate
+
+test:
+  commands:
+    - ntstat --version
+    - ntstat count --help
+
+about:
+  home: https://github.com/bcgsc/ntStat
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: 'a toolkit for statistical analysis of k-mer frequency and depth'
diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml
index 130360639928b..1d4c106c71408 100644
--- a/recipes/oakvar/meta.yaml
+++ b/recipes/oakvar/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.11.14" %}
-{% set sha256 = "241caad69d828731603d540c0881c3c87422aea470061d3b7d4c9bda924034ae" %}
+{% set version = "2.12.4" %}
+{% set sha256 = "f0d9e783e56a29ca41ff83016e5f2fe01d17940d571e7f0da54bdb4b19ae3427" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/oarfish/build.sh b/recipes/oarfish/build.sh
index 580d388d2cf18..fc13873f768bd 100644
--- a/recipes/oarfish/build.sh
+++ b/recipes/oarfish/build.sh
@@ -2,5 +2,9 @@
 
 set -xe
 
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain stable --profile=minimal -y
+export PATH="$HOME/.cargo/bin:$PATH"
+
+
 # build statically linked binary with Rust
-RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path .
+RUST_BACKTRACE=1 RUSTFLAGS="-C linker=$CC" cargo install --verbose --root $PREFIX --path .
diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml
index 41e7e84dcf8ce..68d8da9dc8667 100644
--- a/recipes/oarfish/meta.yaml
+++ b/recipes/oarfish/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.6.2" %}
+{% set version = "0.6.4" %}
 
 package:
   name: oarfish
@@ -11,13 +11,15 @@ build:
     
 source:
   url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz
-  sha256: 78b523fc459fec5ae3680395925862b4d367bd56d051120f28c689dd387e1758
+  sha256: 56c900b5d0ffcfee875e414513d9a638b1f936c4e31748b459b9e1b649fce5dd
 
 requirements:
   build:
     - make
-    - {{ compiler('rust') }} 
+    #- rust >=1.82.0
+    #- {{ compiler('rust') }} >=1.82.0
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
     - zlib
   run:
diff --git a/recipes/omamer/meta.yaml b/recipes/omamer/meta.yaml
index 2efe270cd63c8..d3fa8987df269 100644
--- a/recipes/omamer/meta.yaml
+++ b/recipes/omamer/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "omamer" %}
-{% set version = "2.0.4" %}
+{% set version = "2.0.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,28 +7,29 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omamer-{{ version }}.tar.gz
-  sha256: 292a9bc0534452f0480144620a57135a498b5e54cb252f1ee6f93a816037e3e0
+  sha256: eb1e62703c6b68a345880294ddac73721d753364dbde4f3a75f17d8a13a2d0da
 
 build:
   entry_points:
     - omamer = omamer.main:main
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
   number: 0
   run_exports:
-    - {{ pin_subpackage(name, max_pin="x.x") }}
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - alive-progress
     - biopython
     - ete3
     - numba
-    - numpy
+    - numpy <2
     - pandas >2.0.0
     - property-manager
     - rmath4
diff --git a/recipes/orthodb/build.sh b/recipes/orthodb/build.sh
new file mode 100644
index 0000000000000..5b807e129ac0a
--- /dev/null
+++ b/recipes/orthodb/build.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+$PYTHON -m pip install . --no-deps --ignore-installed -vv
diff --git a/recipes/orthodb/meta.yaml b/recipes/orthodb/meta.yaml
new file mode 100644
index 0000000000000..144090650d1e4
--- /dev/null
+++ b/recipes/orthodb/meta.yaml
@@ -0,0 +1,56 @@
+{% set name = "orthodb" %}
+{% set version = "0.9.1" %}
+{% set sha256 = "366160d5924870b37b0e86456eaac667ae194745fe78e16ede25f29299e34870" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  noarch: python
+  run_exports:
+    - {{ pin_subpackage('orthodb', max_pin="x") }}
+
+source:
+  url: https://gitlab.com/ezlab/orthodb_py/-/archive/{{ version }}/orthodb_py-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+files:
+  - LICENSE
+
+requirements:
+  build:
+    - python >=3.7
+    - pip
+    - setuptools
+  host:
+    - python >=3.7
+    - pip
+    - setuptools
+  run:
+    - python >=3.7
+    - requests
+
+test:
+  commands:
+    - python -c 'import orthodb'
+    - python -c 'from orthodb import OdbAPI'
+
+about:
+  home: https://www.ezlab.org/orthodb_v12_userguide.html
+  license: GPL3
+  license_family: GPL3
+  license_file: LICENSE
+  summary: Interface to OrthoDB REST API.
+  description: Python interface to OrthoDB REST API with some additional functionality.
+  dev_url: https://gitlab.com/ezlab/orthodb_py
+  doc_url: https://www.ezlab.org/orthodb_v12_userguide.html#api
+
+extra:
+  identifiers:
+    - biotools:orthodb
+    - doi:10.1093/nar/gkac996
+    - PMID:36350662
+  recipe-maintainers:
+    - ftegenfe
diff --git a/recipes/pacu_snp/meta.yaml b/recipes/pacu_snp/meta.yaml
index 6798465c0519a..8c18219362599 100644
--- a/recipes/pacu_snp/meta.yaml
+++ b/recipes/pacu_snp/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.0.5" %}
+{% set version = "0.0.6" %}
 
 package:
   name: pacu_snp
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/p/pacu_snp/pacu_snp-{{ version }}.tar.gz
-  sha256: 68979d53d8a591351a3de4edcde38bb508a8fcf8a4b1878999c9e63c932ffeb6
+  sha256: 5ba982f196852e380a130897108bedf401a1a256fc1bd262a2ec3dac42cfd8d1
 
 build:
   noarch: python
diff --git a/recipes/palantir/meta.yaml b/recipes/palantir/meta.yaml
index 6bb03200b5f4c..6945a69eccdf6 100644
--- a/recipes/palantir/meta.yaml
+++ b/recipes/palantir/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "palantir" %}
-{% set version = "1.3.3" %}
+{% set version = "1.3.4" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 915bb802e01f282d309fab02062caa4e790535279c14f6c15823cdaa01ba7a56
+  sha256: 467aa9fbf9f6d2df2b3fe7ad148ad1675becf3682744b837b70941547bccbbb0
 
 build:
   number: 0
diff --git a/recipes/panacus/meta.yaml b/recipes/panacus/meta.yaml
index af5bddd58cb9b..fa4b81e48bfac 100644
--- a/recipes/panacus/meta.yaml
+++ b/recipes/panacus/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "panacus" %}
-{% set version = "0.2.4" %}
+{% set version = "0.2.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/marschall-lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: e4709c5e3e4b5c445789406a0ebf06a2052e24bc5fcc3b540cacf8064c2ab478
+  sha256: 7b4e4aee52528c569ad663d0fcd00bd42f221f29f93f0768f18c2ac2d3f0d769
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
diff --git a/recipes/panfeed/meta.yaml b/recipes/panfeed/meta.yaml
index 833ba2d123065..7e053b67e7b36 100644
--- a/recipes/panfeed/meta.yaml
+++ b/recipes/panfeed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.6.2" %}
+{% set version = "1.7.0" %}
 {% set name = "panfeed" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 71e6e97b29784396421b59511dbca27103acfe31a3f392324d4d0419179340be
+  sha256: dd75396f5fd6cbb27163559f813ea7c2802e2d4444271a2e30190727785811e2
 
 build:
   entry_points:
diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml
index 8c9f30d0327ae..054c230131bfd 100644
--- a/recipes/pango-designation/meta.yaml
+++ b/recipes/pango-designation/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.30" %}
+{% set version = "1.31" %}
 
 package:
   name: pango-designation
@@ -6,12 +6,12 @@ package:
 
 source:
   url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 835075a7410d4d3a59003105a993358ce20f4ee744231f9728092756a8f2e8d6
+  sha256: 6e82abfbb368023bd07d409d4c4f04473fa3aa36a76bb22a564b4d3cb98ddfda
 
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv .
   entry_points:
     - pango_designation = pango_designation.command:main
   run_exports:
@@ -21,6 +21,7 @@ requirements:
   host:
     - python >=3.7
     - pip
+    - setuptools
   run:
     - python >=3.7
 
@@ -30,9 +31,10 @@ test:
 
 about:
   home: https://github.com/cov-lineages/pango-designation
-  license: CC-BY-NC-4.0
-  license_file: LICENSE.md
-  summary: Repository for suggesting new lineages that should be added to the current
+  license: "CC-BY-NC-4.0"
+  license_file: "LICENSE.md"
+  summary: "Repository for suggesting new lineages that should be added to the current scheme."
+  dev_url: https://github.com/cov-lineages/pango-designation
 
 extra:
   recipe-maintainers:
diff --git a/recipes/pangolin/meta.yaml b/recipes/pangolin/meta.yaml
index 8a8e2c1ced076..49e39138cca80 100644
--- a/recipes/pangolin/meta.yaml
+++ b/recipes/pangolin/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "4.3" %}
+{% set version = "4.3.1" %}
 
 package:
   name: pangolin
@@ -6,27 +6,29 @@ package:
 
 source:
   url: https://github.com/cov-lineages/pangolin/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: daf13c111799943b05bc2c8eee8deb2316e1347ca8f40f0b40d22cdbcc72e3c1
+  sha256: 79f958cfc1b3a01144b138b9ca34ab010aa4ec72499a29ea41acaa57b0bfe7c0
 
 build:
-  number: 2
+  number: 0
   noarch: python
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --ignore-installed .
+  run_exports:
+    - {{ pin_subpackage('pangolin', max_pin="x") }}
 
 requirements:
   host:
     - python >=3.7
     - pip
+    - setuptools
   run:
     - python >=3.7
-    - biopython ==1.74
+    - biopython >=1.74
     - pandas >=1.0.1
-    - tabulate
     - joblib >=0.11
-    - scikit-learn <1.3.0
+    - scikit-learn >=0.23.1,<1.3.0
     - pulp >=2
     - minimap2 >=2.16
-    - snakemake-minimal >=5.13,<=7.30.1
+    - snakemake-minimal >=5.13,!=7.30.1,<8
     - gofasta
     - usher >=0.6.2
     - ucsc-fatovcf >=426
diff --git a/recipes/pangolin/run_test.py b/recipes/pangolin/run_test.py
index 61701e399aa4b..56c68067a019c 100644
--- a/recipes/pangolin/run_test.py
+++ b/recipes/pangolin/run_test.py
@@ -2,10 +2,12 @@
 
 from pathlib import Path
 from subprocess import run, PIPE, STDOUT
+import sys
 
 import pangolin
 
 test_data = Path(pangolin.__file__).parent / 'data/reference.fasta'
 cmd = ['pangolin', str(test_data)]
 pangolin_proc = run(cmd, stdout=PIPE, stderr=STDOUT)
-assert b'Output file written to' in pangolin_proc.stdout, pangolin_proc.stdout
+print(pangolin_proc.stdout.decode(), file=sys.stderr)
+assert b'Output file written to' in pangolin_proc.stdout
diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml
index 43aa89fff9051..f5ad767d5bbf3 100644
--- a/recipes/parm/meta.yaml
+++ b/recipes/parm/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.0.6" %}
-{% set sha256 = "58853578e42e76ecb9e609cb9b292fa979ae5a999d28126f3c43ac0e986f44a5" %}
+{% set version = "0.0.7" %}
+{% set sha256 = "5f6a94d86ba026ac816eae8e27fbec00d2b25a7c5f5729101474f758d7dcbcc9" %}
 
 package:
   name: parm
@@ -10,7 +10,7 @@ source:
     sha256: {{ sha256 }}
 build:
   noarch: python
-  number: 2
+  number: 0
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage('parm', max_pin="x.x") }}
diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml
index db629d9a89746..12cf7af7e81d4 100644
--- a/recipes/pathogen-profiler/meta.yaml
+++ b/recipes/pathogen-profiler/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pathogen-profiler" %}
-{% set version = "4.4.0" %}
-{% set sha256 = "42a82777c01f26f1a5c85185960873e173329f9f84e081a1eef0fe66ac940f2e" %}
+{% set version = "4.5.1" %}
+{% set sha256 = "e48994cb52005f1c2eb5a963bcf9c60d596352d80bf2bcb1e6475653caaf91fb" %}
 
 package:
   name: {{name}}
@@ -31,7 +31,7 @@ requirements:
     - samtools >=1.12
     - bcftools >=1.12
     - tqdm
-    - delly >=1.2.6
+    - delly =1.2.6
     - gatk4
     - bedtools
     - freebayes =1.3.6
diff --git a/recipes/pbaa/meta.yaml b/recipes/pbaa/meta.yaml
index af1f362975501..ae13eeaf6993c 100644
--- a/recipes/pbaa/meta.yaml
+++ b/recipes/pbaa/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbaa" %}
-{% set version = "1.0.3" %}
-{% set pbaa_sha256 = "39ee21fc8b94d15f2004afeb34c6370bcb7661f8e29d35ebd50349f0dced472c" %}
+{% set version = "1.1.0" %}
+{% set pbaa_sha256 = "fb94e8122593a3a6ce6405239645f2f3b15a996113c00ce3872058be9caa1b89" %}
 
 package:
   name: {{ name }}
@@ -18,10 +18,16 @@ about:
 extra:
   recipe-maintainers:
     - zeeev
-    
+  skip-lints:
+    #repackaged binary
+    - should_be_noarch_generic
+
 build:
   number: 0
-  noarch: generic
+  skip: True  # [osx]
+  binary_relocation: False
+  run_exports:
+    - {{ pin_subpackage('pbaa', max_pin='x.x') }}
 
 test:
   commands:
diff --git a/recipes/pbjasmine/build.sh b/recipes/pbjasmine/build.sh
index 6b3a4f5a12308..1a89008b66dab 100644
--- a/recipes/pbjasmine/build.sh
+++ b/recipes/pbjasmine/build.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
 
-mkdir -p "${PREFIX}"/bin
-cp jasmine "${PREFIX}"/bin/
-chmod +x "${PREFIX}"/bin/jasmine
+mkdir -p "${PREFIX}/"{bin,lib}
+cp bin/* "${PREFIX}/bin"
+cp lib/* "${PREFIX}/lib"
diff --git a/recipes/pbjasmine/meta.yaml b/recipes/pbjasmine/meta.yaml
index b78cf8d9ba46b..e73d1f40afbb0 100644
--- a/recipes/pbjasmine/meta.yaml
+++ b/recipes/pbjasmine/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pbjasmine" %}
-{% set version = "2.0.0" %}
-{% set sha256 = "7a93e2b3932ed4701ae437f69a9c82b00b6b0718998ba2b137e0b06df0272e1c" %}
+{% set version = "2.4.0" %}
+{% set sha256 = "c987777320b8ef5ff838a9a893b3baf0de5aaa58fbcf9a25e6ec7b4ad0b88231" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://github.com/PacificBiosciences/jasmine/releases/download/v{{ version }}/jasmine
+  url: https://github.com/PacificBiosciences/jasmine/releases/download/v{{ version }}/jasmine.tar.xz
   sha256: {{ sha256 }}
 
 about:
@@ -26,6 +26,12 @@ extra:
 build:
   number: 0
   skip: True  # [osx]
+  binary_relocation: False
+  run_exports:
+    - {{ pin_subpackage('pbjasmine', max_pin='x.x') }}
+requirements:
+  build:
+    - {{ compiler('cxx') }}
 
 test:
   commands:
diff --git a/recipes/pbmarkdup/meta.yaml b/recipes/pbmarkdup/meta.yaml
index be7bb4d807002..7fa8439d87dfd 100644
--- a/recipes/pbmarkdup/meta.yaml
+++ b/recipes/pbmarkdup/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbmarkdup" %}
-{% set version = "1.0.3" %}
-{% set sha256 = "96907ba4873f377c79b3c74128ae45307e75e7c42dd90b0ddf7fe8b4684b723a" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "a6bbcd71cce4a90202f5d7a7882f982e876212dbc237095418a72d0b7eea6e61" %}
 
 package:
   name: {{ name }}
@@ -26,6 +26,8 @@ extra:
 build:
   number: 0
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('pbmarkdup', max_pin='x.x') }}
 
 test:
   commands:
diff --git a/recipes/pbmm2/meta.yaml b/recipes/pbmm2/meta.yaml
index 348e04b135e2e..e9a1fe4dc9195 100644
--- a/recipes/pbmm2/meta.yaml
+++ b/recipes/pbmm2/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbmm2" %}
-{% set version = "1.14.99" %}
-{% set sha256 = "5cf873325a39aae70b806b8ede27426b3bad779f808379acc517f2349ad256fb" %}
+{% set version = "1.16.0" %}
+{% set sha256 = "80a194cdd0b8b065ff2632b88e054489fc582a49d7f23f5d0423bbb8753b9c82" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/pbpigeon/meta.yaml b/recipes/pbpigeon/meta.yaml
index 20965d16c23e4..1f109235cc705 100644
--- a/recipes/pbpigeon/meta.yaml
+++ b/recipes/pbpigeon/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pbpigeon" %}
-{% set version = "1.2.0" %}
+{% set version = "1.3.0" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   - url: https://github.com/PacificBiosciences/pigeon/releases/download/v{{ version }}/pigeon
-    sha256: 0202818fed1247d21b79bf58811402f7af2481b3731ebc1094b161cf03c0e009
+    sha256: daa61a0067a6bc3c166fd90ab027ed0674e46395f7c4e96fd3561695ef2ab778
 
 build:
   # repackaged binaries
diff --git a/recipes/pbskera/meta.yaml b/recipes/pbskera/meta.yaml
index 39a8c65d89706..1671d1e3eeafd 100644
--- a/recipes/pbskera/meta.yaml
+++ b/recipes/pbskera/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbskera" %}
-{% set version = "1.2.0" %}
-{% set pbskera_sha256 = "0385ab4d67377cd6ed596eccd5df973c03d78561db639d84f9ff557332f745be" %}
+{% set version = "1.3.0" %}
+{% set pbskera_sha256 = "1784969ff410da7d53b1bd0432f3d4f825524e5b99bfa7956aa7dab33a28cedc" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml
index 8d3f1cf875a11..2df50edefe340 100644
--- a/recipes/pbstarphase/meta.yaml
+++ b/recipes/pbstarphase/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbstarphase" %}
-{% set version = "0.14.2" %}
-{% set sha256 = "c8694b47f164db08074cee118238694d8383c0df526637ec1068ae8e93494b75" %}
+{% set version = "1.0.0" %}
+{% set sha256 = "26d76e2a428b9a076ac83255d68598967c9cb46ad113d677483faf4dc6e41167" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/pbsv/meta.yaml b/recipes/pbsv/meta.yaml
index 261ac6727ee49..23b592f884aa0 100644
--- a/recipes/pbsv/meta.yaml
+++ b/recipes/pbsv/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbsv" %}
-{% set version = "2.9.0" %}
-{% set sha256 = "3daf41d28f5d0063f68c49ce790ab17b648f1d2459122f5c13704598342db97c" %}
+{% set version = "2.10.0" %}
+{% set sha256 = "5b640017716efb2d30a75f5af5fd566eae8ee4d6b9517c0a903296b7d298121c" %}
 
 package:
   name: {{ name }}
@@ -13,6 +13,10 @@ source:
 build:
   number: 0
   skip: True  # [osx]
+  binary_relocation: False
+  run_exports:
+    - {{ pin_subpackage('pbsv', max_pin='x.x') }}
+
 
 test:
   commands:
diff --git a/recipes/pbtk/meta.yaml b/recipes/pbtk/meta.yaml
index 6192456fd7a53..1119bb9f94a25 100644
--- a/recipes/pbtk/meta.yaml
+++ b/recipes/pbtk/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pbtk" %}
-{% set version = "3.1.1" %}
-{% set sha256 = "4dbe08d880a4b54d7c84ecdf9849feead71ac5330277a66f57a2915447169814" %}
+{% set version = "3.4.0" %}
+{% set sha256 = "31ff50c9a182b25f1d7e717e3ad764ec106a2ca81dc307a7c76242230e884b92" %}
 
 package:
   name: {{ name }}
@@ -26,6 +26,7 @@ extra:
 build:
   number: 0
   skip: True  # [osx]
+  binary_relocation: False
   run_exports:
     - {{ pin_subpackage('pbtk', max_pin='x.x') }}
 
diff --git a/recipes/pcst-fast/meta.yaml b/recipes/pcst-fast/meta.yaml
deleted file mode 100644
index ede0000d553e5..0000000000000
--- a/recipes/pcst-fast/meta.yaml
+++ /dev/null
@@ -1,44 +0,0 @@
-{% set name = "pcst-fast" %}
-{% set version = "1.0.10" %}
-
-package:
-  name: "{{ name }}"
-  version: "{{ version }}"
-
-source:
-  url: https://files.pythonhosted.org/packages/d4/fd/64b51c867bad63e6622ff97cad6230b94b19b5a61e30424cd69c8353091c/pcst_fast-{{ version }}.tar.gz
-  sha256: 3b5694110ce2e004471f383267d5e4ab7fe1ba9828954e8c42560ac1e42b25e6
-
-build:
-  number: 1
-  skip: True  # [py < 38]
-  script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --use-pep517 -vvv
-  run_exports:
-    - {{ pin_subpackage('pcst-fast', max_pin="x") }}
-
-requirements:
-  build:
-    - {{ compiler('cxx') }}
-  host:
-    - pip
-    - pybind11 >=2.4
-    - python
-    - setuptools_scm
-  run:
-    - pybind11 >=2.4
-    - python
-
-test:
-  commands:
-    - python --version
-
-about:
-  home: https://github.com/fraenkel-lab/pcst_fast
-  license: MIT
-  license_family: MIT
-  license_file: LICENSE.txt
-  summary: "A fast implementation of the Goemans-Williamson scheme for the PCST (prize-collecting Steiner tree/forest) problem."
-
-extra:
-  recipe-maintainers:
-    - hag007
diff --git a/recipes/perl-bloom-faster/meta.yaml b/recipes/perl-bloom-faster/meta.yaml
index 1e48e5ac526a3..29341c0aa36d2 100644
--- a/recipes/perl-bloom-faster/meta.yaml
+++ b/recipes/perl-bloom-faster/meta.yaml
@@ -1,8 +1,9 @@
+{% set name = "perl-bloom-faster" %}
 {% set version = "1.7" %}
 {% set sha256 = "02cfde4f6aca6f7453edb93ba70d36d08081f5ebad8b023188da6379ff1d4a75" %}
 
 package:
-  name: perl-bloom-faster
+  name: {{ name }}
   version: {{ version }}
 
 source:
@@ -10,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 6
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+  number: 7
 
 requirements:
   build:
@@ -30,3 +33,8 @@ about:
   home: http://metacpan.org/pod/Bloom-Faster
   license: unknown
   summary: 'Perl extension for the c library libbloom.'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-class-methodmaker/meta.yaml b/recipes/perl-class-methodmaker/meta.yaml
index 54ecf065f40b3..008ce2d081dce 100644
--- a/recipes/perl-class-methodmaker/meta.yaml
+++ b/recipes/perl-class-methodmaker/meta.yaml
@@ -1,18 +1,20 @@
 {% set name = "perl-class-methodmaker" %}
-{% set version = "2.24" %}
-{% set sha256 = "5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328" %}
+{% set version = "2.25" %}
+{% set sha256 = "70bd3a6595cc40e54a9521eae3247e7d69166e6783ea5faebd59b84537e1b588" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: http://search.cpan.org/CPAN/authors/id/S/SC/SCHWIGON/class-methodmaker/Class-MethodMaker-2.24.tar.gz
+  url: https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker/Class-MethodMaker-2.25.tar.gz
   sha256: {{ sha256 }}
 
 
 build:
-  number: 4
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+  number: 0
 
 requirements:
   build:
@@ -43,3 +45,8 @@ about:
   home: http://search.cpan.org/~schwigon/Class-MethodMaker-2.24/
   license: perl_5
   summary: 'Create generic methods for OO Perl'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-class-xsaccessor/meta.yaml b/recipes/perl-class-xsaccessor/meta.yaml
index 72fef7ce450a1..40daa3938c895 100644
--- a/recipes/perl-class-xsaccessor/meta.yaml
+++ b/recipes/perl-class-xsaccessor/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 6
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+  number: 7
 
 requirements:
   build:
@@ -35,3 +37,8 @@ about:
   home: http://metacpan.org/pod/Class::XSAccessor
   license: perl_5
   summary: 'Generate fast XS accessors without runtime compilation'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-config-any/meta.yaml b/recipes/perl-config-any/meta.yaml
index 12977756b8234..cbc8b71ec8028 100644
--- a/recipes/perl-config-any/meta.yaml
+++ b/recipes/perl-config-any/meta.yaml
@@ -1,14 +1,18 @@
+{% set name = "perl-config-any" %}
+{% set version = "0.33" %}
+
 package:
-  name: perl-config-any
-  version: "0.33"
+  name : {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Config-Any-0.33.tar.gz
+  url: https://cpan.metacpan.org/authors/id/H/HA/HAARG/Config-Any-{{ version }}.tar.gz
   sha256: c0668eb5f2cd355bf20557f04dc18a25474b7a0bcfa79562e3165d9a3c789333
 
 build:
-  #skip: True # [osx]
-  number: 2
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 3
 
 requirements:
   build:
@@ -50,3 +54,8 @@ about:
 # See
 # http://docs.continuum.io/conda/build.html for
 # more information about meta.yaml
+
+extra:
+  # linux-aarch64 is erroring during build.
+  additional-platforms:
+    - osx-arm64
diff --git a/recipes/perl-crypt-openssl-random/0.11/meta.yaml b/recipes/perl-crypt-openssl-random/0.11/meta.yaml
index 0e5abb3119a95..93c01b767e90c 100644
--- a/recipes/perl-crypt-openssl-random/0.11/meta.yaml
+++ b/recipes/perl-crypt-openssl-random/0.11/meta.yaml
@@ -7,13 +7,15 @@ package:
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/R/RU/RURBAN/Crypt-OpenSSL-Random-0.11.tar.gz
+  url: https://cpan.metacpan.org/authors/id/R/RU/RURBAN/Crypt-OpenSSL-Random-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 # If this is a new build for the same version, increment the build
 # number. If you do not include this key, it defaults to 0.
 build:
-  number: 5
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 6
 
 requirements:
   build:
@@ -45,6 +47,11 @@ about:
   license: perl_5
   summary: 'OpenSSL/LibreSSL pseudo-random number generator access'
 
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+
 # See
 # http://docs.continuum.io/conda/build.html for
 # more information about meta.yaml
diff --git a/recipes/perl-crypt-openssl-rsa/meta.yaml b/recipes/perl-crypt-openssl-rsa/meta.yaml
index b7bf758c6afb5..53b6430a88360 100644
--- a/recipes/perl-crypt-openssl-rsa/meta.yaml
+++ b/recipes/perl-crypt-openssl-rsa/meta.yaml
@@ -13,7 +13,7 @@ source:
 # If this is a new build for the same version, increment the build
 # number. If you do not include this key, it defaults to 0.
 build:
-  number: 2
+  number: 3
   run_exports:
     weak:
       - {{ name }} ={{ version }}
@@ -47,3 +47,8 @@ about:
 # See
 # https://docs.conda.io/projects/conda-build for
 # more information about meta.yaml
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-datetime-locale/meta.yaml b/recipes/perl-datetime-locale/meta.yaml
index 471c43e093dce..40db36081f33a 100644
--- a/recipes/perl-datetime-locale/meta.yaml
+++ b/recipes/perl-datetime-locale/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "perl-datetime-locale" %}
-{% set version = "1.43" %}
-{% set sha256 = "6c859c17cf274749dfc2c6aaf6bf4b492b605fabdddd23712efbbd5caf601de1" %}
+{% set version = "1.44" %}
+{% set sha256 = "12a584a4a43c46114cd41ab6981be3609588604a906463fe4f844bb88a31c2de" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/DateTime-Locale-1.43.tar.gz
+  url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/DateTime-Locale-1.44.tar.gz
   sha256: {{ sha256 }}
 
 build:
diff --git a/recipes/perl-devel-size/meta.yaml b/recipes/perl-devel-size/meta.yaml
index c74ef7d91f2b7..c1eb19414e9e9 100644
--- a/recipes/perl-devel-size/meta.yaml
+++ b/recipes/perl-devel-size/meta.yaml
@@ -1,13 +1,18 @@
+{% set name = "perl-devel-size" %}
+{% set version = "0.84" %}
+
 package:
-  name: perl-devel-size
-  version: "0.83"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.83.tar.gz
-  sha256: 757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3
+  url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-{{ version }}.tar.gz
+  sha256: db2e4d65f688dbf59273b5e82101ac3f1a66f665afb0594dce168b8650a4d0e4
 
 build:
-  number: 4
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 0
 
 requirements:
   build:
@@ -30,3 +35,8 @@ about:
   home: http://metacpan.org/pod/Devel::Size
   license: perl_5
   summary: 'Perl extension for finding the memory usage of Perl variables'
+
+extra:
+  # osx-arm64 is erroring due to missing perl-storable in conda forge
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/perl-file-copy-recursive/meta.yaml b/recipes/perl-file-copy-recursive/meta.yaml
index 07675bb8d2156..f3c7e267bfb2c 100644
--- a/recipes/perl-file-copy-recursive/meta.yaml
+++ b/recipes/perl-file-copy-recursive/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 4
 
 requirements:
   build:
@@ -37,3 +39,8 @@ about:
   home: https://metacpan.org/pod/File::Copy::Recursive
   license: Perl
   summary: 'Perl extension for recursively copying files and directories'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-filesys-df/meta.yaml b/recipes/perl-filesys-df/meta.yaml
index f15d1946acf04..e489baf31724f 100644
--- a/recipes/perl-filesys-df/meta.yaml
+++ b/recipes/perl-filesys-df/meta.yaml
@@ -1,8 +1,9 @@
+{% set name = "perl-filesys-df" %}
 {% set version = "0.92" %}
 {% set sha256 = "fe89cbb427e0e05f1cd97c2dd6d3866ac6b21bc7a85734ede159bdc35479552a" %}
 
 package:
-  name: "perl-filesys-df"
+  name: {{ name }}
   version: {{ version }}
 
 source:
@@ -10,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 7
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 8
 
 requirements:
   build:
@@ -29,3 +32,8 @@ about:
   home: http://metacpan.org/pod/Filesys-Df
   license: unknown
   summary: 'Perl extension for filesystem disk space information.'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-heap-simple-xs/meta.yaml b/recipes/perl-heap-simple-xs/meta.yaml
index 86f2ab0436cfb..f71773be3e19d 100644
--- a/recipes/perl-heap-simple-xs/meta.yaml
+++ b/recipes/perl-heap-simple-xs/meta.yaml
@@ -1,13 +1,18 @@
+{% set name = "perl-heap-simple-xs" %}
+{% set version = "0.10" %}
+
 package:
-  name: perl-heap-simple-xs
-  version: "0.10"
+  name: {{ name }}
+  version: {{ version }} 
 
 source:
-  url: http://cpan.metacpan.org/authors/id/T/TH/THOSPEL/Heap-Simple-XS-0.10.tar.gz
+  url: http://cpan.metacpan.org/authors/id/T/TH/THOSPEL/Heap-Simple-XS-{{ version }}.tar.gz
   md5: 0611ac7984f6ddc3aaa60c75d2257803
 
 build:
-  number: 6
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 7
 
 requirements:
   build:
@@ -28,3 +33,8 @@ about:
   home: http://metacpan.org/pod/Heap::Simple::XS
   license: unknown
   summary: 'An XS implementation of the Heap::Simple interface'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-indirect/meta.yaml b/recipes/perl-indirect/meta.yaml
index 02cb6e6267eca..67179c8f741d1 100644
--- a/recipes/perl-indirect/meta.yaml
+++ b/recipes/perl-indirect/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 4
 
 requirements:
   build:
@@ -35,3 +37,8 @@ about:
   home: http://search.cpan.org/dist/indirect/
   license: perl_5
   summary: 'Lexically warn about using the indirect method call syntax.'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-io-compress/meta.yaml b/recipes/perl-io-compress/meta.yaml
index 8622771c8e1e5..ec9551d86e261 100644
--- a/recipes/perl-io-compress/meta.yaml
+++ b/recipes/perl-io-compress/meta.yaml
@@ -1,5 +1,6 @@
+{% set name = "perl-io-compress" %}
 package:
-  name: perl-io-compress
+  name: {{ name }}
   version: 2.201
 
 source:
@@ -7,8 +8,10 @@ source:
   sha256: f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad
 
 build:
-  number: 2
-
+  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+    
 requirements:
   build:
     - make
@@ -55,6 +58,11 @@ test:
     - IO::Uncompress::RawInflate
     - IO::Uncompress::Unzip
 
+extra:
+  additional-platforms:
+    - linux-aarch64
+    #  perl-compress-raw-bzip2 and perl-scalar-list-utils missing
+    # - osx-arm64
 about:
   home: http://metacpan.org/pod/IO-Compress
   license: perl_5
diff --git a/recipes/perl-ipc-sharelite/meta.yaml b/recipes/perl-ipc-sharelite/meta.yaml
index fc2cce94f329d..c0b03629528c8 100644
--- a/recipes/perl-ipc-sharelite/meta.yaml
+++ b/recipes/perl-ipc-sharelite/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 5
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 6
 
 requirements:
   build:
@@ -33,3 +35,8 @@ about:
   home: http://metacpan.org/pod/IPC::ShareLite
   license: perl_5
   summary: 'Lightweight interface to shared memory'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-json-create/meta.yaml b/recipes/perl-json-create/meta.yaml
index 1f6281fa604f1..8ce75d9a58407 100644
--- a/recipes/perl-json-create/meta.yaml
+++ b/recipes/perl-json-create/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 3
 
 requirements:
   build:
@@ -39,3 +41,8 @@ about:
   home: http://metacpan.org/pod/JSON::Create
   license: perl_5
   summary: 'fast, minimal, UTF-8-only serialization of data to JSON'
+
+extra:
+  # osx-arm64 is erroring due to missing perl-encode in conda forge
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/perl-json-parse/meta.yaml b/recipes/perl-json-parse/meta.yaml
index 1adc509494ebc..23d23915f13fd 100644
--- a/recipes/perl-json-parse/meta.yaml
+++ b/recipes/perl-json-parse/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 4
 
 requirements:
   build:
@@ -33,3 +35,8 @@ about:
   home: http://metacpan.org/pod/JSON::Parse
   license: perl_5
   summary: 'Read JSON into a Perl variable'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-list-moreutils-xs/meta.yaml b/recipes/perl-list-moreutils-xs/meta.yaml
index 4d35dd71519b8..4f65724892370 100644
--- a/recipes/perl-list-moreutils-xs/meta.yaml
+++ b/recipes/perl-list-moreutils-xs/meta.yaml
@@ -11,7 +11,8 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 3
+  run_exports: '{{ pin_subpackage(name,  max_pin="x.x") }}'
 
 requirements:
   build:
@@ -33,6 +34,10 @@ test:
   imports:
     - List::MoreUtils::XS
 
+extra:
+  additional-platforms:
+  - linux-aarch64
+    
 about:
   home: https://metacpan.org/release/List-MoreUtils-XS
   license: apache_2_0
diff --git a/recipes/perl-math-cdf/meta.yaml b/recipes/perl-math-cdf/meta.yaml
index 864e4029f59d6..aa9058106d27c 100644
--- a/recipes/perl-math-cdf/meta.yaml
+++ b/recipes/perl-math-cdf/meta.yaml
@@ -1,13 +1,18 @@
+{% set name = "perl-math-cdf" %}
+{% set version = "0.1" %}
+
 package:
-  name: perl-math-cdf
-  version: "0.1"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: http://cpan.metacpan.org/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz
+  url: http://cpan.metacpan.org/authors/id/C/CA/CALLAHAN/Math-CDF-{{ version }}.tar.gz
   md5: 7866c7b6b9d27f0ce4b7637334478ab7
 
 build:
-  number: 9
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 10
 
 requirements:
   build:
@@ -27,3 +32,8 @@ about:
   home: http://metacpan.org/pod/Math-CDF
   license: Public Domain
   summary: 'Generate probabilities and quantiles from several statistical probability functions'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-math-random/meta.yaml b/recipes/perl-math-random/meta.yaml
index 090563a437962..3b45dcebed81a 100644
--- a/recipes/perl-math-random/meta.yaml
+++ b/recipes/perl-math-random/meta.yaml
@@ -1,13 +1,20 @@
+{% set name = "perl-math-random" %}
+{% set version = "0.72" %}
+
 package:
-  name: perl-math-random
-  version: "0.72"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/G/GR/GROMMEL/Math-Random-0.72.tar.gz
+  url: https://cpan.metacpan.org/authors/id/G/GR/GROMMEL/Math-Random-{{ version }}.tar.gz
   md5: b0b961e2ae06920801a9c9843c48d0bc
 
 build:
-  number: 6
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 7
+  # skip osx on x86 - builds fail in CI
+  skip: True # [osx]
 
 requirements:
   build:
@@ -29,3 +36,8 @@ about:
   home: http://metacpan.org/pod/Math-Random
   license: unknown
   summary: 'Random Number Generators'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-ole-storage_lite/meta.yaml b/recipes/perl-ole-storage_lite/meta.yaml
index 74dfa61ad513a..0656e9a786df7 100644
--- a/recipes/perl-ole-storage_lite/meta.yaml
+++ b/recipes/perl-ole-storage_lite/meta.yaml
@@ -1,19 +1,20 @@
 {% set name = "perl-ole-storage_lite" %}
-{% set version = "0.20" %}
-{% set sha256 = "ab18a6171c0e08ea934eea14a0ab4f3a8909975dda9da42124922eb41e84f8ba" %}
+{% set version = "0.22" %}
+{% set sha256 = "d0566d6c29d397ea736379dc515c36849f6b97107cf700ba8250505c984cf965" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.20.tar.gz
+  url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.22.tar.gz
   sha256: {{ sha256 }}
 
 # If this is a new build for the same version, increment the build
 # number. If you do not include this key, it defaults to 0.
 build:
   number: 0
+  noarch: generic
   run_exports:
     weak:
       - {{ name }} ={{ version }}
@@ -41,3 +42,4 @@ about:
 # See
 # https://docs.conda.io/projects/conda-build for
 # more information about meta.yaml
+
diff --git a/recipes/perl-padwalker/meta.yaml b/recipes/perl-padwalker/meta.yaml
index e525214f7f5e1..1099d70539734 100644
--- a/recipes/perl-padwalker/meta.yaml
+++ b/recipes/perl-padwalker/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+  number: 4
 
 requirements:
   build:
@@ -33,3 +35,8 @@ about:
   home: http://metacpan.org/pod/PadWalker
   license: unknown
   summary: "play with other peoples' lexical variables"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-perl-unsafe-signals/meta.yaml b/recipes/perl-perl-unsafe-signals/meta.yaml
index c0b257a47b4e2..14ece03872921 100644
--- a/recipes/perl-perl-unsafe-signals/meta.yaml
+++ b/recipes/perl-perl-unsafe-signals/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 7
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 8
 
 requirements:
   build:
@@ -32,3 +34,8 @@ about:
   home: http://metacpan.org/pod/Perl::Unsafe::Signals
   license: perl_5
   summary: 'Allow unsafe handling of signals in selected blocks'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-perlio-gzip/meta.yaml b/recipes/perl-perlio-gzip/meta.yaml
index a603090dc0a80..bf37a23f9a7f4 100644
--- a/recipes/perl-perlio-gzip/meta.yaml
+++ b/recipes/perl-perlio-gzip/meta.yaml
@@ -1,13 +1,18 @@
+{% set name = "perl-perlio-gzip" %}
+{% set version = "0.20" %}
+
 package:
-  name: perl-perlio-gzip
-  version: "0.20"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/PerlIO-gzip-0.20.tar.gz
+  url: https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/PerlIO-gzip-{{ version }}.tar.gz
   sha256: "4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5"
 
 build:
-  number: 5
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 6
 
 requirements:
   build:
@@ -29,3 +34,8 @@ about:
   home: http://metacpan.org/pod/PerlIO-gzip
   license: perl_5
   summary: 'PerlIO interface to gzip/gunzip'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-scalar-util-numeric/meta.yaml b/recipes/perl-scalar-util-numeric/meta.yaml
index 6573f32e7d397..a5eed6627236f 100644
--- a/recipes/perl-scalar-util-numeric/meta.yaml
+++ b/recipes/perl-scalar-util-numeric/meta.yaml
@@ -1,13 +1,18 @@
+{% set name = "perl-scalar-util-numeric" %}
+{% set version = "0.40" %}
+
 package:
-  name: perl-scalar-util-numeric
-  version: "0.40"
+  name:  {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/Scalar-Util-Numeric-0.40.tar.gz
+  url: https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/Scalar-Util-Numeric-{{ version }}.tar.gz
   md5: 6a5451f33c3ec5c17d0672a4d5b0d24c
 
 build:
-  number: 5
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 6
 
 requirements:
   build:
@@ -28,3 +33,8 @@ about:
   home: http://metacpan.org/pod/Scalar-Util-Numeric
   license: perl_5
   summary: 'numeric tests for perl scalars'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-set-object/meta.yaml b/recipes/perl-set-object/meta.yaml
index c07c9b0944918..7fb3c667489ca 100644
--- a/recipes/perl-set-object/meta.yaml
+++ b/recipes/perl-set-object/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  number: 4
   run_exports:
     weak:
       - {{ name }} ={{ version }}
@@ -34,3 +34,8 @@ about:
   home: http://metacpan.org/pod/Set-Object
   license: artistic_2
   summary: 'Unordered collections (sets) of Perl Objects'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-socket6/meta.yaml b/recipes/perl-socket6/meta.yaml
index a8a000a43df6c..bbb6526df15eb 100644
--- a/recipes/perl-socket6/meta.yaml
+++ b/recipes/perl-socket6/meta.yaml
@@ -1,13 +1,18 @@
+{% set name = "perl-socket6" %}
+{% set version = "0.29" %}
+
 package:
-  name: perl-socket6
-  version: "0.29"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: http://cpan.metacpan.org/authors/id/U/UM/UMEMOTO/Socket6-0.29.tar.gz
+  url: http://cpan.metacpan.org/authors/id/U/UM/UMEMOTO/Socket6-{{ version }}.tar.gz
   sha256: 468915fa3a04dcf6574fc957eff495915e24569434970c91ee8e4e1459fc9114
 
 build:
-  number: 4
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 5
 
 requirements:
   build:
@@ -28,3 +33,8 @@ about:
   home: http://metacpan.org/pod/Socket6
   license: unknown
   summary: 'IPv6 related part of the C socket.h defines and structure manipulators'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-term-table/meta.yaml b/recipes/perl-term-table/meta.yaml
index 90c7601d8941b..c2c092b1d7bdd 100644
--- a/recipes/perl-term-table/meta.yaml
+++ b/recipes/perl-term-table/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "perl-term-table" %}
-{% set version = "0.022" %}
-{% set sha256 = "b9dbdacfa7362846e3c4a100081832db9da74b7356828ef9d92869c44642e0b8" %}
+{% set version = "0.023" %}
+{% set sha256 = "e45042face1801d99c0bead6ca5f363a34e0e055f4fe6b0ccb208de481072bd3" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.022.tar.gz
+  url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.023.tar.gz
   sha256: {{ sha256 }}
 
 build:
diff --git a/recipes/perl-time-hires/meta.yaml b/recipes/perl-time-hires/meta.yaml
index 760b297eb6ffd..29a2702b32606 100644
--- a/recipes/perl-time-hires/meta.yaml
+++ b/recipes/perl-time-hires/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 4
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+  number: 5
 
 requirements:
   build:
@@ -36,3 +38,8 @@ about:
   home: http://metacpan.org/pod/Time::HiRes
   license: perl_5
   summary: 'High resolution alarm, sleep, gettimeofday, interval timers'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-unicode-map/meta.yaml b/recipes/perl-unicode-map/meta.yaml
index 9e9c878fe529d..2628f73f65d49 100644
--- a/recipes/perl-unicode-map/meta.yaml
+++ b/recipes/perl-unicode-map/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 7
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 8
 
 requirements:
   build:
@@ -35,3 +37,8 @@ about:
   home: http://metacpan.org/pod/Unicode::Map
   license: unknown
   summary: 'An utility to map texts from and to unicode'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-unicode-normalize/meta.yaml b/recipes/perl-unicode-normalize/meta.yaml
index 24ec84e9aaa00..96a87f3761326 100644
--- a/recipes/perl-unicode-normalize/meta.yaml
+++ b/recipes/perl-unicode-normalize/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 5
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+  number: 6
 
 requirements:
   build:
@@ -39,3 +41,8 @@ about:
   home: http://metacpan.org/pod/Unicode::Normalize
   license: perl_5
   summary: 'Unicode Normalization Forms'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/perl-unicode-utf8/meta.yaml b/recipes/perl-unicode-utf8/meta.yaml
index 5e23f0cf4f885..311d5ce748c39 100644
--- a/recipes/perl-unicode-utf8/meta.yaml
+++ b/recipes/perl-unicode-utf8/meta.yaml
@@ -11,7 +11,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 6
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+  number: 7
 
 requirements:
   build:
@@ -38,3 +40,8 @@ about:
   home: http://metacpan.org/pod/Unicode::UTF8
   license: perl_5
   summary: 'Encoding and decoding of UTF-8 encoding form'
+
+extra:
+  # osx-arm64 is erroring due to missing perl-encode in conda forge
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/perl-url-encode/meta.yaml b/recipes/perl-url-encode/meta.yaml
index fd8f343642c49..a46f36be411c5 100644
--- a/recipes/perl-url-encode/meta.yaml
+++ b/recipes/perl-url-encode/meta.yaml
@@ -13,13 +13,14 @@ source:
 # If this is a new build for the same version, increment the build
 # number. If you do not include this key, it defaults to 0.
 build:
-  number: 0
+  number: 1
   run_exports:
     weak:
       - {{ name }} ={{ version }}
 
 requirements:
   build:
+    - make
 
   # Run exports are used now
   host:
@@ -45,3 +46,8 @@ about:
 # See
 # https://docs.conda.io/projects/conda-build for
 # more information about meta.yaml
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/pggb/meta.yaml b/recipes/pggb/meta.yaml
index 77a7157fb194c..6497a8b080682 100644
--- a/recipes/pggb/meta.yaml
+++ b/recipes/pggb/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pggb" %}
-{% set version = "0.7.1" %}
+{% set version = "0.7.2" %}
 
 package:
   name: "{{ name }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 9faa14c9924a7fbf17e9df26a88c2764315842994cdbee155fb4cf0fbfce187e
+  sha256: a687d5268b77d6bbbdb026d379975eed2afff148d7d73697a8421ca39b3ddbe9
 
 build:
   number: 0
diff --git a/recipes/pgscatalog-utils/meta.yaml b/recipes/pgscatalog-utils/meta.yaml
index 9f2ccfa52bfaf..912fd1d00bbab 100644
--- a/recipes/pgscatalog-utils/meta.yaml
+++ b/recipes/pgscatalog-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pgscatalog-utils" %}
-{% set version = "1.4.1" %}
+{% set version = "1.4.4" %}
 
 package:
   name: {{ name|lower }}
@@ -7,12 +7,12 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pgscatalog_utils-{{ version }}.tar.gz
-  sha256: e54e67f9a372e91a7cc640528c66a9989258bc5ae61e7d6972a5b8ef4e1aa2da
+  sha256: dd431b3e064194d6febb1d41e8c9f558cd4421d1e94d7d42e3f42f3f100ac2ae
 
 build:
   noarch: python
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('pgscatalog-utils', max_pin='x.x') }}  
 
@@ -24,7 +24,7 @@ requirements:
   run:
     - python >=3.10.0,<4.0.0
     - pgscatalog.calc >=0.3.0,<0.4.0
-    - pgscatalog.core >=0.3.1,<0.4.0
+    - pgscatalog.core >=0.3.3,<0.4.0
     - pgscatalog.match >=0.3.3,<0.4.0
 
 test:
diff --git a/recipes/pgscatalog.core/meta.yaml b/recipes/pgscatalog.core/meta.yaml
index 5d51c105d3fcc..c7a45cf48520e 100644
--- a/recipes/pgscatalog.core/meta.yaml
+++ b/recipes/pgscatalog.core/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pgscatalog.core" %}
-{% set version = "0.3.1" %}
+{% set version = "0.3.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pgscatalog_core-{{ version }}.tar.gz
-  sha256: 612cc10afc4bea0dc5edfc6b279fc92b76e6833a9152e5bd63a7f98da4a125ad
+  sha256: 5b2851860e3dda29ec4863701cf2acb9e1007549960b24e1dcdfec4258f6792f
 
 build:
   entry_points:
diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml
index 014462e5a79f6..940dad736add2 100644
--- a/recipes/phabox/meta.yaml
+++ b/recipes/phabox/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "PhaBOX" %}
-{% set version = "2.0.0" %}
+{% set version = "2.1.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,49 +7,60 @@ package:
 
 source:
   url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 3e120da4b6c37d1ae9f7291382365012a4efa0c4e704068c1ecd897e5fd8178a
-  patches:
-    - setup.patch
+  sha256: 875124cd1568fcb706662e7f86ff7e1ef79b38944156c8c5d0b1b329d983d73a
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  entry_points:
+    - phabox2=phabox2.phabox2:main
   run_exports:
     - {{ pin_subpackage('phabox', max_pin="x.x") }}
 
 requirements:
   host:
+    - python >=3.8
     - pip
-    - python
     - setuptools
   run:
-    - python
+    - python >=3.8
     - biopython >=1.84
+    - datasets >=3
+    - kcounter >=0.1.1
+    - fasttree >=2.1.11
+    - mafft >=7.525
     - networkx >=3.4
-    - numpy >=2
+    - numpy >=1.26
     - pandas >=2
-    - pprodigal >=1
-    - scipy >=1.14
+    - prodigal-gv >=2.11.0
+    - pyarrow >=16
     - pytorch >=2.4
-    - transformers >=4.40
-    - datasets >=3
-    - pyarrow >=17
-
+    - scipy >=1.14
+    - seaborn-base >=0.13.2
+    - transformers >=4
+    - blast >=2.16.0
+    - diamond <=0.9.14
+    - mcl >=22.282
+    - accelerate >=1.0.1
+    
 test:
   commands:
-    - phabox --help
-    - Cherry_single --help
-    - PhaGCN_single --help
-    - PhaMer_single --help
-    - PhaTYP_single --help
+    - phabox2 --help
 
 about:
   home: https://github.com/KennthShang/PhaBOX
-  license: AFL
-  license_file: LICENSE.md 
-  summary: Phage BOX is a Python library for phage-related tasks
+  license: "AFL-3.0"
+  license_family: OTHER
+  license_file: "LICENSE.md"
+  summary: Virus identification and analysis tool set
+  dev_url: "https://github.com/KennthShang/PhaBOX"
+  doc_url: "https://github.com/KennthShang/PhaBOX/wiki"
 
 extra:
   recipe-maintainers:
-    - bernt-matthias
+    - SHANG Jiayu
+    - PENG Cheng
+  identifiers:
+    - doi:10.1093/bioadv/vbad101
+    - biotools:phabox
diff --git a/recipes/phabox/setup.patch b/recipes/phabox/setup.patch
deleted file mode 100644
index b5213da9b8f34..0000000000000
--- a/recipes/phabox/setup.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-diff -ruN PhaBOX-1.0.0-org/Cherry_single.py PhaBOX-1.0.0/Cherry_single.py
---- PhaBOX-1.0.0-org/Cherry_single.py	2024-09-30 10:20:05.496290778 +0200
-+++ PhaBOX-1.0.0/Cherry_single.py	2024-09-30 13:26:23.735605652 +0200
-@@ -16,21 +16,21 @@
- from torch import optim
- from torch.nn import functional as F
- 
--from scripts.ulity import *
--from scripts.preprocessing import *
--from scripts.cnnscript import *
-+from phabox.scripts.ulity import *
-+from phabox.scripts.preprocessing import *
-+from phabox.scripts.cnnscript import *
- from shutil import which
- from collections import Counter
- from Bio import SeqIO
- from Bio.SeqRecord import SeqRecord
- from Bio.Blast.Applications import NcbiblastnCommandline
--from models.phamer import Transformer
--from models.CAPCNN import WCNN
--from models.PhaGCN import GCN
--from models import Cherry
--from draw import draw_network, drop_network
-+from phabox.models.phamer import Transformer
-+from phabox.models.CAPCNN import WCNN
-+from phabox.models.PhaGCN import GCN
-+from phabox.models import Cherry
-+from phabox.draw import draw_network, drop_network
- from scipy.special import softmax
--from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
-+from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
- 
- 
- 
-diff -ruN PhaBOX-1.0.0-org/draw.py PhaBOX-1.0.0/draw.py
---- PhaBOX-1.0.0-org/draw.py	2024-09-30 10:20:05.500290882 +0200
-+++ PhaBOX-1.0.0/draw.py	2024-09-30 13:27:20.231425936 +0200
-@@ -4,8 +4,8 @@
- import numpy as np
- import argparse
- import subprocess
--from scripts.ulity import *
--from scripts.preprocessing import *
-+from phabox.scripts.ulity import *
-+from phabox.scripts.preprocessing import *
- import math
- import os
- import pandas as pd
-diff -ruN PhaBOX-1.0.0-org/main.py PhaBOX-1.0.0/main.py
---- PhaBOX-1.0.0-org/main.py	2024-09-30 10:20:05.500290882 +0200
-+++ PhaBOX-1.0.0/main.py	2024-09-30 13:27:33.651385105 +0200
-@@ -16,22 +16,22 @@
- from torch import optim
- from torch.nn import functional as F
- 
--from scripts.ulity import *
--from scripts.preprocessing import *
--from scripts.cnnscript import *
-+from phabox.scripts.ulity import *
-+from phabox.scripts.preprocessing import *
-+from phabox.scripts.cnnscript import *
- from shutil import which
- from collections import Counter
- from Bio import SeqIO
- from Bio.SeqRecord import SeqRecord
- from Bio.Blast.Applications import NcbiblastnCommandline
--from models.phamer import Transformer
--from models.CAPCNN import WCNN
--from models.PhaGCN import GCN
--from models import Cherry
--from draw import draw_network, drop_network
-+from phabox.models.phamer import Transformer
-+from phabox.models.CAPCNN import WCNN
-+from phabox.models.PhaGCN import GCN
-+from phabox.models import Cherry
-+from phabox.draw import draw_network, drop_network
- from collections import Counter
- from scipy.special import softmax
--from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
-+from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
- 
- 
- 
-diff -ruN PhaBOX-1.0.0-org/PhaGCN_single.py PhaBOX-1.0.0/PhaGCN_single.py
---- PhaBOX-1.0.0-org/PhaGCN_single.py	2024-09-30 10:20:05.496290778 +0200
-+++ PhaBOX-1.0.0/PhaGCN_single.py	2024-09-30 13:26:46.099532952 +0200
-@@ -13,21 +13,21 @@
- import scipy.sparse as sparse
- 
- 
--from scripts.ulity import *
--from scripts.preprocessing import *
--from scripts.cnnscript import *
-+from phabox.scripts.ulity import *
-+from phabox.scripts.preprocessing import *
-+from phabox.scripts.cnnscript import *
- from shutil import which
- from collections import Counter
- from Bio import SeqIO
- from Bio.SeqRecord import SeqRecord
- from Bio.Blast.Applications import NcbiblastnCommandline
--from models.phamer import Transformer
--from models.CAPCNN import WCNN
--from models.PhaGCN import GCN
--from models import Cherry
--from draw import draw_network, drop_network
-+from phabox.models.phamer import Transformer
-+from phabox.models.CAPCNN import WCNN
-+from phabox.models.PhaGCN import GCN
-+from phabox.models import Cherry
-+from phabox.draw import draw_network, drop_network
- from scipy.special import softmax
--from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
-+from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
- 
- from torch import nn
- from torch import optim
-diff -ruN PhaBOX-1.0.0-org/PhaMer_single.py PhaBOX-1.0.0/PhaMer_single.py
---- PhaBOX-1.0.0-org/PhaMer_single.py	2024-09-30 10:20:05.500290882 +0200
-+++ PhaBOX-1.0.0/PhaMer_single.py	2024-09-30 13:26:53.231510206 +0200
-@@ -16,20 +16,20 @@
- from torch import optim
- from torch.nn import functional as F
- 
--from scripts.ulity import *
--from scripts.preprocessing import *
--from scripts.cnnscript import *
-+from phabox.scripts.ulity import *
-+from phabox.scripts.preprocessing import *
-+from phabox.scripts.cnnscript import *
- from shutil import which
- from collections import Counter
- from Bio import SeqIO
- from Bio.SeqRecord import SeqRecord
- from Bio.Blast.Applications import NcbiblastnCommandline
--from models.phamer import Transformer
--from models.CAPCNN import WCNN
--from models.PhaGCN import GCN
--from models import Cherry
-+from phabox.models.phamer import Transformer
-+from phabox.models.CAPCNN import WCNN
-+from phabox.models.PhaGCN import GCN
-+from phabox.models import Cherry
- from scipy.special import softmax
--from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
-+from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
- 
- 
- 
-diff -ruN PhaBOX-1.0.0-org/PhaTYP_single.py PhaBOX-1.0.0/PhaTYP_single.py
---- PhaBOX-1.0.0-org/PhaTYP_single.py	2024-09-30 10:20:05.500290882 +0200
-+++ PhaBOX-1.0.0/PhaTYP_single.py	2024-09-30 13:27:03.755477016 +0200
-@@ -16,20 +16,20 @@
- from torch import optim
- from torch.nn import functional as F
- 
--from scripts.ulity import *
--from scripts.preprocessing import *
--from scripts.cnnscript import *
-+from phabox.scripts.ulity import *
-+from phabox.scripts.preprocessing import *
-+from phabox.scripts.cnnscript import *
- from shutil import which
- from collections import Counter
- from Bio import SeqIO
- from Bio.SeqRecord import SeqRecord
- from Bio.Blast.Applications import NcbiblastnCommandline
--from models.phamer import Transformer
--from models.CAPCNN import WCNN
--from models.PhaGCN import GCN
--from models import Cherry
-+from phabox.models.phamer import Transformer
-+from phabox.models.CAPCNN import WCNN
-+from phabox.models.PhaGCN import GCN
-+from phabox.models import Cherry
- from scipy.special import softmax
--from scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
-+from phabox.scripts.data import load_data, preprocess_features, preprocess_adj, sample_mask
- 
- 
- 
-diff -ruN PhaBOX-1.0.0-org/scripts/cnnscript.py PhaBOX-1.0.0/scripts/cnnscript.py
---- PhaBOX-1.0.0-org/scripts/cnnscript.py	2024-09-30 10:20:05.608293722 +0200
-+++ PhaBOX-1.0.0/scripts/cnnscript.py	2024-09-30 13:25:46.367731972 +0200
-@@ -3,7 +3,7 @@
- import  numpy as np
- import  torch
- import  torch.utils.data as Data
--from    models.CAPCNN import WCNN
-+from    phabox.models.CAPCNN import WCNN
- from    Bio import SeqIO
- from    Bio.SeqRecord import SeqRecord   
- from    torch import nn
-diff -ruN PhaBOX-1.0.0-org/scripts/data.py PhaBOX-1.0.0/scripts/data.py
---- PhaBOX-1.0.0-org/scripts/data.py	2024-09-30 10:20:05.608293722 +0200
-+++ PhaBOX-1.0.0/scripts/data.py	2024-09-30 13:26:08.807655370 +0200
-@@ -2,6 +2,7 @@
- import  pickle as pkl
- import  networkx as nx
- import  scipy.sparse as sp
-+from scipy.sparse.linalg import eigsh
- import  sys
- 
- 
-diff -ruN PhaBOX-1.0.0-org/setup.py PhaBOX-1.0.0/setup.py
---- PhaBOX-1.0.0-org/setup.py	2024-09-30 10:20:05.500290882 +0200
-+++ PhaBOX-1.0.0/setup.py	2024-09-30 10:21:12.297733200 +0200
-@@ -3,7 +3,20 @@
- setup(
-     name='phabox',
-     version='1.0',
--    packages=find_packages(),
-+    packages=["phabox"],
-+    package_dir={'phabox': '.'},
-+    package_data={
-+        '': ['scripts/*.py', 'models/*.py', 'GTDB/*.py']
-+    },
-+    entry_points={
-+        'console_scripts': [
-+            'phabox=phabox.main:main',  # Allows running the script with `phabox` command
-+            'Cherry_single=phabox.Cherry_single:main',
-+            'PhaGCN_single=phabox.PhaGCN_single:main',
-+            'PhaMer_single=phabox.PhaMer_single:main',
-+            'PhaTYP_single=phabox.PhaTYP_single:main',
-+        ]
-+    },
-     install_requires=[
-         'numpy==1.21.2',
-         'pandas==1.3.4',
diff --git a/recipes/phenograph/meta.yaml b/recipes/phenograph/meta.yaml
new file mode 100644
index 0000000000000..7e233c8624fc6
--- /dev/null
+++ b/recipes/phenograph/meta.yaml
@@ -0,0 +1,48 @@
+{% set name = "phenograph" %}
+{% set version = "1.5.7" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/PhenoGraph-{{ version }}.tar.gz
+  sha256: 46b28f9e043a00deba53bb5f35dd84793669ab2bd4ce78900bf7f15f1321515a
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('phenograph', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.6
+    - pip
+    - setuptools
+  run:
+    - python >=3.6
+    - leidenalg >=0.8.2
+    - setuptools >=18.0.1
+    - numpy >=1.12
+    - scipy >=1.5.1
+    - scikit-learn >=0.17
+    - psutil >4
+
+test:
+  imports:
+    - phenograph
+
+about:
+  home: https://github.com/dpeerlab/PhenoGraph
+  summary: "Graph-based clustering for high-dimensional single-cell data."
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  dev_url: https://github.com/dpeerlab/PhenoGraph
+  doc_url: "https://github.com/dpeerlab/PhenoGraph/blob/v{{ version }}/README.md"
+
+extra:
+  identifiers:
+    - doi:10.1016/j.cell.2015.05.047
diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml
index 23e84b018047c..98a200dc4142d 100644
--- a/recipes/phykit/meta.yaml
+++ b/recipes/phykit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "phykit" %}
-{% set version = "2.0.0" %}
+{% set version = "2.0.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 32358dc24e564860ce56fa71772599a00d12dc746b6ca2fb046fbca9f4c1e2c3
+  sha256: 34799da77c621afdd50afd3411449a4460f15a52a56bff38b5c9ab7def864302
 
 build:
   noarch: python
@@ -129,8 +129,9 @@ requirements:
   host:
     - pip
     - python >=3
+    - setuptools
   run:
-    - biopython >=1.81
+    - biopython >=1.82
     - numpy >=1.24.0
     - python >=3
     - scipy >=1.11.3
diff --git a/recipes/piawka/meta.yaml b/recipes/piawka/meta.yaml
index 873fd2896a466..20a7425ba148d 100644
--- a/recipes/piawka/meta.yaml
+++ b/recipes/piawka/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "piawka" %}
-{% set version = "0.8.6" %}
+{% set version = "0.8.8" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/novikovalab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 5da0029ef43fbe159052e5523bcd7db69a4566bf8268fcd2db44d91521e028f6
+  sha256: 9a89ba6f23470f5127d30c3b6b55c64e27612fd7d98028c3d69b077676832e08
 
 build:
   noarch: generic
diff --git a/recipes/piscem/build.sh b/recipes/piscem/build.sh
index 482a75a82dec1..b2d78efc2f3e2 100644
--- a/recipes/piscem/build.sh
+++ b/recipes/piscem/build.sh
@@ -4,7 +4,13 @@ unamestr=`uname`
 
 if [ "$unamestr" == 'Darwin' ];
 then
+  if [[ $(uname -m) == 'x86_64' ]]; then
+    echo "OSX x86-64: attempting to fix broken (old) SDK behavior"
+    export CFLAGS="${CFLAGS} -D_LIBCPP_HAS_NO_C11_ALIGNED_ALLOC"
+    export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_HAS_NO_C11_ALIGNED_ALLOC"
+  fi
   export MACOSX_DEPLOYMENT_TARGET=10.15
+  export MACOSX_SDK_VERSION=10.15
   export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
   export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
 else 
diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml
index 0c261497c9b1d..ce3baa0e0adef 100644
--- a/recipes/piscem/meta.yaml
+++ b/recipes/piscem/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.10.3" %}
+{% set version = "0.10.4" %}
 {% set name = "piscem" %}
-{% set sha256 = "5bb7d856e28f7090456bbc9aa81120169cff76b66c47a642916d8d53e35bec8a" %}
+{% set sha256 = "665d3dc54bf4b9c50c02d190112177e270c1b992e61608f34c3e95b0e4a5b5d6" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh
index 343b7d9d0f89f..fd7226afabb7c 100644
--- a/recipes/polap/build.sh
+++ b/recipes/polap/build.sh
@@ -6,14 +6,72 @@ files=(polap
 	polap-conda-environment-fmlrc.yaml
 	polap-conda-environment.yaml
 	polap-mt.1.c70.3.faa
-	polap-parsing.sh
 	polap-pt.2.c70.3.faa
-	polap.sh
-	run-polap-genes.R
-	run-polap-jellyfish.R
-	run-polap-mtcontig.R
 	run-polap-ncbitools
-	run-polap-pairs.R)
+	polap-command-completion.sh
+	polap-constants.sh
+	polap-function-set-variables.sh
+	polap-git-hash-version.sh
+	polap-parsing.sh
+	polap-test-variables.sh
+	polap-variables-common.sh
+	polap-variables-main.sh
+	polap-variables-mtcontigs.sh
+	polap-version.sh
+	run-polap-function-annotate-contig.sh
+	run-polap-function-annotate.sh
+	run-polap-function-archive.sh
+	run-polap-function-assemble.sh
+	run-polap-function-bioproject.sh
+	run-polap-function-include.sh
+	run-polap-function-log.sh
+	run-polap-function-menus.sh
+	run-polap-function-miscellaneous.sh
+	run-polap-function-mtdna.sh
+	run-polap-function-oga.sh
+	run-polap-function-polishing.sh
+	run-polap-function-seeds.sh
+	run-polap-function-template.sh
+	run-polap-function-utilities.sh
+	run-polap-function-wga.sh
+	run-polap-sh-create-depth-file.sh
+	run-polap-sh-half-cut.sh
+	run-polap-sh-minimap2-paf2tab.sh
+	run-polap-py-find-cc.py
+	run-polap-py-select-mtdna-2-nx-find-circular-path.py
+	run-polap-py-select-mtdna-2-nx-simple-cycles.py
+	run-polap-pairs.R
+	run-polap-r-assemble-bioproject-3-length-match.R
+	run-polap-r-blast-mtdna-1-determine-gene.R
+	run-polap-r-bridge.R
+	run-polap-r-cc2mtcontig.R
+	run-polap-r-depth-distribution.R
+	run-polap-r-depthfilter-gfa.R
+	run-polap-r-determine-depth-range.R
+	run-polap-r-determine-depth-range_1.R
+	run-polap-r-determine-depth-range_2.R
+	run-polap-r-determine-depth-range_3.R
+	run-polap-r-determine-depth-range_4.R
+	run-polap-r-determine-depth-range_5.R
+	run-polap-r-edges-stats.R
+	run-polap-r-final-filter-mtcontig.R
+	run-polap-r-final-mtcontig.R
+	run-polap-r-final-seed-mtcontig.R
+	run-polap-r-genes-bed4.R
+	run-polap-r-genes.R
+	run-polap-r-get-bioproject-1.R
+	run-polap-r-jellyfish.R
+	run-polap-r-mtcontig-contig.R
+	run-polap-r-mtcontig.R
+	run-polap-r-pairs.R
+	run-polap-r-plastid-determine-depth-range.R
+	run-polap-r-plot-mtdna.R
+	run-polap-r-prepare-cc.R
+	run-polap-r-preselect-annotation.R
+	run-polap-r-select-mtdna-1-nx-gfa-links.R
+	run-polap-r-template.R
+	run-polap-r-test-reads-bar-graph.R
+	polap.sh)
 
 for i in "${files[@]}"; do
 	cp src/$i $PREFIX/bin
@@ -21,4 +79,3 @@ done
 
 chmod +x $PREFIX/bin/polap
 chmod +x $PREFIX/bin/polap.sh
-chmod +x $PREFIX/bin/run-polap-*
diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml
index eacc9680c84a3..2ca4d29359c56 100644
--- a/recipes/polap/meta.yaml
+++ b/recipes/polap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "polap" %}
-{% set version = "0.2.6" %}
-{% set sha256 = "6d9b5ffc26ce6feeaa6119d0dda57e07af9e9def55e5510b0ddf237699b15948" %}
+{% set version = "0.3.7.2" %}
+{% set sha256 = "7ac79618aa16cacd8bb5dd6fa7a1284b75bbbeeb526a418c9297d7324e9359c7" %}
 
 package:
   name: "{{ name }}"
@@ -20,33 +20,37 @@ requirements:
   run:
     - python
     - flye >=2.9.2
-    - seqkit
     - minimap2 >=2.24
-    - blast
+    - seqkit
     - bedtools
     - seqtk
-    - bioawk
-    - entrez-direct
-    - sra-tools
     - csvtk
-    - gfastats
     - kmer-jellyfish
-    - clustalw
+    - blast
+    - entrez-direct
+    - sra-tools
     - samtools
-    - assembly-stats
     - orthofinder
     - bioconductor-ggtree
-    - perl-xml-libxml
-    - icu
-    - libxml2
-    - perl
-    - r-base
+    - networkx
+    - pandas
+    - gfatools
+    - r-optparse
     - r-dplyr
     - r-readr
-    - r-optparse
     - r-stringr
     - r-tidyr
     - parallel
+    - r-base
+    - bioawk
+    - assembly-stats
+    - progressivemauve
+    - clustalw
+    - gfastats
+    - perl-xml-libxml
+    - icu
+    - libxml2
+    - perl
 
 test:
   commands:
diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml
index 802e0ca68a124..da399ad941f42 100644
--- a/recipes/poppunk/meta.yaml
+++ b/recipes/poppunk/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.7.0" %}
+{% set version = "2.7.2" %}
 {% set name = "PopPUNK" %}
 
 package:
@@ -7,12 +7,12 @@ package:
 
 source:
   url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz
-  sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067
+  sha256: 1ea36fd3dee28b47c7e629eacd5ae5bf6dda3e464c23cfa5f51e63dc3d06e371
 
 build:
   number: 0
-  skip: true  # [py < 38]
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
+  skip: True # [py < 39]
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - poppunk = PopPUNK.__main__:main
     - poppunk_assign = PopPUNK.assign:main
@@ -27,13 +27,12 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ compiler('fortran') }}
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux64]
     - cmake >=3.18
     - make
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   host:
     # python
     - python
@@ -64,7 +63,6 @@ requirements:
     - treeswift
     - requests
     # C++ extension
-    - zlib
     # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool.
     - xorg-libxi
     - xorg-libxcursor
@@ -80,7 +78,6 @@ test:
   imports:
     - PopPUNK
     - poppunk_refine
-
   commands:
     - poppunk --help
     - poppunk_assign --help
@@ -92,16 +89,17 @@ test:
     - poppunk_lineages_from_strains --help
 
 about:
-  home: https://poppunk.bacpop.org/
-  license: Apache-2.0
+  home: "https://poppunk.bacpop.org"
+  license: "Apache-2.0"
   license_family: APACHE
+  license_file: LICENSE
   summary: 'PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'
+  dev_url: "https://github.com/bacpop/PopPUNK"
+  doc_url: "https://poppunk.bacpop.org/index.html"
 
 extra:
   identifiers:
     - doi:10.1101/gr.241455.118
-  # enabling this would require arm64 packages for: mandrake, pp-sketchlib,
-  # rapidnj
-  # additional-platforms:
-  #  - linux-aarch64
-  #  - osx-arm64
+    - biotools:poppunk
+  additional-platforms:
+    - osx-arm64
diff --git a/recipes/poseidon-trident/meta.yaml b/recipes/poseidon-trident/meta.yaml
index 12b4892d889dc..abb6356acd5b8 100644
--- a/recipes/poseidon-trident/meta.yaml
+++ b/recipes/poseidon-trident/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.5.4.0" %}
+{% set version = "1.5.7.0" %}
 package:
   name: poseidon-trident
   version: {{ version }}
@@ -7,11 +7,11 @@ package:
 # https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#preprocessing-selectors
 source:
   - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-conda-linux # [linux]
-    md5: 626dc6fde74f532e505bdded4742886f # [linux]
+    md5: de1e15f936cca94ffac240863bf95127 # [linux]
   - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-macOS-X64 # [osx and x86_64]
-    md5: 88fc51b50a17cf3c05e66f0a4e701d03 # [osx and x86_64]
+    md5: 4ed4a2a827ab454e88bec1850250d7fe # [osx and x86_64]
   - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-macOS-ARM64 # [osx and arm64]
-    md5: 0cc0186736b8a3d380e23bfa242f9a98 # [osx and arm64]
+    md5: 949200977a85883a078f1ee8ed0292a9 # [osx and arm64]
 
 build:
   number: 0 
diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml
index 0f5d28be758ff..bf568d621e2c8 100644
--- a/recipes/ppanggolin/meta.yaml
+++ b/recipes/ppanggolin/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.1.2" %}
+{% set version = "2.2.0" %}
 
 package:
   name: ppanggolin
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz
-  sha256: ecb5cc4bc4db3a1e842a4085d6aec3a25a12513215523797723e325f96d1158d
+  sha256: c061d622ce9e334be8ed571decdd8ce113967e4d1e314cf840e87497377211a6
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage("ppanggolin", max_pin="x") }}
 
diff --git a/recipes/pretextgraph/build.sh b/recipes/pretextgraph/build.sh
index e9ec56d912ec1..4c7699c6851e5 100755
--- a/recipes/pretextgraph/build.sh
+++ b/recipes/pretextgraph/build.sh
@@ -5,7 +5,7 @@ set -eo pipefail
 if [ `uname` == Darwin ]; then
     meson setup --buildtype=release --prefix=$PREFIX --unity on builddir
 else
-    env CC=clang CXX=clang meson setup --buildtype=release --prefix=$PREFIX --unity on builddir
+    env CC=clang CXX=clang++ meson setup --buildtype=release --prefix=$PREFIX --unity on builddir
 fi
 
 cd builddir
diff --git a/recipes/pretextgraph/meta.yaml b/recipes/pretextgraph/meta.yaml
index 42027ecad8f8a..e93bc950bbaac 100644
--- a/recipes/pretextgraph/meta.yaml
+++ b/recipes/pretextgraph/meta.yaml
@@ -1,23 +1,26 @@
 {% set name = "PretextGraph" %}
-{% set version = "0.0.6" %}
-{% set sha256 = "94e69e9c99f62d6112a8e48db4cf9ff92102c2704dacff01924cce5799a6807f" %}
+{% set version = "0.0.7" %}
+{% set sha256 = "4c99c46105cf4de3f22ab3065b0e5445cdf3caed8f66aafaf08249c365455d37" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://github.com/wtsi-hpag/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.xz
+  url: https://github.com/sanger-tol/PretextGraph/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  number: 0 # the build number should be incremented if the same version of the package is built with different build settings
+  run_exports:
+    - {{ pin_subpackage('pretextgraph', max_pin="x.x") }}
 
 requirements:
   build:
     - {{ compiler('cxx') }}
-    - clang>=9.0.1 # [linux] 
-    - meson>=0.57.1
+    - clang >=11.0.1 # [linux] 
+    - clangxx >=11.0.1 # [linux]
+    - meson >=0.57.1
 
 test:
   commands:
diff --git a/recipes/prodigal-gv/build.sh b/recipes/prodigal-gv/build.sh
index 15bf945056cfe..86994efd62287 100644
--- a/recipes/prodigal-gv/build.sh
+++ b/recipes/prodigal-gv/build.sh
@@ -1,8 +1,10 @@
 #!/bin/sh
 
+set -xe
+
 # the executable is not installed in $PREFIX though
 # make install prefix=$PREFIX
 
-make CC=$CC
+make -j"${CPU_COUNT}" CC=$CC
 mkdir -p $PREFIX/bin
 cp $PKG_NAME $PREFIX/bin
diff --git a/recipes/prodigal-gv/meta.yaml b/recipes/prodigal-gv/meta.yaml
index e322b1fd68b4d..1221209bd1622 100644
--- a/recipes/prodigal-gv/meta.yaml
+++ b/recipes/prodigal-gv/meta.yaml
@@ -9,7 +9,9 @@ source:
   sha256: 1fb40a8ae204ce2f41a413edb1edf5b8f22c28c2812320e2807ab48f8e8ce795
 
 build:
-  number: 2
+  number: 4
+  run_exports:
+    - {{ pin_subpackage('prodigal-gv', max_pin="x") }}
 
 requirements:
   build:
@@ -26,5 +28,11 @@ test:
 
 about:
   home: https://github.com/apcamargo/prodigal-gv
-  license: GPL v3
+  license: GPL-3.0-only
+  license_file: LICENSE
   summary: A fork of Prodigal meant to improve gene calling for giant viruses
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
\ No newline at end of file
diff --git a/recipes/proteinortho/build.sh b/recipes/proteinortho/build.sh
index 65cbd9e704393..ea9644d67ef30 100755
--- a/recipes/proteinortho/build.sh
+++ b/recipes/proteinortho/build.sh
@@ -1,12 +1,17 @@
 #!/bin/bash
 
+mkdir -p $PREFIX/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include"
 export STATIC="FALSE"
-if [ `uname` == Darwin ]; then
+
+if [[ `uname` == Darwin ]]; then
     export LDFLAGS="${LDFLAGS} -headerpad_max_install_names"
-#    export STATIC="TRUE"
 fi
 
 make clean
-make CC=$CC CXX=$CXX STATIC=$STATIC all -j${CPU_COUNT}
-mkdir -p $PREFIX/bin
-make install PREFIX=$PREFIX/bin/
+make CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" STATIC="${STATIC}" all -j"${CPU_COUNT}"
+make install PREFIX="${PREFIX}/bin/"
diff --git a/recipes/proteinortho/meta.yaml b/recipes/proteinortho/meta.yaml
index 0d1fa24143b21..be6e3274c7f74 100755
--- a/recipes/proteinortho/meta.yaml
+++ b/recipes/proteinortho/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "proteinortho" %}
-{% set version = "6.3.2" %}
-{% set sha256 = "3b3c58e814ca10f77a25954b0bcddc479b9f61682f3dc5c93d85b07f109342a4" %}
+{% set version = "6.3.3" %}
+{% set sha256 = "989eed292e6e65c3725d4395cb7aed3c59754b5dc60d4a1e034aa1c4a6504c6c" %}
 
 package:
   name: {{ name }}
@@ -13,21 +13,22 @@ source:
 build:
   number: 0
   run_exports:
-    - {{ pin_subpackage('proteinortho', max_pin="x.x.x") }}
-
+    - {{ pin_subpackage('proteinortho', max_pin="x") }}
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
-    - {{ compiler('fortran') }}  
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]  
+    - {{ compiler('fortran') }}
     - cmake
   host:
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - liblapack
     - blis
   run:
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - perl
     - python
     - diamond >=0.9.29
@@ -42,13 +43,20 @@ test:
     - proteinortho_grab_proteins.pl -help
 
 about:
-  home: https://gitlab.com/paulklemm_PHD/proteinortho/
+  home: "https://gitlab.com/paulklemm_PHD/proteinortho"
   license: GPL-3.0-only
   license_family: GPL
   license_file: LICENSE
   summary: "Proteinortho is a tool to detect orthologous genes within different species."
+  dev_url: "https://gitlab.com/paulklemm_PHD/proteinortho"
+  doc_url: "https://gitlab.com/paulklemm_PHD/proteinortho/-/blob/master/README.md"
 
 extra:
   identifiers:
     - biotools:proteinortho
     - doi:10.3389/fbinf.2023.1322477
+    - usegalaxy-eu:proteinortho
+    - usegalaxy-eu:proteinortho_summary
+    - usegalaxy-eu:proteinortho_grab_proteins
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/psm-utils/LICENSE b/recipes/psm-utils/LICENSE
deleted file mode 100644
index 261eeb9e9f8b2..0000000000000
--- a/recipes/psm-utils/LICENSE
+++ /dev/null
@@ -1,201 +0,0 @@
-                                 Apache License
-                           Version 2.0, January 2004
-                        http://www.apache.org/licenses/
-
-   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
-   1. Definitions.
-
-      "License" shall mean the terms and conditions for use, reproduction,
-      and distribution as defined by Sections 1 through 9 of this document.
-
-      "Licensor" shall mean the copyright owner or entity authorized by
-      the copyright owner that is granting the License.
-
-      "Legal Entity" shall mean the union of the acting entity and all
-      other entities that control, are controlled by, or are under common
-      control with that entity. For the purposes of this definition,
-      "control" means (i) the power, direct or indirect, to cause the
-      direction or management of such entity, whether by contract or
-      otherwise, or (ii) ownership of fifty percent (50%) or more of the
-      outstanding shares, or (iii) beneficial ownership of such entity.
-
-      "You" (or "Your") shall mean an individual or Legal Entity
-      exercising permissions granted by this License.
-
-      "Source" form shall mean the preferred form for making modifications,
-      including but not limited to software source code, documentation
-      source, and configuration files.
-
-      "Object" form shall mean any form resulting from mechanical
-      transformation or translation of a Source form, including but
-      not limited to compiled object code, generated documentation,
-      and conversions to other media types.
-
-      "Work" shall mean the work of authorship, whether in Source or
-      Object form, made available under the License, as indicated by a
-      copyright notice that is included in or attached to the work
-      (an example is provided in the Appendix below).
-
-      "Derivative Works" shall mean any work, whether in Source or Object
-      form, that is based on (or derived from) the Work and for which the
-      editorial revisions, annotations, elaborations, or other modifications
-      represent, as a whole, an original work of authorship. For the purposes
-      of this License, Derivative Works shall not include works that remain
-      separable from, or merely link (or bind by name) to the interfaces of,
-      the Work and Derivative Works thereof.
-
-      "Contribution" shall mean any work of authorship, including
-      the original version of the Work and any modifications or additions
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diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml
index 02b60ab80be76..7029e73d9b4c9 100644
--- a/recipes/psm-utils/meta.yaml
+++ b/recipes/psm-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "psm-utils" %}
-{% set version = "1.1.1" %}
-{% set sha256 = "8926d8f5e2e05ac38d54d6ae5c89461568085b60d23414a907c820bc674a4a2b" %}
+{% set version = "1.2.0" %}
+{% set sha256 = "38ead8b9ef6f46552d1016a0947527b68af33b73e9f39177f091136551c23c4a" %}
 
 package:
   name: {{ name|lower }}
@@ -14,18 +14,19 @@ build:
   number: 0
   entry_points:
     - psm_utils=psm_utils.__main__:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   run_exports:
-    - {{ pin_subpackage('psm-utils', max_pin="x.x") }}
+    - {{ pin_subpackage('psm-utils', max_pin="x") }}
 
 requirements:
   host:
     - pip
     - python >=3.7
+    - setuptools
   run:
     - python >=3.7
-    - pyteomics >=4,<4.7
+    - pyteomics >=4
     - pyopenms
     - lxml
     - psims
diff --git a/recipes/pybigtools/build.sh b/recipes/pybigtools/build.sh
index 9f7a317e6924c..ea4ae484cce66 100644
--- a/recipes/pybigtools/build.sh
+++ b/recipes/pybigtools/build.sh
@@ -4,10 +4,6 @@
 # -x = print every executed command
 set -ex
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo"
-
 # There is some issue here building with Python 3.8 on macOS >= 11
 # See https://github.com/pypa/cibuildwheel/issues/1410
 export MACOSX_DEPLOYMENT_TARGET=12.7
@@ -23,12 +19,6 @@ if [[ $target_platform == osx-* ]]; then
     done
 fi
 
-# Use a custom temporary directory as home on macOS.
-# (not sure why this is useful, but people use it in bioconda recipes)
-if [ `uname` == Darwin ]; then
-	export HOME=`mktemp -d`
-fi
-
 # Build statically linked binary with Rust
 # Note: This sdist is a bit wonky because it was generated from a monorepo by running maturin sdist
 RUST_BACKTRACE=1 
@@ -44,4 +34,4 @@ maturin build -m pybigtools/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --relea
 ${PYTHON} -m pip install pybigtools/target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
 
 # Move the LICENSE file to the root dir
-mv pybigtools/LICENSE .
\ No newline at end of file
+mv pybigtools/LICENSE .
diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml
index ccc184ca0c425..c1fe465fc0dd2 100644
--- a/recipes/pybigtools/meta.yaml
+++ b/recipes/pybigtools/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pybigtools" %}
-{% set version = "0.2.0" %}
-{% set sha256 = "7c5d1676c5042b92f3f11bae3166cda92f5b33eb1a0a8c3411eb4c54ed94dd12" %}
+{% set version = "0.2.2" %}
+{% set sha256 = "8fe5e5f04cadca7d1f58653203928455e405a25fbc26d272ce5e443b70533ba3" %}
 
 package:
   name: {{ name }}
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('pybigtools', max_pin="x.x") }}
 
@@ -32,16 +32,17 @@ test:
     - pybigtools
 
 about:
-  home: https://github.com/jackh726/bigtools/
+  home: "https://github.com/jackh726/bigtools"
   license: MIT
   summary: 'pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O'
   license_family: MIT
   license_file: LICENSE
-  doc_url: https://bigtools.readthedocs.io
-  dev_url: https://github.com/jackh726/bigtools/
+  doc_url: "https://bigtools.readthedocs.io"
+  dev_url: "https://github.com/jackh726/bigtools"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - doi:10.5281/zenodo.10606493
diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
index 07f43e97d3b13..b22fd18cf58ee 100644
--- a/recipes/pybiolib/meta.yaml
+++ b/recipes/pybiolib/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.205" %}
+{% set version = "1.2.223" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 79693b4ebc2b89703f6b2dcf1134b65840d3505b32a6c866009f276ce0da99de
+  sha256: 40873a8acc8b30656f3bdb4aa267efef6052b53b83738e6b806615eefe8adbd9
 
 build:
   number: 0
@@ -24,6 +24,7 @@ requirements:
     - poetry >=1.8.0
     - poetry-core
     - pip
+    - setuptools
   run:
     - python >=3.6,<3.13
     - appdirs >=1.4.3
diff --git a/recipes/pycomo/meta.yaml b/recipes/pycomo/meta.yaml
index af10fd414d0aa..a2d092fe9f69e 100644
--- a/recipes/pycomo/meta.yaml
+++ b/recipes/pycomo/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pycomo" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.4" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pycomo-{{ version }}.tar.gz
-  sha256: 242973127addd422bcfabc8db79caaaa88c3a1e87f86b735a4de5449abe99331
+  sha256: 5da3c1e85f0f0ca7b0fda240a7badb9ed8a84d65ec338c4334a0895463b1fb49
 
 build:
   entry_points:
diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml
index 466847c774fb9..a05490fa87488 100644
--- a/recipes/pydeseq2/meta.yaml
+++ b/recipes/pydeseq2/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pydeseq2" %}
-{% set version = "0.4.11" %}
+{% set version = "0.4.12" %}
 
 package:
   name: {{ name|lower }}
@@ -7,19 +7,20 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz
-  sha256: 3eb9ae8fd586c04c03e0fa49f274c2db65d0fad19c91803dda09dccb7aaf598c
+  sha256: dfe1051bd1639caef8be42761f4aa6e93fee0920bb0c35ef51fb454151644015
 
 build:
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
   run_exports:
-    - {{ pin_subpackage('pydeseq2', max_pin="x") }}
+    - {{ pin_subpackage('pydeseq2', max_pin="x.x") }}
 
 requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
     - anndata >=0.8.0
@@ -34,10 +35,6 @@ requirements:
 test:
   imports:
     - pydeseq2
-  commands:
-    - pip check
-  requires:
-    - pip
 
 about:
   home: https://github.com/owkin/PyDESeq2
@@ -45,6 +42,8 @@ about:
   license: MIT
   license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/owkin/PyDESeq2
+  doc_url: https://pydeseq2.readthedocs.io/en/latest
 
 extra:
   identifiers:
diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml
index 5cb5faa479d92..a08d3a6682906 100644
--- a/recipes/pyfamsa/meta.yaml
+++ b/recipes/pyfamsa/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pyfamsa" %}
-{% set version = "0.5.2" %}
+{% set version = "0.5.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 5715eccfaf0ac38f9eba951285de900086e10007b0e2508e3735879d7e4e5fce
+  sha256: d5492e885c71dedfd3ddb1fc16b02981388f7fcb7dbb152c37b8bffa5f760ce5
 
 build:
   number: 0
@@ -19,11 +19,13 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - cmake
+    - make
   host:
     - python
     - pip
     - cython
-    - semantic_version
+    - scikit-build-core
     - scoring-matrices >=0.2
   run:
     - python
diff --git a/recipes/pyjess/meta.yaml b/recipes/pyjess/meta.yaml
new file mode 100644
index 0000000000000..82ed92722ed9e
--- /dev/null
+++ b/recipes/pyjess/meta.yaml
@@ -0,0 +1,51 @@
+{% set name = "pyjess" %}
+{% set version = "0.3.3" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: dc7d9a39ce75112d672780a57a9629afb3a78af6194028d8fad7a7138024de6f
+
+build:
+  number: 0
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv"
+  run_exports:
+    - {{ pin_subpackage("pyjess", max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - cmake >=3.20
+    - make
+  host:
+    - python
+    - pip
+    - cython
+    - scikit-build-core
+  run:
+    - python
+
+test:
+  imports:
+    - {{ name }}
+  commands:
+    - python -m unittest -vv {{ name }}.tests
+
+about:
+  home: "https://github.com/althonos/pyjess"
+  license: "MIT"
+  license_family: MIT
+  license_file: COPYING
+  summary: "Cython bindings and Python interface to JESS, a 3D template matching software."
+  doc_url: "https://pyjess.readthedocs.org"
+  dev_url: "https://github.com/althonos/pyjess"
+
+extra:
+  recipe-maintainers:
+    - althonos
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/pyopal/build_failure.osx-64.yaml b/recipes/pyopal/build_failure.osx-64.yaml
deleted file mode 100644
index 2d7f45a8d11c0..0000000000000
--- a/recipes/pyopal/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 97120fb97215d81e614d54e48a5765c4bb1401d5962f33775f32d47c962fab3d  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  LIPO=x86_64-apple-darwin13.4.0-lipo
-  MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
-  NM=x86_64-apple-darwin13.4.0-nm
-  NMEDIT=x86_64-apple-darwin13.4.0-nmedit
-  OBJC=x86_64-apple-darwin13.4.0-clang
-  OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  OTOOL=x86_64-apple-darwin13.4.0-otool
-  PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
-  RANLIB=x86_64-apple-darwin13.4.0-ranlib
-  REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
-  SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk
-  SEGEDIT=x86_64-apple-darwin13.4.0-segedit
-  SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
-  SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
-  SIZE=x86_64-apple-darwin13.4.0-size
-  STRINGS=x86_64-apple-darwin13.4.0-strings
-  STRIP=x86_64-apple-darwin13.4.0-strip
-  _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
-  ac_cv_func_malloc_0_nonnull=yes
-  ac_cv_func_realloc_0_nonnull=yes
-  build_alias=x86_64-apple-darwin13.4.0
-  host_alias=x86_64-apple-darwin13.4.0
-  INFO: activate_clangxx_osx-64.sh made the following environmental changes:
-  CLANGXX=x86_64-apple-darwin13.4.0-clang
-  CXX=x86_64-apple-darwin13.4.0-clang
-  CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pyopal-0.6.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pyopal-0.6.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  Using pip 24.0 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10)
-  Non-user install because user site-packages disabled
-  Ignoring indexes: https://pypi.org/simple
-  Created temporary directory: /private/tmp/pip-build-tracker-tis4zq2n
-  Initialized build tracking at /private/tmp/pip-build-tracker-tis4zq2n
-  Created build tracker: /private/tmp/pip-build-tracker-tis4zq2n
-  Entered build tracker: /private/tmp/pip-build-tracker-tis4zq2n
-  Created temporary directory: /private/tmp/pip-install-_gf39vkr
-  Created temporary directory: /private/tmp/pip-ephem-wheel-cache-8_pk_ilh
-  Processing $SRC_DIR
-    Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-tis4zq2n'
-    Created temporary directory: /private/tmp/pip-modern-metadata-8ma8_ihc
-    Preparing metadata (pyproject.toml): started
-    Preparing metadata (pyproject.toml): finished with status 'done'
-    Source in $SRC_DIR has version 0.6.1, which satisfies requirement pyopal==0.6.1 from file://$SRC_DIR
-    Removed pyopal==0.6.1 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-tis4zq2n'
-  Created temporary directory: /private/tmp/pip-unpack-fzs6hzuk
-  Building wheels for collected packages: pyopal
-    Created temporary directory: /private/tmp/pip-wheel-njzbb_zu
-    Destination directory: /private/tmp/pip-wheel-njzbb_zu
-    Building wheel for pyopal (pyproject.toml): started
-    Building wheel for pyopal (pyproject.toml): finished with status 'done'
-    Created wheel for pyopal: filename=pyopal-0.6.1-cp310-cp310-macosx_10_13_x86_64.whl size=515862 sha256=a38f136881522e429a78dbe17e4c6cc8f971793618ddbac5d30b23cffff24a7d
-    Stored in directory: /private/tmp/pip-ephem-wheel-cache-8_pk_ilh/wheels/b1/80/41/acf0f7026053655891e76f1f15adb5e2a74199a76839144c8d
-  Successfully built pyopal
-  Installing collected packages: pyopal
-
-  Successfully installed pyopal-0.6.1
-  Removed build tracker: '/private/tmp/pip-build-tracker-tis4zq2n'
-
-  Resource usage statistics from building pyopal:
-     Process count: 5
-     CPU time: Sys=0:00:01.5, User=0:00:24.7
-     Memory: 434.8M
-     Disk usage: 17.2K
-     Time elapsed: 0:00:40.0
-
-
-  Packaging pyopal
-  Packaging pyopal-0.6.1-py310h04ad86b_1
-  compiling .pyc files...
-  number of files: 40
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2711, in build
-      newly_built_packages = bundlers[pkg_type](output_d, m, env, stats)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1850, in bundle_conda
-      files = post_process_files(metadata, initial_files)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1664, in post_process_files
-      post_build(m, new_files, build_python=python)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1727, in post_build
-      post_process_shared_lib(m, f, prefix_files, host_prefix)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1603, in post_process_shared_lib
-      mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 481, in mk_relative_osx
-      existing_rpaths = macho.get_rpaths(path, build_prefix=prefix)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 252, in get_rpaths
-      dylib_loads = otool(path, build_prefix, is_rpath)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool
-      lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8")
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output
-      return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run
-      raise CalledProcessError(retcode, process.args,
-  subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/pyopal_1718320809916/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/pyopal_1718320809916/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.10/site-packages/pyopal/platform/sse2.cpython-310-darwin.so']' died with <Signals.SIGABRT: 6>.
-# Last 100 lines of the build log.
diff --git a/recipes/pyopal/meta.yaml b/recipes/pyopal/meta.yaml
index e7a82782a5ad7..f0cb6488709ba 100644
--- a/recipes/pyopal/meta.yaml
+++ b/recipes/pyopal/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pyopal" %}
-{% set version = "0.6.1" %}
+{% set version = "0.7.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,28 +7,29 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 039487f2ffeae29962e1ed38db401fbe2c295f894461f1dd9af09e94e1feccb0
+  sha256: 690b46fb158f10c663e14cf51a50060a27adb51e113ed1cdfbe50b4b9b1d7689
 
 build:
-  number: 1
+  number: 0
   skip: True  #[py2k]
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - cmake
+    - make
   host:
     - python
     - pip
     - cython
-    - setuptools
+    - scikit-build-core
     - scoring-matrices >=0.2
   run:
     - python
-    - setuptools
     - archspec
     - scoring-matrices >=0.2
 
@@ -41,9 +42,11 @@ test:
 about:
   home: https://github.com/althonos/pyopal
   license: MIT
+  license_family: MIT
   license_file: COPYING
   summary: Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
-  doc_url: https://pyopal.readthedocs.org/
+  doc_url: https://pyopal.readthedocs.org
+  dev_url: https://github.com/althonos/pyopal
 
 extra:
   recipe-maintainers:
diff --git a/recipes/pyopenms/build_failure.linux-64.yaml b/recipes/pyopenms/build_failure.linux-64.yaml
deleted file mode 100644
index 1163117bd07fe..0000000000000
--- a/recipes/pyopenms/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: cef771a499e1d08792062492677584c7f734492305e7c2bb29e8d1dddf2e2dc4  # The commit at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-   - numpy 1.23.*
-   - libopenms 2.9.1.*
-   - qt 5.12.*
-   - cython >=0.25.2
-   - matplotlib-base
-   - wheel
-   - boost-cpp 1.78.0.*
-   - pandas
-   - xerces-c 3.2.*
-   - libgcc-ng >=12
-
-  with channels:
-   - conda-forge
-   - bioconda
-   - defaults
-
-  The reported errors are:
-  - Encountered problems while solving:
-  -   - package libopenms-2.9.1-h135471a_1 requires qt >=5.12.9,<5.13.0a0, but none of the providers can be installed
-  -
-
-  Leaving build/test directories:
-    Work:
-   /opt/conda/conda-bld/work
-    Test:
-   /opt/conda/conda-bld/test_tmp
-  Leaving build/test environments:
-    Test:
-  source activate  /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
-    Build:
-  source activate  /opt/conda/conda-bld/_build_env
-
-
-  Traceback (most recent call last):
-    File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions
-      solution = solver.solve_for_action(_specs, prefix)
-    File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 230, in solve_for_action
-      t = self.solve(specs)
-    File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 220, in solve
-      raise RuntimeError("Solver could not find solution."  error_string)
-  RuntimeError: Solver could not find solution.Mamba failed to solve:
-   - libstdcxx-ng >=12
-   - autowrap >=0.22.10
-   - pip
-   - python 3.11.*
-   - libsvm 325.*
-   - setuptools
-   - numpy 1.23.*
-   - libopenms 2.9.1.*
-   - qt 5.12.*
-   - cython >=0.25.2
-   - matplotlib-base
-   - wheel
-   - boost-cpp 1.78.0.*
-   - pandas
-   - xerces-c 3.2.*
-   - libgcc-ng >=12
-
-  with channels:
-   - conda-forge
-   - bioconda
-   - defaults
-
-  The reported errors are:
-  - Encountered problems while solving:
-  -   - package libopenms-2.9.1-h135471a_1 requires qt >=5.12.9,<5.13.0a0, but none of the providers can be installed
-  -
-
-  During handling of the above exception, another exception occurred:
-
-  Traceback (most recent call last):
-    File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
-      sys.exit(main())
-    File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
-      call_conda_build(action, config)
-    File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
-      result = api.build(
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
-      return build_tree(
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
-      packages_from_this = build(metadata, stats,
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build
-      output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs
-      for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False):
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set
-      conda_packages = finalize_outputs_pass(
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass
-      fm = finalize_metadata(
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata
-      build_unsat, host_unsat = add_upstream_pins(m,
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins
-      host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host',
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files
-      deps, actions, unsat = get_env_dependencies(m, env, m.config.variant,
-    File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies
-      actions = environ.get_install_actions(tmpdir, tuple(dependencies), env,
-    File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions
-      raise err
-  conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libopenms==2.9.1=h135471a_1"), MatchSpec("qt[version='>=5.12.9,<5.13.0a0']")}
-# Last 100 lines of the build log.
diff --git a/recipes/pyopenms/conda_build_config.yaml b/recipes/pyopenms/conda_build_config.yaml
deleted file mode 100644
index adf8945de603d..0000000000000
--- a/recipes/pyopenms/conda_build_config.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-python:
-  - 3.9.*
-  - 3.10.*
-  - 3.11.*
-python_impl:
-  - cpython
-  - cpython
-  - cpython
-numpy:
-  - 1.23.*
-  - 1.23.*
-  - 1.23.*  
-zip_keys:
-  - python
-  - python_impl
-  - numpy
diff --git a/recipes/pyopenms/meta.yaml b/recipes/pyopenms/meta.yaml
index a3376b5a32f13..59cf39da0d5d7 100644
--- a/recipes/pyopenms/meta.yaml
+++ b/recipes/pyopenms/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pyopenms" %}
-{% set version = "3.1.0" %} # if ends with 'dev' it is considered a development release and pulled from GitHub
+{% set version = "3.2.0" %} # if ends with 'dev' it is considered a development release and pulled from GitHub
 package:
   name: {{ name|lower  }}
   version: {{ version  }}
@@ -11,13 +11,13 @@ source:
   git_depth: 1 # (Defaults to -1/not shallow)
 {% else %}
 source:
-  url: https://github.com/OpenMS/OpenMS/releases/download/Release{{ version }}/OpenMS-{{ version }}-src.tar.gz
-  md5: 6a60ef1a95c7ce915cc3a02e5bccd593
+  url: https://github.com/OpenMS/OpenMS/releases/download/release%2F3.2.0/OpenMS-3.2.tar.gz # since we discarded the trailing 0 during the GHA we have to hard code this, fix it next release
+  md5: e15b34a4ccaf7070d186fd01a6d57f3e
 {% endif %}
 
 build:
   skip: True  # [py2k or osx]
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("pyopenms", max_pin="x.x") }}  
 
@@ -26,33 +26,36 @@ requirements:
     - {{ compiler('cxx') }}
     - make
     - cmake
-    - sysroot_linux-64 =2.17 # [linux]    
+    - sysroot_linux-64 =2.17 # [linux]
   host:
-    - libopenms {{ version }}
+    - eigen >=3.3.4
+    - libopenms >={{ version }}
     - llvm-openmp # [osx]
     - libsvm
     - xerces-c
     - boost-cpp
-    - qt-main
-    - python {{ python }}
+    - qt-main >=5.15.8
+    - python >=3.9,<3.13
     - cython >=0.25.2
     - autowrap >=0.22.10
     - setuptools
     - wheel
     - pip
-    - numpy {{ numpy }}
+    - numpy >=1.23.*
     - pandas
     - matplotlib-base
     - sysroot_linux-64 =2.17 # [linux]
+    - icu >=73.2,<74.0a0
   run: # run_exports in libopenms should take care of the libraries. But it does not because of bugs. So copy everthing again and again
-    - libopenms {{ version }}
+    - libopenms >={{ version }}
     - llvm-openmp # [osx]
     - libsvm
     - xerces-c
     - boost-cpp
-    - qt-main
-    - python {{ python }}
-    - numpy {{ numpy }}
+    - qt-main >=5.15.8
+    - eigen >=3.3.4
+    - python >=3.9,<3.13
+    - numpy >=1.23.*
     - pandas
     - matplotlib-base
     - sysroot_linux-64 =2.17 # [linux]
diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml
index 76cfdde6e5ea3..bf4a900db8352 100644
--- a/recipes/pyrodigal/meta.yaml
+++ b/recipes/pyrodigal/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pyrodigal" %}
-{% set version = "3.5.2" %}
+{% set version = "3.6.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 2a40eb6113e720ada51c326958b295944cdc33ecee9f25d5bad4e9a8e6e6f7f5
+  sha256: 3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78
 
 build:
   number: 0
@@ -20,10 +20,13 @@ build:
 requirements:
   build:
     - {{ compiler('c') }}
+    - cmake >=3.20
+    - make
   host:
     - python
     - pip
     - cython
+    - scikit-build-core
   run:
     - python
     - archspec >=0.2.0
diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch
new file mode 100644
index 0000000000000..a01549df70c8c
--- /dev/null
+++ b/recipes/pyscenic/dill_patch.patch
@@ -0,0 +1,11 @@
+--- pyscenic-0.12.1/src/pyscenic/prune.py	2022-11-21 10:38:05.000000000 +0000
++++ pyscenic-0.12.1/src/pyscenic/prune.py	2024-10-02 10:20:58.423708208 +0000
+@@ -20,8 +20,8 @@
+ from dask import delayed
+ from dask.dataframe import from_delayed
+ from dask.distributed import Client, LocalCluster
+-from multiprocessing_on_dill.connection import Pipe
+-from multiprocessing_on_dill.context import Process
++from multiprocessing import Pipe
++from multiprocessing import Process
+ 
diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml
new file mode 100644
index 0000000000000..dfbec6edf7f79
--- /dev/null
+++ b/recipes/pyscenic/meta.yaml
@@ -0,0 +1,80 @@
+{% set name = "pyscenic" %}
+{% set version = "0.12.1" %}
+{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: "{{ sha256 }}"
+  patches:
+    - dill_patch.patch
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - pyscenic = pyscenic.cli.pyscenic:main
+    - db2feather = pyscenic.cli.db2feather:main
+    - csv2loom = pyscenic.cli.csv2loom:main
+    - invertdb = pyscenic.cli.invertdb:main
+    - gmt2regions = pyscenic.cli.gmt2regions:main
+  run_exports:
+    - "{{ pin_subpackage(name, max_pin='x.x') }}"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+
+requirements:
+  host:
+    - python >=3.6
+    - pip
+    - setuptools
+  run:
+    - python >=3.6
+    - aiohttp
+    - arboreto
+    - attrs
+    - boltons
+    - cloudpickle
+    - cytoolz
+    - dill
+    - dask-core >=2023.4.1
+    - distributed >=2023.4.1,<2023.5.0
+    - frozendict
+    - fsspec
+    - llvmlite
+    - loompy
+    - networkx
+    - numba >=0.51.2
+    - numexpr
+    - pandas >=1.3.5
+    - pyyaml
+    - requests
+    - scikit-learn
+    - scipy
+    - tqdm
+    - umap-learn
+    - numpy ==1.23.5
+    - pyarrow
+    - interlap
+    - ctxcore
+
+test:
+  imports:
+    - pyscenic
+
+about:
+  home: "https://github.com/aertslab/pySCENIC"
+  summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments."
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
+  license_file: "LICENSE.txt"
+  dev_url: "https://github.com/aertslab/pySCENIC"
+  doc_url: "https://scenic.aertslab.org"
+
+extra:
+  identifiers:
+    - doi:10.1038/nmeth.4463
+    - doi:10.1038/s41592-023-01938-4
+    - biotools:scenic
diff --git a/recipes/quantms-utils/meta.yaml b/recipes/quantms-utils/meta.yaml
index 0c0457e61496a..5cd911b25e558 100644
--- a/recipes/quantms-utils/meta.yaml
+++ b/recipes/quantms-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "quantms-utils" %}
-{% set version = "0.0.11" %}
+{% set version = "0.0.12" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/quantms_utils-{{ version }}.tar.gz
-  sha256: f1205db7526f09d36606288782363b352546a100b4763c16d988d7cdb45bf26f
+  sha256: 99ecf7e68acad272749040b231701018aaa76c391ceb234eaefd6f6842c2a4e6
 
 build:
   entry_points:
@@ -15,18 +15,20 @@ build:
   noarch: python
   run_exports:
     - {{ pin_subpackage('quantms-utils', max_pin="x.x") }}
-  script: "{{ PYTHON }} -m pip install . --no-deps -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   number: 0
 
 requirements:
   host:
-    - python >=3.8,<4.0
+    - python >=3.8
     - pip
+    - poetry-core
+    - setuptools
   run:
     - python >=3.7.0,<4.0.0
     - click >=7.0
     - pydantic >=1.10,<2
-    - sdrf-pipelines >=0.0.29
+    - sdrf-pipelines >=0.0.31
     - pyopenms >=2.9.1
     - ms2rescore ==3.0.3
     - psm-utils ==0.8.2
@@ -37,21 +39,24 @@ requirements:
     - scipy ==1.13.1
     - scikit-learn
     - deeplcretrainer
+    - protobuf >=3.9.2
+    - pyarrow
+    - pygam
 
 test:
   imports:
     - quantmsutils
   commands:
     - quantmsutilsc --help
-  requires:
-    - pip
 
 about:
-  home: https://www.github.com/bigbio/quantms-utils
-  summary: Python package with scripts and helpers for the quantms workflow
+  home: "https://www.github.com/bigbio/quantms-utils"
+  summary: "Python package with scripts and helpers for the quantms workflow."
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  dev_url: https://www.github.com/bigbio/quantms-utils
+  dev_url: "https://www.github.com/bigbio/quantms-utils"
+  doc_url: "https://quantms.org/home"
 
 extra:
   recipe-maintainers:
diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml
index 4b9f0a96c8548..bbe2024660d3b 100644
--- a/recipes/quast/meta.yaml
+++ b/recipes/quast/meta.yaml
@@ -1,12 +1,14 @@
-{% set version = "5.2.0" %}
-{% set hash = "ccd911087cfa254ad4b8eadac4f95d4685e44c3996f5516b8e0ce6f7cfa7e0db" %}
+{% set version = "5.3.0" %}
+{% set hash = "ac9dba03ef9d0a51d7a9e2c56826104e78f340f6263a3ad393648442debc74ec" %}
 
 package:
   name: quast
   version: {{ version }}
 
 build:
-  number: 4
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("quast", max_pin="x.x") }}
 
 source:
   url:
diff --git a/recipes/quota_anchor/build.sh b/recipes/quota_anchor/build.sh
index 71922513c1169..1688e70c760a7 100644
--- a/recipes/quota_anchor/build.sh
+++ b/recipes/quota_anchor/build.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
-$PYTHON -m pip install --no-deps --ignore-installed . -vv
+
+$PYTHON -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
 echo "[software]
 gffread = ${PREFIX}/bin/gffread
 AnchorWave = ${PREFIX}/bin/anchorwave
diff --git a/recipes/quota_anchor/meta.yaml b/recipes/quota_anchor/meta.yaml
index bd563736d46b1..275adc67bc319 100644
--- a/recipes/quota_anchor/meta.yaml
+++ b/recipes/quota_anchor/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "quota_anchor" %}
-{% set version = "0.0.1a0" %}
-{% set sha256 = "01d8520825fee67f8c73803d3bbe7855291592c064cd2d5712d02e104a71a8fa" %}
+{% set version = "0.0.1a1" %}
+{% set sha256 = "b6eb3ba82a32a8a5e238615dac6ef0eeef5de0d584643132b903dcddb94e760d" %}
 
 package:
   name: {{ name }}
@@ -19,7 +19,8 @@ build:
 requirements:
   host:
     - python >=3
-    - pip 
+    - pip
+    - setuptools
   run:
     - python >=3
     - gffread
@@ -33,18 +34,19 @@ requirements:
     - pal2nal
     - paml
     - plotnine
-    - seaborn
+    - seaborn-base
     - pandas
     - numpy
-
+    - alive-progress
 
 test:
   commands:
-    - 'quota_Anchor 2>&1 | grep "usage: quota_Anchor"'
+    - 'quota_Anchor -h'
 
 about:
   home: https://github.com/baoxingsong/quota_Anchor
   license: MIT
+  license_family: MIT
   summary: 'Strand and WGD aware syntenic gene identification'
   description: "Strand and WGD aware syntenic gene identification for comparative genomics"
   dev_url: https://github.com/baoxingsong/quota_Anchor
diff --git a/recipes/r-facets/meta.yaml b/recipes/r-facets/meta.yaml
index 4bbd9aa678bdd..f0ea43f0f9c9d 100644
--- a/recipes/r-facets/meta.yaml
+++ b/recipes/r-facets/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: aa671d4fc66e10ce2fe4c8b2cbac4946da8a1564627240ea916db6cd8ec2a6c5
 
 build:
-  number: 5
+  number: 6
   run_exports:
     - {{ pin_subpackage("r-facets", max_pin="x") }}
   rpaths:
@@ -39,5 +39,6 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:facets
diff --git a/recipes/r-liger/meta.yaml b/recipes/r-liger/meta.yaml
index bef57845d132b..23c40640860ef 100644
--- a/recipes/r-liger/meta.yaml
+++ b/recipes/r-liger/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "liger" %}
-{% set version = '2.0.1' %}
+{% set version = '2.1.0' %}
 
 package:
   name: r-{{ name }}
@@ -9,7 +9,7 @@ source:
   url:
     - {{ cran_mirror }}/src/contrib/rliger_{{ version }}.tar.gz
     - {{ cran_mirror }}/src/contrib/Archive/rliger/rliger_{{ version }}.tar.gz
-  sha256: e1163722608ba2c2424e87f44b4d62c36dacca429dfb4fee41eb9a0da99703a4
+  sha256: 16b79fdcd1467e4c192f9fb38bb4f35a6710aee319839639edfdf5d87e086e74
 
 build:
   number: 0
diff --git a/recipes/r-locuszoomr/build.sh b/recipes/r-locuszoomr/build.sh
new file mode 100755
index 0000000000000..03cb951f643eb
--- /dev/null
+++ b/recipes/r-locuszoomr/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+if [ ! -f DESCRIPTION ]; then
+    echo "Error: DESCRIPTION file not found"
+    exit 1
+fi
+mv DESCRIPTION DESCRIPTION.old || exit 1
+grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION || exit 1
+${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/recipes/r-locuszoomr/meta.yaml b/recipes/r-locuszoomr/meta.yaml
new file mode 100644
index 0000000000000..10a955fc63a37
--- /dev/null
+++ b/recipes/r-locuszoomr/meta.yaml
@@ -0,0 +1,83 @@
+{% set version = '0.3.5' %}
+
+package:
+  name: r-locuszoomr
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/locuszoomr_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/locuszoomr/locuszoomr_{{ version }}.tar.gz
+  sha256: 92c8bb3a84ceed82e3cf142129eb83c21a1eb780cd6c0fb4b084e099917c2c3d
+
+build:
+  run_exports: 
+    - {{ pin_subpackage("r-locuszoomr", max_pin="x.x") }}
+  noarch: generic
+  merge_build_host: True  # [win]
+  number: 0
+
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  host:
+    - r-base
+    - bioconductor-annotationfilter
+    - bioconductor-biocgenerics
+    - bioconductor-genomeinfodb
+    - bioconductor-genomicranges
+    - bioconductor-iranges
+    - r-ldlinkr
+    - r-cowplot
+    - r-dplyr
+    - bioconductor-ensembldb
+    - r-gggrid
+    - r-ggplot2
+    - r-ggrepel
+    - r-memoise
+    - r-plotly
+    - r-rlang
+    - bioconductor-rtracklayer
+    - r-zoo
+
+  run:
+    - r-base
+    - bioconductor-annotationfilter
+    - bioconductor-biocgenerics
+    - bioconductor-genomeinfodb
+    - bioconductor-genomicranges
+    - bioconductor-iranges
+    - r-ldlinkr
+    - r-cowplot
+    - r-dplyr
+    - bioconductor-ensembldb
+    - r-gggrid
+    - r-ggplot2
+    - r-ggrepel
+    - r-memoise
+    - r-plotly
+    - r-rlang
+    - bioconductor-rtracklayer
+    - r-zoo
+
+test:
+  commands:
+    - $R -e "library('locuszoomr')"
+    - $R -e "packageVersion('locuszoomr')"
+    - $R -e "help(package = 'locuszoomr')"
+
+about:
+  home: https://github.com/myles-lewis/locuszoomr
+  license: GPL-3
+  summary: Publication-ready regional gene locus plots similar to those produced by the web interface
+    'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic
+    data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly',
+    allowing flexibility and easy customisation including laying out multiple locus
+    plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess>
+    to query linkage disequilibrium data from the 1000 Genomes Project and can overlay
+    this on plots.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
diff --git a/recipes/r-mfassignr/meta.yaml b/recipes/r-mfassignr/meta.yaml
index 421e7b81ce8ea..6787db1e2ee5f 100644
--- a/recipes/r-mfassignr/meta.yaml
+++ b/recipes/r-mfassignr/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mfassignr" %}
-{% set version = "1.1.1" %}
+{% set version = "1.1.2" %}
 {% set github = "https://github.com/RECETOX" %}
 
 package:
@@ -8,7 +8,7 @@ package:
 
 source:
   url: "{{ github }}/MFAssignR/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 11d0c871871e52010978df0273221f95ccd21e950585e19a63d8b40ea23aebcb
+  sha256: 99c15cbbb13609d8331e85cba5d3900f7d006dda9798aa778ea48a00436dd327
 
 build:
   number: 0
diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml
index 999f9600bc26a..963fd3894e35a 100644
--- a/recipes/r-oncopharmadb/meta.yaml
+++ b/recipes/r-oncopharmadb/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "r-oncopharmadb" %}
-{% set version = "1.7.0" %}
+{% set version = "1.8.1" %}
 {% set github = "https://github.com/sigven/oncoPharmaDB" %}
 
 package:
@@ -8,7 +8,7 @@ package:
 
 source:
   url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 001e9b133028b00df90fa7081ad315fcb28be671ac7477cf6b689f0e0ca539fb
+  sha256: e21386183a6916c328dac32e0ea92a5d9c1d28921b4e3e14d4b63515335a1f51
   
 build:
   number: 0
diff --git a/recipes/r-quilt/meta.yaml b/recipes/r-quilt/meta.yaml
index b18e2ef0e20cd..6e6ef9613842c 100644
--- a/recipes/r-quilt/meta.yaml
+++ b/recipes/r-quilt/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "r-quilt" %}
-{% set version = "2.0.0" %}
-{% set sha256 = "723c52371fd8c495a54165b168db70d8c4ce001cd4dc902e63db0240318e8a6e" %}
+{% set version = "2.0.1" %}
+{% set sha256 = "6e0f041641c96014b879a7fea6c0cc21351a83e8ba938c828c07a0c297574eba" %}
 
 package:
   name: '{{ name }}'
@@ -11,7 +11,7 @@ source:
     sha256: '{{ sha256 }}'
 
 build:
-  number: 2
+  number: 0
   run_exports:
         - {{ pin_subpackage('r-quilt', max_pin="x") }}
 
diff --git a/recipes/r-recetox-aplcms/meta.yaml b/recipes/r-recetox-aplcms/meta.yaml
index f47239d4c8f56..81fdcd3fa1705 100644
--- a/recipes/r-recetox-aplcms/meta.yaml
+++ b/recipes/r-recetox-aplcms/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "recetox-aplcms" %}
-{% set version = "0.13.3" %}
+{% set version = "0.13.4" %}
 {% set github = "https://github.com/RECETOX/recetox-aplcms" %}
 
 package:
@@ -8,7 +8,7 @@ package:
 
 source:
   url: "https://github.com/RECETOX/recetox-aplcms/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 3b37e51e959cba7cab6691f66dd2bb8279c4112fc5155576e0efef4ded2ad10b
+  sha256: c6c08d7e0def2b4df9f5ae366e0f69bf982d271bb8a4aec165e66c373d45c791
 
 build:
   number: 0
diff --git a/recipes/r-remapenrich/build.sh b/recipes/r-remapenrich/build.sh
new file mode 100644
index 0000000000000..df943f40e3e3d
--- /dev/null
+++ b/recipes/r-remapenrich/build.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# 'Autobrew' is being used by more and more packages these days
+# to grab static libraries from Homebrew bottles. These bottles
+# are fetched via Homebrew's --force-bottle option which grabs
+# a bottle for the build machine which may not be macOS 10.9.
+# Also, we want to use conda packages (and shared libraries) for
+# these 'system' dependencies. See:
+# https://github.com/jeroen/autobrew/issues/3
+export DISABLE_AUTOBREW=1
+
+# R refuses to build packages that mark themselves as Priority: Recommended
+mv DESCRIPTION DESCRIPTION.old
+grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION
+# shellcheck disable=SC2086
+${R} CMD INSTALL --build . ${R_ARGS}
+
+# Add more build steps here, if they are necessary.
+
+# See
+# https://docs.conda.io/projects/conda-build
+# for a list of environment variables that are set during the build process.
diff --git a/recipes/r-remapenrich/meta.yaml b/recipes/r-remapenrich/meta.yaml
new file mode 100644
index 0000000000000..4d73492800c64
--- /dev/null
+++ b/recipes/r-remapenrich/meta.yaml
@@ -0,0 +1,86 @@
+{% set version = '0.99.0' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-remapenrich
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url: https://github.com/nigiord/ReMapEnrich/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 87764400fbe3fbb41fda2395b669c9e926f7e39323a590f53f2944a9cd720aaf
+
+build:
+  noarch: generic
+  merge_build_host: True  # [win]
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  run_exports:
+    - {{ pin_subpackage('r-remapenrich', max_pin='x.x') }}
+
+# Suggests: knitr, rmarkdown
+requirements:
+  build:
+    - {{ posix }}filesystem        # [win]
+    - {{ posix }}git
+    - {{ posix }}zip               # [win]
+
+  host:
+    - r-base >=3.3
+    - bioconductor-genomicranges
+    - r-r.utils
+    - r-rmysql
+    - r-data.table
+
+  run:
+    - r-base >=3.3
+    - bioconductor-genomicranges
+    - r-r.utils
+    - r-rmysql
+    - r-data.table
+
+test:
+  commands:
+    # You can put additional test commands to be run here.
+    - $R -e "library('ReMapEnrich')"           # [not win]
+    - "\"%R%\" -e \"library('ReMapEnrich')\""  # [win]
+
+  # You can also put a file called run_test.py, run_test.sh, or run_test.bat
+  # in the recipe that will be run at test time.
+
+  # requires:
+    # Put any additional test requirements here.
+
+about:
+  home: https://github.com/nigiord/ReMapEnrich
+  license: AGPL-3
+  summary: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap
+    peaks
+  license_family: AGPL
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3'
+
+extra:
+  recipe-maintainers:
+    - nigiord
+
+# The original CRAN metadata for this package was:
+
+# Package: ReMapEnrich
+# Title: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks
+# Version: 0.99.0
+# Authors@R: c(person("Zacharie", "Menetrier", email = "zacharie.menetrier@gmail.com", role = c("aut", "cre")), person("Martin", "Mestdagh", email = "martin.mestdagh@gmail.com", role = c("aut")))
+# Description: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks
+# Depends: R (>= 3.3), GenomicRanges, data.table, R.utils, RMySQL
+# LazyData: true
+# RoxygenNote: 6.1.1
+# License: GNU Affero General Public License
+# Suggests: knitr, rmarkdown
+# VignetteBuilder: knitr
+# biocViews: c("GeneExpression", "GeneSetEnrichment", "GenomeAnnotation", "Software")
+
+# See
+# https://docs.conda.io/projects/conda-build for
+# more information about meta.yaml
diff --git a/recipes/r-seamless/meta.yaml b/recipes/r-seamless/meta.yaml
index 7ab85b48ac9dd..bc06815b02ea7 100644
--- a/recipes/r-seamless/meta.yaml
+++ b/recipes/r-seamless/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '0.1.0' %}
+{% set version = '0.1.1' %}
 
 package:
   name: r-seamless
@@ -8,14 +8,16 @@ source:
   url:
     - {{ cran_mirror }}/src/contrib/seAMLess_{{ version }}.tar.gz
     - {{ cran_mirror }}/src/contrib/Archive/seAMLess/seAMLess_{{ version }}.tar.gz
-  sha256: ab737087b3341884e915530d772948130f60299a65af40c43e101a8c819a37a3
+  sha256: 8bba2ae29cd9b92fad6e5a1b12aed589ee10b49ef81189524236b07d994ea07b
 
 build:
-  number: 3
+  number: 0
   noarch: generic
   rpaths:
     - lib/R/lib/
     - lib/
+  run_exports:
+    - {{ pin_subpackage("r-seamless", max_pin="x.x") }}
 
 requirements:
   host:
@@ -25,6 +27,7 @@ requirements:
     - r-ggtern
     - r-randomforest
     - r-music
+    - r-optparse
   run:
     - r-base
     - bioconductor-biobase
@@ -33,6 +36,7 @@ requirements:
     - r-randomforest
     - r-music
     - xbioc
+    - r-optparse
 
 test:
   commands:
diff --git a/recipes/r-spacexr/meta.yaml b/recipes/r-spacexr/meta.yaml
index 241ba913d5238..2fa7bafc68543 100644
--- a/recipes/r-spacexr/meta.yaml
+++ b/recipes/r-spacexr/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: 7d980ecea377a0e2131a87c3ff2b66f512ac69ecc96c2e2b8c1dd4d4f02403f8
 
 build:
-  number: 0
+  number: 1
   noarch: generic  # Specify that the package is noarch
   run_exports: '{{ pin_compatible("r-spacexr", max_pin="x.x") }}'
   rpaths:
@@ -66,6 +66,7 @@ requirements:
     - r-scales
     - r-lifecycle
     - r-evaluate
+    - openssh
 test:
   commands:
     - $R -e "library(spacexr)"
diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml
index d85b61e5b355c..ba6390ac5ee70 100644
--- a/recipes/rabbitqcplus/meta.yaml
+++ b/recipes/rabbitqcplus/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.2.9" %}
+{% set version = "2.3.0" %}
 
 package:
   name: rabbitqcplus
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 076cb1e11046d5a41464f74d7df363e2ea337e2cf3ad8e8b0712c5c7df746466
+  sha256: 9ce239d998582c50c373eefc8d5f83763439693fe348206107f27105a22d4aaf
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }}
diff --git a/recipes/racon/build.sh b/recipes/racon/build.sh
index 5bca68065ae90..90a870c2c9480 100644
--- a/recipes/racon/build.sh
+++ b/recipes/racon/build.sh
@@ -7,15 +7,26 @@ case $(uname -m) in
     aarch64)
         SPOA_OPTS="-Dspoa_use_simde=ON -Dspoa_use_simde_nonvec=ON -Dspoa_use_simde_openmp=ON -DBUILD_TESTING=OFF"
         ;;
+    arm64)
+	SPOA_OPTS="-Dspoa_optimize_for_portability=ON"
+	;;
     *)
         ;;
 esac
 
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
 mkdir -p $PREFIX/bin
-mkdir build
-cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${PREFIX} -Dracon_build_wrapper=ON ${SPOA_OPTS} ..
-make
-chmod +w bin/racon_wrapper
-make install
-cp bin/racon_wrapper ${PREFIX}/bin
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" -Dracon_build_wrapper=ON \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	"${SPOA_OPTS}" "${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
+
+chmod +w build/bin/racon_wrapper
+cp -f build/bin/racon_wrapper ${PREFIX}/bin
diff --git a/recipes/racon/meta.yaml b/recipes/racon/meta.yaml
index c3070387cb5d0..a853f6be6f209 100644
--- a/recipes/racon/meta.yaml
+++ b/recipes/racon/meta.yaml
@@ -6,15 +6,13 @@ package:
   version: {{ version }}
 
 build:
-  number: 4
+  number: 5
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
 source:
   url: https://github.com/lbcb-sci/racon/archive/refs/tags/{{ version }}.tar.gz
   sha256: 41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a
-  #patches:
-  #  - racon_wrapper.patch
 
 requirements:
   build:
@@ -25,7 +23,6 @@ requirements:
     - zlib
     - boost-cpp
   run:
-    - zlib
     - python
 
 test:
@@ -37,9 +34,16 @@ test:
 about:
   home: https://github.com/lbcb-sci/racon
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
+  summary: "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads."
+  dev_url: https://github.com/lbcb-sci/racon
+  doc_url: "https://github.com/lbcb-sci/racon/blob/{{ version }}/README.md"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - biotools:Racon
+    - usegalaxy-eu:racon
diff --git a/recipes/racon/racon_wrapper.patch b/recipes/racon/racon_wrapper.patch
deleted file mode 100644
index 36a799eca23b8..0000000000000
--- a/recipes/racon/racon_wrapper.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- CMakeLists.txt	2018-05-23 03:59:14.000000000 -0500
-+++ CMakeLists.txt.new	2018-10-19 15:29:39.782104577 -0500
-@@ -57,8 +57,8 @@
- endif(racon_build_tests)
- 
- if (racon_build_wrapper)
--    set(racon_path ${PROJECT_BINARY_DIR}/bin/racon)
--    set(rampler_path ${PROJECT_BINARY_DIR}/vendor/rampler/bin/rampler)
-+    set(racon_path $ENV{PREFIX}/bin/racon)
-+    set(rampler_path $ENV{PREFIX}/bin/rampler)
-     configure_file(${PROJECT_SOURCE_DIR}/scripts/racon_wrapper.py
-         ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper)
-     file(COPY ${PROJECT_BINARY_DIR}/${CMAKE_FILES_DIRECTORY}/racon_wrapper
diff --git a/recipes/rdeval/Makefile.patch b/recipes/rdeval/Makefile.patch
new file mode 100644
index 0000000000000..b9243d5f94b5d
--- /dev/null
+++ b/recipes/rdeval/Makefile.patch
@@ -0,0 +1,25 @@
+--- a/Makefile
++++ b/Makefile
+@@ -12,7 +12,12 @@
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+ 
+-LDFLAGS := -pthread
++ifeq ($(origin LDFLAGS), undefined)
++    LDFLAGS := -pthread
++else
++    LDFLAGS := $(LDFLAGS) -pthread
++endif
++
+ LIBS = -lz
+ 
+ OBJS := main input reads
+@@ -27,7 +32,7 @@
+ all: head validate regenerate
+ 
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
+ 
+ .PHONY: gfalibs
+ gfalibs:
diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh
new file mode 100644
index 0000000000000..3f30b2376ac7a
--- /dev/null
+++ b/recipes/rdeval/build.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+
+if [ -e "$PREFIX/include" ]; then
+    export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include"
+fi
+
+if [ -e "$PREFIX/lib" ]; then
+    export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L$PREFIX/lib"
+fi
+
+echo "CPPFLAGS=\"$CPPFLAGS\""
+echo "LDFLAGS=\"$LDFLAGS\""
+
+cd "$SRC_DIR"
+
+make
+
+install -d "$PREFIX/bin"
+install -v -m 0755 build/bin/rdeval "$PREFIX/bin/"
diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch
new file mode 100644
index 0000000000000..417701560725a
--- /dev/null
+++ b/recipes/rdeval/foo.patch
@@ -0,0 +1,38 @@
+diff --git a/Makefile b/Makefile
+index 5823f28..6f4a60f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+-CXX ?= g++
+-INCLUDE_DIR = -I./include -I./gfalibs/include
++CXX ?= ${CXX}
++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include
+ WARNINGS = -Wall -Wextra
+ 
+ CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS)
+@@ -12,8 +12,8 @@ SOURCE = src
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+ 
+-LDFLAGS := -pthread
+-LIBS = -lz
++LDFLAGS := -pthread -L${PREFIX}/lib
++LIBS := -lz -lpthread
+ 
+ OBJS := main input reads
+ BINS := $(addprefix $(BINDIR)/, $(OBJS))
+@@ -22,12 +22,12 @@ BINS := $(addprefix $(BINDIR)/, $(OBJS))
+ GFALIBS_DIR := $(CURDIR)/gfalibs
+ 
+ head: $(BINS) gfalibs | $(BUILD)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
++	$(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
+ 	
+ all: head validate regenerate
+ 
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++	$(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS)
+ 
+ .PHONY: gfalibs
+ gfalibs:
diff --git a/recipes/rdeval/gfalibs-Makefile.patch b/recipes/rdeval/gfalibs-Makefile.patch
new file mode 100644
index 0000000000000..d43d6346dadaa
--- /dev/null
+++ b/recipes/rdeval/gfalibs-Makefile.patch
@@ -0,0 +1,25 @@
+--- a/gfalibs/Makefile
++++ b/gfalibs/Makefile
+@@ -1,4 +1,4 @@
+-CXX = g++
++CXX ?= g++
+ INCLUDE_DIR = -I./include
+ WARNINGS = -Wall -Wextra
+ 
+@@ -8,15 +8,13 @@
+ BUILD = build/bin
+ SOURCE = src
+ INCLUDE = include
+-LDFLAGS :=
+ 
+ SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
+ 
+ all: $(SOURCES)
+-	@
+ 
+ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
+     
+ clean:
+ 	$(RM) *.o
diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml
new file mode 100644
index 0000000000000..a495d435df647
--- /dev/null
+++ b/recipes/rdeval/meta.yaml
@@ -0,0 +1,43 @@
+{% set name = "rdeval" %}
+{% set version = "0.0.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip
+  sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d
+  patches:
+    - Makefile.patch
+    - gfalibs-Makefile.patch
+
+build: 
+  number: 1
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x.x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make
+  host:
+    - zlib
+
+test:
+  commands:
+    - rdeval --help
+
+about:
+  home: https://github.com/vgl-hub/{{ name }}
+  summary: A general purpose, multithreaded read analysis and manipulation tool.
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  dev_url: https://github.com/vgl-hub/{{ name }}
+  doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/regenie/build.sh b/recipes/regenie/build.sh
index 1b8a8269d4876..2b3f78889c9ab 100644
--- a/recipes/regenie/build.sh
+++ b/recipes/regenie/build.sh
@@ -25,7 +25,7 @@ cmake \
   -S "${SRC_DIR}" \
   -B build
 
-make  -C build -j1 regenie
-make  -C build install
+cmake --build build --target install -j "${CPU_COUNT}"
 
-# bash test/test_conda.sh --path "${SRC_DIR}"
+#make  -C build -j1 regenie
+#make  -C build install
diff --git a/recipes/regenie/build_failure.osx-64.yaml b/recipes/regenie/build_failure.osx-64.yaml
deleted file mode 100644
index e759abd9b6e93..0000000000000
--- a/recipes/regenie/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 79124a9aa8c8c4bfc4ac1b2a6d10a5fa7bbc0886136237cccdac70de0b0ca6bc  # The commit at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  INFO:conda_build.metadata:Attempting to finalize metadata for regenie
-  Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld
-  Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld
-  Mamba failed to solve:
-   - llvm-openmp >=15.0.7
-   - liblapack * *mkl
-   - boost-cpp 1.78.0.*
-   - libcxx >=15.0.7
-   - mkl >=2020.4
-   - bgenix >=1.1.7
-   - zstd 1.5.*
-   - zlib 1.2.*
-   - mkl-include
-   - libgfortran5 >=12.2.0
-   - libgfortran 5.*
-
-  with channels:
-   - conda-forge
-   - bioconda
-   - defaults
-
-  The reported errors are:
-  - Encountered problems while solving:
-  -   - package bgenix-1.1.7-h4a65bee_0 requires boost-cpp 1.63.0.*, but none of the providers can be installed
-  -
-
-  Leaving build/test directories:
-    Work:
-   /opt/mambaforge/envs/bioconda/conda-bld/work
-    Test:
-   /opt/mambaforge/envs/bioconda/conda-bld/test_tmp
-  Leaving build/test environments:
-    Test:
-  source activate  /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
-    Build:
-  source activate  /opt/mambaforge/envs/bioconda/conda-bld/_build_env
-
-
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions
-      solution = solver.solve_for_action(_specs, prefix)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 230, in solve_for_action
-      t = self.solve(specs)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 220, in solve
-      raise RuntimeError("Solver could not find solution."  error_string)
-  RuntimeError: Solver could not find solution.Mamba failed to solve:
-   - llvm-openmp >=15.0.7
-   - liblapack * *mkl
-   - boost-cpp 1.78.0.*
-   - libcxx >=15.0.7
-   - mkl >=2020.4
-   - bgenix >=1.1.7
-   - zstd 1.5.*
-   - zlib 1.2.*
-   - mkl-include
-   - libgfortran5 >=12.2.0
-   - libgfortran 5.*
-
-  with channels:
-   - conda-forge
-   - bioconda
-   - defaults
-
-  The reported errors are:
-  - Encountered problems while solving:
-  -   - package bgenix-1.1.7-h4a65bee_0 requires boost-cpp 1.63.0.*, but none of the providers can be installed
-  -
-
-  During handling of the above exception, another exception occurred:
-
-  Traceback (most recent call last):
-    File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
-      sys.exit(main())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
-      call_conda_build(action, config)
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
-      result = api.build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
-      return build_tree(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
-      packages_from_this = build(metadata, stats,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build
-      output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs
-      for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False):
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set
-      conda_packages = finalize_outputs_pass(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass
-      fm = finalize_metadata(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata
-      build_unsat, host_unsat = add_upstream_pins(m,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins
-      host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host',
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files
-      deps, actions, unsat = get_env_dependencies(m, env, m.config.variant,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies
-      actions = environ.get_install_actions(tmpdir, tuple(dependencies), env,
-    File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions
-      raise err
-  conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("boost-cpp=1.63.0"), MatchSpec("bgenix==1.1.7=h4a65bee_0")}
-# Last 100 lines of the build log.
diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml
index ef14c2e5919c7..a26632ba592ce 100644
--- a/recipes/regenie/meta.yaml
+++ b/recipes/regenie/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "regenie" %}
-{% set version = "3.5" %}
-{% set sha256 = "48dfe8efa7b8acb6771452e3b53008f97d4a5c1241d5dbc3380d994b70a07a8c" %}
+{% set version = "4.0" %}
+{% set sha256 = "8f678d55bccf18ab70680637aca3cfd737060b3da291c803f3016d2ac3a07ccf" %}
 
 package:
   name: {{ name|lower }}
@@ -11,23 +11,10 @@ source:
   sha256: {{ sha256 }}
   patches:
     # Fixing postrelease issues
-    # - patches/0001-use-shared-cxxopts.patch
-    # - patches/0002-import-shared-Eigen3.patch
-    # - patches/0003-use-conda-cmakelists.patch
-    # - patches/0004-fix-fail-exit-on-help.patch
-    # - patches/0005-use-conda-cmakelist-file.patch
-    # - patches/0006-fix-cmakelist-file.patch
-    # - patches/0007-fix-cmakelist-file-for-osx.patch
-    # - patches/0008-fix-cmakelist-file-for-osx-eigen4.patch
-    # - patches/0009-update-cmake-file-for-conda.patch
-    # - patches/0010-update-cmakelist-file-for-v3.2.7.patch
-    # - patches/0011-update-cmakelist-file-for-v3.2.9.patch
-    # - patches/0012-update-cmakelist-file-for-v3.4.patch
-    # - patches/0013-update-cmakelist-file-for-v3.4.1.patch
-    - patches/0014-update-cmakelist.txt-for-v3.5.patch
+    - patches/0015-update-cmakelist.txt-for-v3.6.patch
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('regenie', max_pin="x") }}
     
diff --git a/recipes/regenie/patches/0001-use-shared-cxxopts.patch b/recipes/regenie/patches/0001-use-shared-cxxopts.patch
deleted file mode 100644
index dc705efd27cfa..0000000000000
--- a/recipes/regenie/patches/0001-use-shared-cxxopts.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From 545caf4f8557e056765c61db1b0e3200a0dc39fb Mon Sep 17 00:00:00 2001
-From: Matus Kosut <matus.kosut@ntnu.no>
-Date: Sun, 1 Nov 2020 15:35:40 +0100
-Subject: [PATCH 1/3] use shared cxxopts
-
----
- src/Regenie.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Regenie.cpp b/src/Regenie.cpp
-index 03d0edb..759f95a 100755
---- a/src/Regenie.cpp
-+++ b/src/Regenie.cpp
-@@ -24,7 +24,7 @@
- 
- */
- 
--#include "cxxopts/include/cxxopts.hpp"
-+#include "cxxopts.hpp"
- #include "Regenie.hpp"
- #include "Geno.hpp"
- #include "Step1_Models.hpp"
--- 
-2.23.0
-
diff --git a/recipes/regenie/patches/0002-import-shared-Eigen3.patch b/recipes/regenie/patches/0002-import-shared-Eigen3.patch
deleted file mode 100644
index c2aeeb4414f17..0000000000000
--- a/recipes/regenie/patches/0002-import-shared-Eigen3.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-From 644f0db61395be9283bc7dfe3b6a77a90a50c40b Mon Sep 17 00:00:00 2001
-From: Matus Kosut <matus.kosut@ntnu.no>
-Date: Sun, 1 Nov 2020 15:38:16 +0100
-Subject: [PATCH 2/3] import shared Eigen3
-
----
- src/Regenie.hpp | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/Regenie.hpp b/src/Regenie.hpp
-index a51db25..b6f5506 100644
---- a/src/Regenie.hpp
-+++ b/src/Regenie.hpp
-@@ -58,8 +58,8 @@
- #include <boost/math/distributions.hpp>
- 
- #include "bgen_to_vcf.hpp"
--#include "eigen3.3/Dense"
--#include "eigen3.3/StdVector"
-+#include "Eigen/Dense"
-+#include "Eigen/StdVector"
- 
- #ifdef __linux__
- #include <omp.h>
--- 
-2.23.0
-
diff --git a/recipes/regenie/patches/0003-use-conda-cmakelists.patch b/recipes/regenie/patches/0003-use-conda-cmakelists.patch
deleted file mode 100644
index c496194332944..0000000000000
--- a/recipes/regenie/patches/0003-use-conda-cmakelists.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-From 38cf311fd20dc3a0ec82f2d35af500732d91614a Mon Sep 17 00:00:00 2001
-From: Matus Kosut <matus.kosut@ntnu.no>
-Date: Sun, 1 Nov 2020 15:48:54 +0100
-Subject: [PATCH 3/3] use conda cmakelists
-
----
- CMakeLists.txt | 98 ++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 file changed, 98 insertions(+)
- create mode 100644 CMakeLists.txt
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-new file mode 100644
-index 0000000..b959bef
---- /dev/null
-+++ CMakeLists.txt
-@@ -0,0 +1,98 @@
-+cmake_minimum_required(VERSION 3.15)
-+file(STRINGS "VERSION" PROJECT_VERSION)
-+project(regenie VERSION "${PROJECT_VERSION}")
-+include(CMakePackageConfigHelpers)
-+include(GNUInstallDirs)
-+
-+set(CMAKE_CXX_STANDARD 11)
-+set(CMAKE_CXX_STANDARD_REQUIRED True)
-+
-+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -Wall -ffast-math -std=c++11")
-+set(THREADS_PREFER_PTHREAD_FLAG TRUE CACHE BOOL
-+    "Prefer using the -pthread compiler flag over -lpthread")
-+
-+set(ENV{CFLAGS}  "${CMAKE_C_FLAGS}")
-+set(ENV{CXXFLAGS} "${CMAKE_CXX_FLAGS}")
-+set(ENV{LDFLAGS} "-L${CMAKE_PREFIX_PATH}/lib")
-+set(ENV{MKLROOT} "${CMAKE_PREFIX_PATH}")
-+
-+if(BUILD_SHARED_LIBS)
-+  set(ENV{STATIC} OFF)
-+  set(Boost_USE_STATIC_LIBS OFF)
-+  set(BLA_STATIC OFF)
-+else()
-+  set(ENV{STATIC} ON)
-+  set(BLA_STATIC ON)
-+  set(Boost_USE_STATIC_LIBS ON)
-+  set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
-+  set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc" "-static-libstdc++")
-+endif(BUILD_SHARED_LIBS)
-+set(Boost_USE_DEBUG_LIBS     OFF)
-+set(Boost_USE_MULTITHREADED  ON)
-+set(Boost_USE_STATIC_RUNTIME OFF)
-+
-+find_package(Boost REQUIRED COMPONENTS iostreams system filesystem thread)
-+find_library(ZLIB_LIBRARY z)
-+find_library(MLIB_LIBRARY m)
-+find_library(DLLIB_LIBRARY dl)
-+find_library(ZSTD_LIBRARY zstd)
-+find_library(BGEN_LIBRARY bgen)
-+find_library(SQLITE3_LIBRARY sqlite3)
-+find_library(DB_LIBRARY db)
-+find_package(Threads)
-+find_package(BLAS)
-+find_package(LAPACK)
-+find_package(Eigen3 3.3 REQUIRED NO_MODULE)
-+
-+if(Boost_FOUND)
-+  add_definitions(${Boost_DEFINITIONS})
-+  if(Boost_iostreams_FOUND)
-+    add_definitions(-DHAS_BOOST_IOSTREAM=1)
-+    add_definitions(-DVERSION_NUMBER="${PROJECT_VERSION}.gz")
-+  else()
-+    add_definitions(-DVERSION_NUMBER="${PROJECT_VERSION}")
-+  endif(Boost_iostreams_FOUND)
-+endif(Boost_FOUND)
-+
-+if(BLAS_FOUND)
-+  if(LAPACK_FOUND)
-+    add_definitions(-DWITH_MKL)
-+    add_definitions(-DEIGEN_USE_BLAS)
-+    add_definitions(-DEIGEN_USE_LAPACKE)
-+  endif(LAPACK_FOUND)
-+endif(BLAS_FOUND)
-+
-+set(SIMDE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs/pgenlib/simde")
-+file(GLOB SIMDE_SOURCES "${SIMDE_PATH}/*.h" "${SIMDE_PATH}/x86/*.h")
-+add_library(simde INTERFACE)
-+target_sources(simde INTERFACE "${SIMDE_SOURCES}")
-+target_compile_options(simde BEFORE INTERFACE "-fopenmp-simd")
-+target_include_directories(simde INTERFACE $<BUILD_INTERFACE:${SIMDE_PATH}> $<BUILD_INTERFACE:${SIMDE_PATH}/x86>)
-+
-+set(PGEN_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs/pgenlib")
-+file(GLOB PGEN_SOURCES "${PGEN_PATH}/*.cpp" "${PGEN_PATH}/*.h" "${PGEN_PATH}/**/*.cc" "${PGEN_PATH}/**/*.h")
-+add_library(pgen INTERFACE)
-+target_link_libraries(pgen INTERFACE simde)
-+target_sources(pgen INTERFACE "${PGEN_SOURCES}")
-+target_include_directories(pgen INTERFACE $<BUILD_INTERFACE:${PGEN_PATH}>)
-+
-+file(GLOB REGENIE_PATHS "${CMAKE_CURRENT_SOURCE_DIR}/src/*.cpp" "${CMAKE_CURRENT_SOURCE_DIR}/src/*.hpp")
-+add_executable(regenie "${REGENIE_PATHS}")
-+target_link_libraries(regenie pgen ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} Boost::iostreams Boost::system Boost::filesystem Boost::thread LAPACK::LAPACK Eigen3::Eigen ${ZLIB_LIBRARY} ${ZSTD_LIBRARY} ${MLIB_LIBRARY} ${DLLIB_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})
-+target_include_directories(regenie PUBLIC
-+                           $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+                           $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+                           $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+                           $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>)
-+
-+install(TARGETS regenie
-+        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-+        OPTIONAL)
-+
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
---
-2.23.0
diff --git a/recipes/regenie/patches/0004-fix-fail-exit-on-help.patch b/recipes/regenie/patches/0004-fix-fail-exit-on-help.patch
deleted file mode 100644
index 64208c97416ec..0000000000000
--- a/recipes/regenie/patches/0004-fix-fail-exit-on-help.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From 28910770bb6b31df80f2c9eff25f517e6bc86432 Mon Sep 17 00:00:00 2001
-From: Matus Kosut <matus.kosut@ntnu.no>
-Date: Sun, 1 Nov 2020 18:11:11 +0100
-Subject: [PATCH] fix fail exit on help
-
----
- src/Regenie.cpp | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/Regenie.cpp b/src/Regenie.cpp
-index 759f95a..bf8f020 100755
---- a/src/Regenie.cpp
-+++ b/src/Regenie.cpp
-@@ -190,11 +190,11 @@ void read_params_and_check(int argc, char *argv[], struct param* params, struct
-     if (vm.count("help")){
-       print_header(std::cout);
-       std::cout << AllOptions.help({"", "Main"}) << '\n' << webinfo << "\n\n";
--      exit(-1);
-+      exit(0);
-     } else if (vm.count("helpFull")) {
-       print_header(std::cout);
-       std::cout << AllOptions.help({"", "Main", "Additional"}) << '\n' << webinfo << "\n\n";
--      exit(-1);
-+      exit(0);
-     } 
-     
-     if (!vm.count("out")){
--- 
-2.23.0
-
diff --git a/recipes/regenie/patches/0005-use-conda-cmakelist-file.patch b/recipes/regenie/patches/0005-use-conda-cmakelist-file.patch
deleted file mode 100644
index 0acc076f1749f..0000000000000
--- a/recipes/regenie/patches/0005-use-conda-cmakelist-file.patch
+++ /dev/null
@@ -1,307 +0,0 @@
-From c18d1f024eeddd844c91da835009a0d9fb698cae Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Thu, 17 Mar 2022 18:47:15 -0500
-Subject: [PATCH] use conda cmakelist file
-
----
-
- CMakeLists.txt | 203 ++++++++++++++++++++++++++-------------------------------
- 1 file changed, 93 insertions(+), 110 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 5153c91..6c9e934 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -100,32 +61,60 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp
-   ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY 
-+  NAMES libzstd.a zstd 
-+  REQUIRED
-+  )
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY 
-+  NAMES libsqlite3.a sqlite3 
-+  REQUIRED
-+  )
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
-+
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -134,7 +123,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -144,7 +133,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -154,7 +143,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -164,59 +153,51 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB 
-+    NAMES libmkl_intel_lp64.a mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  find_library(MKL_THREAD_LIB 
-+    NAMES libmkl_gnu_thread.a mkl_gnu_thread 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  find_library(MKL_CORE_LIB 
-+    NAMES libmkl_core.a mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen3/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen3/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY 
-+  NAMES libz.a z 
-+  REQUIRED
-+  )
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -224,14 +205,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
diff --git a/recipes/regenie/patches/0006-fix-cmakelist-file.patch b/recipes/regenie/patches/0006-fix-cmakelist-file.patch
deleted file mode 100644
index 5e615abe7f77d..0000000000000
--- a/recipes/regenie/patches/0006-fix-cmakelist-file.patch
+++ /dev/null
@@ -1,317 +0,0 @@
-From ec72f5a52a7116f79778d0c94bd9559cb2c30792 Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Fri, 18 Mar 2022 11:28:08 -0500
-Subject: [PATCH] fix cmakelist file
-
----
- CMakeLists.txt | 211 +++++++++++++++++++++++--------------------------
- 1 file changed, 101 insertions(+), 110 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 5153c91..3206f61 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -100,32 +61,60 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp
-   ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY 
-+  NAMES libzstd.a zstd 
-+  REQUIRED
-+  )
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY 
-+  NAMES libsqlite3.a sqlite3 
-+  REQUIRED
-+  )
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -134,7 +123,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -144,7 +133,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -154,7 +143,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -164,59 +153,59 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB 
-+    NAMES libmkl_intel_lp64.a mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB 
-+      NAMES libmkl_gnu_thread.a mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB 
-+      NAMES libmkl_intel_thread.a libmkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB 
-+    NAMES libmkl_core.a mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen3/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen3/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY 
-+  NAMES libz.a z 
-+  REQUIRED
-+  )
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -224,14 +213,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.24.3 (Apple Git-128)
-
diff --git a/recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch b/recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch
deleted file mode 100644
index 96ebbcff9360c..0000000000000
--- a/recipes/regenie/patches/0007-fix-cmakelist-file-for-osx.patch
+++ /dev/null
@@ -1,306 +0,0 @@
-From a9b92e4a59ff5ef6dd030257cf7e943705130cf2 Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Fri, 18 Mar 2022 16:18:21 -0500
-Subject: [PATCH] fix cmakelist file for osx
-
----
- CMakeLists.txt | 200 ++++++++++++++++++++++---------------------------
- 1 file changed, 90 insertions(+), 110 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 5153c91..eb42dc0 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -100,32 +61,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp
-   ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -134,7 +117,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -144,7 +127,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -154,7 +137,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -164,59 +147,54 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen3/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen3/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY z REQUIRED)
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -224,14 +202,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.24.3 (Apple Git-128)
-
diff --git a/recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch b/recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch
deleted file mode 100644
index 9eabffee7acef..0000000000000
--- a/recipes/regenie/patches/0008-fix-cmakelist-file-for-osx-eigen4.patch
+++ /dev/null
@@ -1,306 +0,0 @@
-From b58421061df0fd430f2543df4d63f2d1aa1ba6b3 Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Fri, 6 May 2022 09:52:15 -0500
-Subject: [PATCH] fix cmakelist file for osx with eigen 3.4
-
----
- CMakeLists.txt | 200 ++++++++++++++++++++++---------------------------
- 1 file changed, 90 insertions(+), 110 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 3c8567b..be834ab 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -100,32 +61,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/Step1_Models.cpp
-   ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -134,7 +117,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -144,7 +127,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -154,7 +137,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -164,59 +147,54 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY z REQUIRED)
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -224,14 +202,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.24.3 (Apple Git-128)
-
diff --git a/recipes/regenie/patches/0009-update-cmake-file-for-conda.patch b/recipes/regenie/patches/0009-update-cmake-file-for-conda.patch
deleted file mode 100644
index 43ad9b33cceed..0000000000000
--- a/recipes/regenie/patches/0009-update-cmake-file-for-conda.patch
+++ /dev/null
@@ -1,306 +0,0 @@
-From 9bf99e79a94e10430f6695b5fb1b21dd407a7486 Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Fri, 10 Jun 2022 14:18:59 -0400
-Subject: [PATCH] update cmake file for conda
-
----
- CMakeLists.txt | 200 ++++++++++++++++++++++---------------------------
- 1 file changed, 90 insertions(+), 110 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 38ef1d7..7e39c4f 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -101,32 +62,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/Step2_Models.cpp
-   ${CMAKE_SOURCE_DIR}/src/MultiTrait_Tests.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -135,7 +118,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -145,7 +128,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -155,7 +138,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -165,59 +148,54 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY z REQUIRED)
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -225,14 +203,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.24.3 (Apple Git-128)
-
diff --git a/recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch b/recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch
deleted file mode 100644
index 0998cd21e430c..0000000000000
--- a/recipes/regenie/patches/0010-update-cmakelist-file-for-v3.2.7.patch
+++ /dev/null
@@ -1,306 +0,0 @@
-From ff9af7e2ed26995c99a879b2813adc12a986b64e Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <s.joelle.mbatchou@.regeneron.com>
-Date: Wed, 17 May 2023 16:19:07 -0400
-Subject: [PATCH] update cmakelist file for v3.2.7
-
----
- CMakeLists.txt | 200 ++++++++++++++++++++++---------------------------
- 1 file changed, 90 insertions(+), 110 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index e81d7c8..cd376c6 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -102,32 +63,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/MultiTrait_Tests.cpp
-   ${CMAKE_SOURCE_DIR}/src/MCC.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -136,7 +119,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -146,7 +129,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -156,7 +139,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -166,59 +149,54 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY z REQUIRED)
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -226,14 +204,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.17.1
-
diff --git a/recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch b/recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch
deleted file mode 100644
index fe8e0d4233d31..0000000000000
--- a/recipes/regenie/patches/0011-update-cmakelist-file-for-v3.2.9.patch
+++ /dev/null
@@ -1,300 +0,0 @@
-commit 975bd4a5a757eeaae1f7db62977d97de94a1fabd
-Author: Joelle Mbatchou <s.joelle.mbatchou@.regeneron.com>
-Date:   Mon Jul 31 17:48:11 2023 -0400
-
-    cmakelist file for v3.2.9
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 4e0bfac..3609ab4 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake 
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake 
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,48 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC}) 
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM}) 
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -83,6 +43,7 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
- # list each file specifically 
- add_executable(regenie 
-@@ -103,32 +64,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/MCC.cpp
-   ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -137,7 +120,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -147,7 +130,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -157,7 +140,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -167,59 +150,54 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # Intel MKL
--if(EXISTS ${MKLROOT}) 
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM}) 
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
-+find_library(ZLIB_LIBRARY z REQUIRED)
- find_library(M_LIB m REQUIRED) 
- find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-@@ -227,14 +205,16 @@ if("${UNAME_S}" STREQUAL "Linux")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(regenie PRIVATE ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
diff --git a/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch b/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch
deleted file mode 100644
index 0e6278d726201..0000000000000
--- a/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch
+++ /dev/null
@@ -1,348 +0,0 @@
-From 918db42f41961bd4556662ade1edc6ca3378da7f Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Thu, 14 Dec 2023 17:33:24 -0500
-Subject: [PATCH] pdate cmakelist file for v3.4
-
----
- CMakeLists.txt | 243 +++++++++++++++++++------------------------------
- 1 file changed, 94 insertions(+), 149 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 5bb60d3..3609ab4 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC})
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM})
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check HTSlib
--if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "")
--  set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path")
--  if (NOT EXISTS ${HTSLIB_PATH})
--    message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist")
--  endif()
--  message( STATUS "Will compile with HTSlib")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
--# list each file specifically
--add_executable(regenie
-+# list each file specifically 
-+add_executable(regenie 
-   ${CMAKE_SOURCE_DIR}/src/Data.cpp
-   ${CMAKE_SOURCE_DIR}/src/Files.cpp
-   ${CMAKE_SOURCE_DIR}/src/Geno.cpp
-@@ -112,32 +64,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/MCC.cpp
-   ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -146,7 +120,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -156,7 +130,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -166,7 +140,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -176,100 +150,71 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
--# REMETA library
--if(EXISTS ${HTSLIB_PATH})
--  set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta")
--  add_custom_target(
--     remeta
--     COMMAND make HTSLIB_PATH=${HTSLIB_PATH}
--     WORKING_DIRECTORY ${REMETA_PATH}
--  )
--  target_link_libraries(regenie PUBLIC ${REMETA_PATH}/remeta.a)
--  target_include_directories(regenie PUBLIC ${REMETA_PATH})
--  add_dependencies(regenie remeta)
--
--  add_definitions(-DWITH_HTSLIB)
--  find_library(HTSLIB libhts.a HINTS ${HTSLIB_PATH})
--  target_link_libraries(regenie PUBLIC ${HTSLIB})
--endif()
--
- # Intel MKL
--if(EXISTS ${MKLROOT})
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM})
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
--find_library(M_LIB m REQUIRED)
--find_library(DL_LIB dl REQUIRED)
--find_library(BZ2_LIB libbz2.so)
--find_library(LZMA_LIB liblzma.so)
--find_library(CURL_LIB libcurl.so)
--find_library(CRYPTO_LIB libcrypto.so)
-+find_library(ZLIB_LIBRARY z REQUIRED)
-+find_library(M_LIB m REQUIRED) 
-+find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-   set(GFORTRAN_LIBRARY "-lgfortran")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(
--  regenie PRIVATE
--  ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB}
--  ${BZ2_LIB} ${LZMA_LIB}
--  ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY}
--)
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.34.1
-
diff --git a/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch b/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch
deleted file mode 100644
index a3072766dad91..0000000000000
--- a/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch
+++ /dev/null
@@ -1,343 +0,0 @@
-From 40a095edbac9478fe818b43ae49c0d5e958d632f Mon Sep 17 00:00:00 2001
-From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Thu, 1 Feb 2024 17:14:05 -0500
-Subject: [PATCH] update cmakelist file for v3.4.1
-
----
- CMakeLists.txt | 228 +++++++++++++++++++++----------------------------
- 1 file changed, 95 insertions(+), 133 deletions(-)
- mode change 100755 => 100644 CMakeLists.txt
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-old mode 100755
-new mode 100644
-index 4368ce0..2dc15fd
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,11 +1,3 @@
--# For Intel MKL, set MKLROOT=<MKL_path> when running cmake
--#   e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/
--# For OpenBLAS, set OPENBLAS_ROOT=<OpenBLAS_path> when running cmake
--#   note: it also requires lapacke library
--# For static compilation on Linux systems, set STATIC=1 when running cmake
--#   -> this excludes GLIBC
--
--
- cmake_minimum_required(VERSION 3.13)
- 
- # detect OS architecture
-@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF)  # Ensures -std=c++11
- ######################################
- ######## check input variables
- 
--# check BGEN_PATH
--if("$ENV{BGEN_PATH}" STREQUAL "")
--  message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'")
--else()
--  set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path")
--  if (NOT EXISTS ${BGEN_PATH})
--    message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist")
--  endif()
--endif()
--
- # check for static compilation
--if($ENV{STATIC})
-+if(BUILD_SHARED_LIBS)
-+  set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation")
-+  set(Boost_USE_STATIC_LIBS OFF)
-+else()
-   set(BUILD_STATIC ON CACHE INTERNAL "Static compilation")
-+  set(Boost_USE_STATIC_LIBS ON)
-   message( STATUS "Static compilation mode")
- endif()
- 
--# check Boost IOStreams
--if($ENV{HAS_BOOST_IOSTREAM})
--  set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO")
--  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
--else()
--  set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO")
--endif()
--
--# check MKL
--if(NOT "$ENV{MKLROOT}" STREQUAL "")
--  set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path")
--  if (NOT EXISTS ${MKLROOT})
--    message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with Intel MKL library")
--endif()
--
--# check HTSlib
--if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "")
--  set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path")
--  if (NOT EXISTS ${HTSLIB_PATH})
--    message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist")
--  endif()
--  message( STATUS "Will compile with HTSlib")
--endif()
--
--# check OpenBLAS
--if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "")
--  set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path")
--  if (NOT EXISTS ${OPENBLAS_ROOT})
--    message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist")
--  endif()
--  message( STATUS "Will compile with OpenBLAS library")
--endif()
--
- ######################################
- ######## set flags and required libraries
- 
-@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS    ${BUILD_STATIC})
- set(Boost_USE_DEBUG_LIBS     OFF)
- set(Boost_USE_MULTITHREADED  ON)
- set(Boost_USE_STATIC_RUNTIME OFF)
-+set(MKLROOT "${CMAKE_PREFIX_PATH}")
- 
--# list each file specifically
--add_executable(regenie
-+# list each file specifically 
-+add_executable(regenie 
-   ${CMAKE_SOURCE_DIR}/src/Data.cpp
-   ${CMAKE_SOURCE_DIR}/src/Files.cpp
-   ${CMAKE_SOURCE_DIR}/src/Geno.cpp
-@@ -112,32 +64,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/MCC.cpp
-   ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp
-   )
--target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
-+target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
- 
- set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
--add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
- 
-+find_package(OpenMP REQUIRED)
-+target_link_libraries(regenie OpenMP::OpenMP_CXX)
- if("${UNAME_S}" STREQUAL "Linux")
--  find_package(OpenMP REQUIRED)
--  target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX)
-   if(${BUILD_STATIC})
--    target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++)
-+    target_link_options(regenie BEFORE -static-libgcc -static-libstdc++)
-   endif()
- elseif("${UNAME_S}" STREQUAL "Darwin")
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
- endif()
- 
--set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs")
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/)
-+set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs")
-+target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/)
-+
-+# for BGEN (choose static if present first)
-+find_library(ZSTD_LIBRARY zstd REQUIRED)
-+find_library(DB_LIBRARY 
-+  NAMES libdb.a db 
-+  REQUIRED
-+  )
-+find_library(SQLITE3_LIBRARY sqlite3 REQUIRED)
-+find_package(Boost 
-+  REQUIRED COMPONENTS system filesystem thread 
-+  OPTIONAL_COMPONENTS iostreams
-+  )
-+find_library(BGEN_LIBRARY 
-+  NAMES libbgen.a 
-+  REQUIRED
-+  )
-+target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES})
-+target_include_directories(regenie 
-+  PUBLIC
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/genfile>
-+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/db>
-+  $<INSTALL_INTERFACE:${BOOST_INCLUDEDIR}>
-+  )
-+add_definitions(${Boost_DEFINITIONS})
- 
--# BGEN library and its dependencies
--find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED)
--find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED)
--find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED)
--find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED)
--find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED)
--target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY})
--target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3)
-+# Boost IO
-+if(Boost_iostreams_FOUND) 
-+  add_definitions(-DHAS_BOOST_IOSTREAM)
-+  set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version")
-+  message( STATUS "Will compile with Boost Iostreams library")
-+endif()
- 
- # MVTNorm library
- set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -146,7 +120,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${MVTN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a)
-+target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a)
- add_dependencies(regenie libMvtnorm)
- 
- # QF library
-@@ -156,7 +130,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QF_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a)
-+target_link_libraries(regenie ${QF_PATH}/qf.a)
- add_dependencies(regenie libqf)
- 
- # Quadpack library
-@@ -166,7 +140,7 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${QUAD_PATH}
- )
--target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a)
-+target_link_libraries(regenie ${QUAD_PATH}/libquad.a)
- add_dependencies(regenie libquad)
- 
- # PGEN library
-@@ -176,12 +150,12 @@ add_custom_target(
-    COMMAND make
-    WORKING_DIRECTORY ${PGEN_PATH}
- )
--target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a)
--target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
-+target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a)
-+target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/)
- add_dependencies(regenie pgenlib)
- 
- # REMETA library
--if(EXISTS ${HTSLIB_PATH})
-+if(DEFINED HTSLIB_PATH)
-   set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta")
-   add_custom_target(
-      remeta
-@@ -198,78 +172,66 @@ if(EXISTS ${HTSLIB_PATH})
- endif()
- 
- # Intel MKL
--if(EXISTS ${MKLROOT})
-+if(DEFINED MKLROOT) 
-   add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${MKLROOT}/include/)
--  if(${BUILD_STATIC}) # specify static libs
--    find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-+  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
-+  find_library(MKL_LP64_LIB mkl_intel_lp64 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Linux")
-+    find_library(MKL_THREAD_LIB mkl_gnu_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  elseif("${UNAME_S}" STREQUAL "Darwin")
-+    find_library(MKL_THREAD_LIB mkl_intel_thread 
-+      HINTS "${MKLROOT}/lib/" 
-+      REQUIRED
-+      )
-+  endif()
-+  find_library(MKL_CORE_LIB mkl_core 
-+    HINTS "${MKLROOT}/lib/" 
-+    REQUIRED
-+    )
-+  if("${UNAME_S}" STREQUAL "Darwin")
-+    target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB})
-+  elseif(${BUILD_STATIC})
-+    target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp)
-   else() # use dynamic libs
--    find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED)
--    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-+    target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
-   endif()
--elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS
--  add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE)
--  target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/)
--  find_library(LAPACK_LIB lapack REQUIRED)
--  find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED)
--  target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB})
-+  message( STATUS "Will compile with Intel MKL library")
- endif()
- 
- # cxxopts (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/)
- 
- # LBFGS (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/)
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/)
- 
- # Eigen (header-only)
--target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/)
--
--# Boost IO
--if(${HAS_BOOST_IOSTREAM})
--  if("${UNAME_S}" STREQUAL "Darwin")
--    find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  elseif(${BUILD_STATIC})
--    find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED)
--    target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO})
--  else()
--    target_link_libraries(regenie PRIVATE -lboost_iostreams)
--  endif()
--  add_definitions(-DHAS_BOOST_IOSTREAM)
--  message( STATUS "Will compile with Boost Iostreams library")
--endif()
-+target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
- 
- # Other libraries
--find_library(ZLIB_LIBRARY libz.a z REQUIRED)
--find_library(M_LIB m REQUIRED)
--find_library(DL_LIB dl REQUIRED)
--find_library(BZ2_LIB bz2)
--find_library(LZMA_LIB lzma)
--find_library(CURL_LIB curl)
--find_library(CRYPTO_LIB crypto)
-+find_library(ZLIB_LIBRARY z REQUIRED)
-+find_library(M_LIB m REQUIRED) 
-+find_library(DL_LIB dl REQUIRED) 
- if("${UNAME_S}" STREQUAL "Linux")
-   set(GFORTRAN_LIBRARY "-lgfortran")
- elseif("${UNAME_S}" STREQUAL "Darwin")
-   find_library(GFORTRAN_LIBRARY gfortran REQUIRED)
- endif()
--target_link_libraries(
--  regenie PRIVATE
--  ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB}
--  ${BZ2_LIB} ${LZMA_LIB}
--  ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY}
--)
-+target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY})
- 
--install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-+add_definitions(-DVERSION_NUMBER="${RG_VERSION}")
-+install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL)
- message( STATUS "REGENIE v" ${RG_VERSION})
- 
--add_custom_target(full-clean
--  COMMAND cd "${MVTN_PATH}" && make clean
--  COMMAND cd "${QF_PATH}" && make clean
--  COMMAND cd "${QUAD_PATH}" && make clean
--  COMMAND cd "${PGEN_PATH}" && make clean
--  )
-+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
-+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})
-+
-+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
-+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
-+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
-+include(CPack)
--- 
-2.34.1
-
diff --git a/recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch b/recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch
similarity index 96%
rename from recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch
rename to recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch
index 0637586f8c9c0..affa55bdb51bb 100644
--- a/recipes/regenie/patches/0014-update-cmakelist.txt-for-v3.5.patch
+++ b/recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch
@@ -1,14 +1,14 @@
-From 70b5249cb7a454d7eeaa94c262050adee124aea6 Mon Sep 17 00:00:00 2001
+From eac9852f500ba04d75e7f4ad178f365ce690bfa9 Mon Sep 17 00:00:00 2001
 From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
-Date: Wed, 3 Jul 2024 16:15:46 -0400
-Subject: [PATCH] update cmakelist.txt for v3.5
+Date: Tue, 3 Sep 2024 12:29:13 -0400
+Subject: [PATCH] update cmakelist file for v3.6
 
 ---
  CMakeLists.txt | 241 ++++++++++++++++++++-----------------------------
  1 file changed, 97 insertions(+), 144 deletions(-)
 
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index b955d8e..02bdbbb 100644
+index b874c33..b3b9950 100755
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -1,11 +1,3 @@
@@ -99,9 +99,9 @@ index b955d8e..02bdbbb 100644
    ${CMAKE_SOURCE_DIR}/src/Data.cpp
    ${CMAKE_SOURCE_DIR}/src/Files.cpp
    ${CMAKE_SOURCE_DIR}/src/Geno.cpp
-@@ -112,32 +64,54 @@ add_executable(regenie
-   ${CMAKE_SOURCE_DIR}/src/MCC.cpp
-   ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp
+@@ -116,32 +68,54 @@ add_executable(regenie
+   ${CMAKE_SOURCE_DIR}/src/cox_score.cpp
+   ${CMAKE_SOURCE_DIR}/src/cox_firth.cpp
    )
 -target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src)
 +target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include)
@@ -170,7 +170,7 @@ index b955d8e..02bdbbb 100644
  
  # MVTNorm library
  set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm")
-@@ -146,7 +120,7 @@ add_custom_target(
+@@ -150,7 +124,7 @@ add_custom_target(
     COMMAND make
     WORKING_DIRECTORY ${MVTN_PATH}
  )
@@ -179,7 +179,7 @@ index b955d8e..02bdbbb 100644
  add_dependencies(regenie libMvtnorm)
  
  # QF library
-@@ -156,7 +130,7 @@ add_custom_target(
+@@ -160,7 +134,7 @@ add_custom_target(
     COMMAND make
     WORKING_DIRECTORY ${QF_PATH}
  )
@@ -188,7 +188,7 @@ index b955d8e..02bdbbb 100644
  add_dependencies(regenie libqf)
  
  # Quadpack library
-@@ -166,7 +140,7 @@ add_custom_target(
+@@ -170,7 +144,7 @@ add_custom_target(
     COMMAND make
     WORKING_DIRECTORY ${QUAD_PATH}
  )
@@ -197,7 +197,7 @@ index b955d8e..02bdbbb 100644
  add_dependencies(regenie libquad)
  
  # PGEN library
-@@ -176,12 +150,12 @@ add_custom_target(
+@@ -180,12 +154,12 @@ add_custom_target(
     COMMAND make
     WORKING_DIRECTORY ${PGEN_PATH}
  )
@@ -213,7 +213,7 @@ index b955d8e..02bdbbb 100644
    set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta")
    add_custom_target(
       remeta
-@@ -205,91 +179,70 @@ if(EXISTS ${HTSLIB_PATH})
+@@ -209,91 +183,70 @@ if(EXISTS ${HTSLIB_PATH})
  endif()
  
  # Intel MKL
diff --git a/recipes/reseek/build.sh b/recipes/reseek/build.sh
new file mode 100644
index 0000000000000..db61203aa3f99
--- /dev/null
+++ b/recipes/reseek/build.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+mkdir -p ${PREFIX}/bin
+cd src || exit 1
+echo "0" > gitver.txt
+
+cp ${RECIPE_DIR}/vcxproj_make.py .
+chmod +x vcxproj_make.py
+./vcxproj_make.py --openmp --cppcompiler ${CXX} --ccompiler ${CC}
+
+# Verify binary exists and is executable
+if [ ! -f ../bin/reseek ]; then
+    echo "Error: reseek binary not found"
+    exit 1
+fi
+
+cp ../bin/reseek ${PREFIX}/bin/reseek
diff --git a/recipes/reseek/meta.yaml b/recipes/reseek/meta.yaml
new file mode 100644
index 0000000000000..8b59a2d8fb690
--- /dev/null
+++ b/recipes/reseek/meta.yaml
@@ -0,0 +1,32 @@
+{% set name = "reseek" %}
+{% set version = "2.02" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rcedgar/reseek/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 83296e5edcdccdf4848f52ff34f35b753fa9ae1d383c3347eee41ef7d26888b1
+
+build:
+  number: 0
+  skip: True  #[osx]
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
+
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+    - {{ compiler("c") }}
+    - make
+
+test:
+  commands:
+    - reseek -version
+about:
+  home: https://github.com/rcedgar/reseek
+  license: GPL-3.0-only
+  license_file: LICENSE
+  summary: Protein structure alignment and search algorithm
diff --git a/recipes/reseek/vcxproj_make.py b/recipes/reseek/vcxproj_make.py
new file mode 100644
index 0000000000000..739663b29c933
--- /dev/null
+++ b/recipes/reseek/vcxproj_make.py
@@ -0,0 +1,225 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+Usage = (
+    "Convert Visual Studio .vcxproj file in current directory to Makefile and run make."
+)
+
+AP = argparse.ArgumentParser(description=Usage)
+
+# Value opts
+AP.add_argument(
+    "--std",
+    required=False,
+    help="C++ standard option for GCC, e.g. c++11 or c++17 (default none)",
+)
+AP.add_argument(
+    "--cppcompiler",
+    required=False,
+    default="g++",
+    help="C++ compiler command name default g++)",
+)
+AP.add_argument(
+    "--ccompiler",
+    required=False,
+    default="gcc",
+    help="C++ compiler command name default gcc)",
+)
+
+# Flag opts
+AP.add_argument("--debug", required=False, action="store_true", help="Debug build")
+AP.add_argument("--openmp", required=False, action="store_true", help="Requires OMP")
+AP.add_argument(
+    "--pthread", required=False, action="store_true", help="Requires pthread"
+)
+AP.add_argument("--lrt", required=False, action="store_true", help="Requires lrt")
+AP.add_argument(
+    "--symbols",
+    required=False,
+    action="store_true",
+    help="Debug symbols (default if --debug)",
+)
+AP.add_argument(
+    "--nostrip",
+    required=False,
+    action="store_true",
+    help="Don't strip symbols (default if --debug or --symbols)",
+)
+
+Args = AP.parse_args()
+debug = Args.debug
+std = Args.std
+cppcompiler = Args.cppcompiler
+ccompiler = Args.ccompiler
+nostrip = debug or Args.symbols
+symbols = debug or Args.symbols
+
+ProjFileName = None
+HdrNames = []
+for FileName in os.listdir("."):
+    if FileName.endswith(".vcxproj"):
+        ProjFileName = FileName
+    elif FileName.endswith(".h"):
+        HdrNames.append(FileName)
+if ProjFileName is None:
+    sys.stderr.write("\nProject file not found in current directory\n")
+    sys.exit(1)
+
+binary = ProjFileName.replace(".vcxproj", "")
+sys.stderr.write("binary=" + binary + "\n")
+
+compiler_opts = " -ffast-math -march=native"
+linker_opts = " -ffast-math -march=native"
+
+if std:
+    compiler_opts += " --std=" + std
+
+if debug:
+    compiler_opts += " -O0 -DDEBUG"
+    linker_opts += " -O0"
+else:
+    compiler_opts += " -O3 -DNDEBUG"
+    linker_opts += " -O3"
+
+if symbols:
+    compiler_opts += " -g3"
+    linker_opts += " -g3"
+
+if Args.openmp:
+    compiler_opts += " -fopenmp"
+    linker_opts += " -fopenmp"
+
+if Args.pthread:
+    compiler_opts += " -pthread"
+    linker_opts += " -lpthread"
+
+rc = os.system(r"rm -rf o/ ../bin/%s*" % binary)
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- failed to clean\n\n")
+    sys.exit(1)
+sys.stderr.write("clean done.\n")
+
+OBJDIR = "o"
+BINDIR = "../bin"
+
+Fields = ProjFileName.split("/")
+n = len(Fields)
+Name = Fields[n - 1]
+Fields = Name.split(".")
+binary = Fields[0]
+
+CXXNames = []
+CNames = []
+with open(ProjFileName) as File:
+    for Line in File:
+        Line = Line.strip()
+        Line = Line.replace('"', "")
+        Line = Line.replace(" ", "")
+        # <ClCompile Include="betadiv.cpp" />
+        if Line.startswith("<ClCompileInclude"):
+            Fields = Line.split("=")
+            if len(Fields) != 2:
+                continue
+            FileName = Fields[1]
+            FileName = FileName.replace("/>", "")
+            if FileName.endswith(".cpp"):
+                FileName = FileName.replace(".cpp", "")
+                CXXNames.append(FileName)
+            elif FileName.endswith(".c"):
+                FileName = FileName.replace(".c", "")
+                CNames.append(FileName)
+
+assert len(CXXNames) > 0 or len(CNames) > 0
+
+with open("Makefile", "w") as f:
+
+    def Out(s):
+        print(s, file=f)
+
+    BINPATH = "$(BINDIR)/%s" % (binary)
+
+    Out("######################################################")
+    Out("# Makefile is generated by " + sys.argv[0])
+    Out("# Don't edit the Makefile -- update the python script")
+    Out("######################################################")
+    Out("")
+    Out("BINDIR := %s" % BINDIR)
+    Out("OBJDIR := %s" % OBJDIR)
+    Out("BINPATH := %s" % BINPATH)
+
+    if CNames:
+        Out("")
+        Out("CC = " + ccompiler)
+        Out("CFLAGS := $(CFLAGS) " + compiler_opts)
+
+    if CXXNames:
+        Out("")
+        Out("CXX = " + cppcompiler)
+        Out("CXXFLAGS := $(CFLAGS) " + compiler_opts)
+
+    Out("")
+    Out("UNAME_S := $(shell uname -s)")
+    Out("LDFLAGS := $(LDFLAGS) " + linker_opts)
+    Out("ifeq ($(UNAME_S),Linux)")
+    Out("    LDFLAGS += -static")
+    Out("endif")
+
+    Out("")
+    Out("HDRS = \\")
+    for Name in sorted(HdrNames):
+        Out("  %s \\" % Name)
+
+    Out("")
+    Out("OBJS = \\")
+    for Name in CXXNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    for Name in CNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    Out("")
+    Out(".PHONY: clean")
+
+    Out("")
+    Out("$(BINPATH) : $(BINDIR)/ $(OBJDIR)/ $(OBJS)")
+
+    if len(CXXNames) > 0:
+        Cmd = "\t$(CXX) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+    else:
+        Cmd = "\t%(CC) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+
+    if Args.lrt:
+        Cmd += " -lrt"
+    Out(Cmd)
+
+    if not nostrip:
+        Out("	strip $(BINPATH)")
+
+    Out("")
+    Out("$(OBJDIR)/ :")
+    Out("	mkdir -p $(OBJDIR)/")
+
+    Out("")
+    Out("$(BINDIR)/ :")
+    Out("	mkdir -p $(BINDIR)/")
+
+    if CNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.c $(HDRS)")
+        Out("	$(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<")
+
+    if CXXNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.cpp $(HDRS)")
+        Out("	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<")
+
+sys.stderr.write("Makefile done.\n")
+
+rc = os.system("make")
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- make failed\n\n")
+    sys.exit(1)
+sys.stderr.write("make done.\n")
diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml
index 08e802612190e..6a2defda2afbc 100644
--- a/recipes/resistify/meta.yaml
+++ b/recipes/resistify/meta.yaml
@@ -1,13 +1,14 @@
 {% set name = "resistify" %}
-{% set version = "0.4.0" %}
+{% set version = "0.5.2" %}
+{% set sha256 = "2c8e71e4ce52f014a62e5a5a5b32c04ed67af3651ddf9013f96953e711f4d234" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: ba06333873fcb1e07820cb0895755b42a615d289437749846e280bc87d6abf2c
+  url: https://github.com/SwiftSeal/resistify/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
 
 build:
   noarch: python
@@ -21,16 +22,23 @@ build:
 requirements:
   host:
     - pip
-    - python >=3.9
+    - python >=3.9,<3.10
     - hatchling
+    - cython <3
   run:
-    - python >=3.9
+    - python >=3.9,<3.10
     - scikit-learn ==0.24.2
+    - numpy <1.23.0
     - biopython
-    - numpy
     - rich
     - rich-argparse
     - hmmer
+    - pytorch
+    - torchvision
+    - torchaudio
+    - fair-esm
+    - transformers ==4.31.0
+    - sentencepiece
 
 test:
   imports:
@@ -40,5 +48,14 @@ test:
 
 about:
   home: https://github.com/swiftseal/resistify
-  license: MIT
+  dev_url: https://github.com/SwiftSeal/resistify
+  doc_url: https://github.com/SwiftSeal/resistify/blob/main/README.md
+  license: GPL-3.0
+  license_file: LICENSE
+  license_url: https://github.com/SwiftSeal/resistify/blob/main/LICENSE
   summary: A resistance gene annotation tool
+  description: |
+    Resistify is a nucleotide-binding leucine rich repeat (NLR) annotation
+    program, for the purpose of identifying putative disease resistance
+    genes in plant genomes.
+  
diff --git a/recipes/revbayes/build.sh b/recipes/revbayes/build.sh
index 7f0287067d5c3..763ae5c759945 100644
--- a/recipes/revbayes/build.sh
+++ b/recipes/revbayes/build.sh
@@ -1,53 +1,47 @@
-#!/usr/bin/env bash
+#!/bin/bash
 
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+mkdir -p $PREFIX/bin
 cd projects/cmake
 
-if [ ! -d build ]; then
-	mkdir build
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
 fi
 
-./generate_version_number.sh
-mv GitVersion.cpp ../../src/revlanguage/utils/
-
 # MPI version
 ./regenerate.sh -mpi true
 
-cd build
+./build.sh -mpi true -help2yml true \
+	-DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_PREFIX_PATH="${PREFIX}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-boost_root "${PREFIX}" \
+	-j "${CPU_COUNT}" \
+	"${CONFIG_ARGS}"
 
-# If cmake finds a boost version compiled with cmake, it always links to it unless both
-# Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake)
-cmake -DCMAKE_PREFIX_PATH=$PREFIX \
-	-DBOOST_ROOT=$PREFIX \
-	-DBoost_NO_SYSTEM_PATHS=ON \
-	-DBoost_NO_BOOST_CMAKE=ON \
-	.
-
-make
-
-cd ..
-mkdir -p $PREFIX/bin
-mv rb $PREFIX/bin/rb-mpi
+chmod 0755 rb-mpi rb-mpi-help2yml
+mv rb-mpi rb-mpi-help2yml $PREFIX/bin/
 
 
 # Non-mpi version
-rm -rf build
-mkdir build
+rm -rf build-mpi
 
 ./regenerate.sh
 
-cd build
-
-# If cmake finds a boost version compiled with cmake, it always links to it unless both
-# Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake)
-cmake -DCMAKE_PREFIX_PATH=$PREFIX \
-	-DBOOST_ROOT=$PREFIX \
-	-DBoost_NO_SYSTEM_PATHS=ON \
-	-DBoost_NO_BOOST_CMAKE=ON \
-	.
+./build.sh -mpi false -help2yml true \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_PREFIX_PATH="${PREFIX}" \
+        -DCMAKE_CXX_COMPILER="${CXX}" \
+        -boost_root "${PREFIX}" \
+        -j "${CPU_COUNT}" \
+        "${CONFIG_ARGS}"
 
-make
-
-cd ..
-mkdir -p $PREFIX/bin
-mv rb $PREFIX/bin
+chmod 0755 rb rb-help2yml
+mv rb rb-help2yml $PREFIX/bin/
 
+rm -rf build
diff --git a/recipes/revbayes/meta.yaml b/recipes/revbayes/meta.yaml
index cd5f05e04d604..befcec1bb08bb 100644
--- a/recipes/revbayes/meta.yaml
+++ b/recipes/revbayes/meta.yaml
@@ -1,43 +1,57 @@
-{% set version = "1.0.13" %}
+{% set name = "revbayes" %}
+{% set version = "1.2.4" %}
 
 package:
-  name: revbayes
+  name: {{ name }}
   version: {{ version }}
 
-build:
-  number: 7
-
 source:
-  url: https://github.com/revbayes/revbayes.archive/archive/v{{ version }}.tar.gz
-  sha256: e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9
+  url: https://github.com/revbayes/revbayes/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 020aa32b32db5896b081e14613c754fbb5523f01fa64262f502a6b693db9058a
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('revbayes', max_pin="x") }}
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - cmake >=2.6
+    - cmake
   host:
-    - boost-cpp >=1.60
+    - boost-cpp >=1.71
     - openmpi
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   run:
-    - boost-cpp >=1.60
+    - boost-cpp >=1.71
     - openmpi
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
 
 test:
   commands:
-    - rb -v
     - rb -h
-    - rb-mpi -v
     - rb-mpi -h
 
 about:
-  home: https://revbayes.github.io/
-  license: GPLv3
+  home: "https://revbayes.github.io"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.
+  summary: "Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language."
+  dev_url: "https://github.com/revbayes/revbayes"
+  doc_url: "https://revbayes.github.io/tutorials"
 
 extra:
   container:
     # openmpi needs ssh/rsh
-    extended-base: true
+    extended-base: True
+  identifiers:
+    - biotools:revbayes
+    - doi:10.1093/sysbio/syw021
+    - doi:10.1093/sysbio/syu039
+  additional-platforms:
+    - osx-arm64
diff --git a/recipes/rotate/build.sh b/recipes/rotate/build.sh
new file mode 100644
index 0000000000000..5c030d5e0f3a9
--- /dev/null
+++ b/recipes/rotate/build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+set -xe
+make  CC=$CC INCLUDES="-I$PREFIX/include" CFLAGS+="-g -Wall -O2 -L$PREFIX/lib"
+chmod +x rotate
+chmod +x composition
+mkdir -p ${PREFIX}/bin
+cp -f rotate composition ${PREFIX}/bin
diff --git a/recipes/rotate/meta.yaml b/recipes/rotate/meta.yaml
new file mode 100644
index 0000000000000..1b9ef48f14fe2
--- /dev/null
+++ b/recipes/rotate/meta.yaml
@@ -0,0 +1,34 @@
+{% set name = "rotate" %}
+{% set version = "1.0" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://github.com/richarddurbin/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: "da8a3c848cc05d59b579c375824008dd2d533c28d8a436a6e4761312d2152906"
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("rotate", max_pin="x") }}
+
+requirements:
+  build:
+    - make
+    - {{ compiler('c') }}
+  host:
+    - zlib
+
+
+test:
+  commands:
+    - rotate 
+
+about:
+  home: "https://github.com/richarddurbin/rotate"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Simple program to rotate a circular sequence to start at a given position or string."
diff --git a/recipes/rpsbproc/build.sh b/recipes/rpsbproc/build.sh
index dbaea1d1ac5e7..a152fae34917c 100755
--- a/recipes/rpsbproc/build.sh
+++ b/recipes/rpsbproc/build.sh
@@ -125,9 +125,11 @@ CONFIGURE_FLAGS="$CONFIGURE_FLAGS --without-dll --with-static-exe"
 # Platform-specific flags
 if [[ "$(uname)" = "Linux" ]]; then
 	# --with(out)-64:
-	#   Compile in 64-bit mode instead of 32-bit.
+	#   Compile in 64-bit mode instead of 32-bit on x86_64 platforms.
 	#   Flag not available for osx build.
-	CONFIGURE_FLAGS="$CONFIGURE_FLAGS --with-64"
+        if [[ "$(arch)" = "x86_64" ]]; then
+	    CONFIGURE_FLAGS="$CONFIGURE_FLAGS --with-64"
+	fi
 	# --with(out)-openmp:
 	#   Enable OpenMP extensions for all projects.
 	#   Does not work without hacks for OSX
@@ -154,7 +156,7 @@ cd "$NCBI_CXX_TOOLKIT"
 # Run GNU Make
 cd "$RESULT_PATH/build"
 echo "RUNNING MAKE" >&2
-make -j1 -f Makefile.flat rpsbproc.exe >&2
+make -j 4 -f Makefile.flat rpsbproc.exe >&2
 
 # Copy compiled binaries to the Conda $PREFIX
 mkdir -p "$PREFIX/bin"
diff --git a/recipes/rpsbproc/meta.yaml b/recipes/rpsbproc/meta.yaml
index e6f28433383b3..6f42c04bad539 100644
--- a/recipes/rpsbproc/meta.yaml
+++ b/recipes/rpsbproc/meta.yaml
@@ -24,7 +24,7 @@ source:
       - update_configsub.patch
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -81,3 +81,7 @@ about:
 extra:
   identifiers:
     - doi:10.1002/cpbi.90
+  additional-platforms:
+    - linux-aarch64
+    # osx-arm64 is encountering issues with Xcode and make during builds
+    # - osx-arm64
diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml
index 9fc2b851b8369..804d07d108d74 100644
--- a/recipes/saccharis/meta.yaml
+++ b/recipes/saccharis/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "SACCHARIS" %}
 {% set version = "2.0.1.dev21" %}
-{% set hash = "327FCE45E7B50BF0C52064DA883CC4A21BCE183EBACF4C4A827FE2C5BE934CB3" %}
+{% set hash = "0CC50F3A1D80C4FC8F84783A46E122BC4E382E00B8AD15EF10E985AAF100F43B" %}
 
 
 package:
@@ -9,12 +9,13 @@ package:
 
 source:
   #  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz
-  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_2.tar.gz
+  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_9.tar.gz
   sha256: {{ hash|lower }}
 
 build:
   noarch: python
-  number: 2
+  number: 9
+
   script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt
   preserve_egg_dir: True  # added because the entry points below seem to be causing a build error
   entry_points:
@@ -36,7 +37,7 @@ requirements:
     - python
     - setuptools
   host:
-    - python >=3.6
+    - python >=3.11
     - setuptools
     - pip
   run:
@@ -52,9 +53,8 @@ requirements:
     - modeltest-ng >=0.1.7  # [not win]
     - muscle >=3.8  # [not win]
     - psutil
-    - python >=3.8
+    - python >=3.11
     - python-dotenv >=0.20.0
-    - python-wget >=3.2
     - raxml >=8.2.12 # [not win]
     - raxml-ng >=1.2 # [not win]
     - requests >=2.28.0
diff --git a/recipes/sainsc/meta.yaml b/recipes/sainsc/meta.yaml
index b6417121ec76a..1edc3e2d2120a 100644
--- a/recipes/sainsc/meta.yaml
+++ b/recipes/sainsc/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "sainsc" %}
-{% set version = "0.2.0" %}
+{% set version = "0.2.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,11 +7,11 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sainsc-{{ version }}.tar.gz
-  sha256: af964871f73b31177cf1a31844b6c40323384e0bd3c97ab2520ecbec23036d72
+  sha256: f710579c01809110c280bee838607fc6b961ca2f27b54aa7d431e25fe97b3872
 
 build:
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
-  number: 0
+  number: 1
   skip: True  # [(osx and not arm64) or py < 310]
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
diff --git a/recipes/samshee/meta.yaml b/recipes/samshee/meta.yaml
index 103a21643be3f..94f9f8837d82d 100644
--- a/recipes/samshee/meta.yaml
+++ b/recipes/samshee/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "samshee" %}
-{% set version = "0.2.1" %}
+{% set version = "0.2.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://files.pythonhosted.org/packages/82/fa/895448adfc9be87b7af0a46b5c84eeae752d685966eba02d572e5c670f08/samshee-0.2.1.tar.gz
-  sha256: e85d9363de533dab91e3190c52eda9034cbaf1e53c03f0b33f4f9b433e800b76
+  url: https://files.pythonhosted.org/packages/38/04/edcd9859eb00dd3b0258aba128890d7d537b72e227b96a5f19837b54afd9/samshee-0.2.2.tar.gz
+  sha256: 360427adb2d3913c3eca4d97ff55933a51dcb3d7d82559c44d9323f69e98addc
 
 build:
   noarch: python
diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml
index f9c03bb28ca14..30c1107c415c2 100644
--- a/recipes/savana/meta.yaml
+++ b/recipes/savana/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "savana" %}
-{% set version = "1.2.3" %}
+{% set version = "1.2.4" %}
 
 package:
   name: "{{ name }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz"
-  sha256: 3d7b7258b59b7f8bc2704eed131df81db77931f790c86b7af19100554fa9d44f
+  sha256: 3d9f341259a41a964341fad1ce08f1a58d980bc75d2659181c6d41f8acc68204
 
 build:
   number: 0
diff --git a/recipes/sawfish/meta.yaml b/recipes/sawfish/meta.yaml
index 68d579f6bfc88..97818ecfc31b2 100644
--- a/recipes/sawfish/meta.yaml
+++ b/recipes/sawfish/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "sawfish" %}
-{% set version = "0.12.6" %}
+{% set version = "0.12.7" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/PacificBiosciences/sawfish/releases/download/v{{ version }}/sawfish-v{{ version }}-x86_64-unknown-linux-gnu.tar.gz
-  sha256: 15e9c190877bde4b01b3c72037459fa67d5183ad1172878ccd364807fcff51a8
+  sha256: 6af341da0452856da58e77f6e843275b9d6811114c222cef05f2e78add58bb4a
 
 build:
   number: 0
diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml
index 8fe28e48762f4..59ce888960c89 100644
--- a/recipes/scirpy/meta.yaml
+++ b/recipes/scirpy/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "scirpy" %}
-{% set version = "0.18.0" %}
+{% set version = "0.19.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 7d8f5deb2f6d83aa6f719b051c2d7c8cd1fb27589b64796be4b1a64ec76a708e
+  sha256: 83bc3663e49d7f5ae26e1a54229085af4fcd103304842b23d0aaddae1796e9ba
   folder: "{{ name }}-{{ version }}"
 
 build:
@@ -26,7 +26,7 @@ requirements:
     - hatch-vcs
   run:
     - python >=3.10
-    - anndata >=0.9,<0.10.9
+    - anndata >=0.9
     - awkward >=2.1.0
     - mudata >=0.2.3
     - scanpy >=1.9.3
diff --git a/recipes/search_ncbi/meta.yaml b/recipes/search_ncbi/meta.yaml
new file mode 100644
index 0000000000000..3385465789e9d
--- /dev/null
+++ b/recipes/search_ncbi/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = "0.1.1" %}
+
+package:  
+  name: search_ncbi  
+  version: {{ version }}
+
+source:  
+  url: https://pypi.io/packages/source/s/search_ncbi/search_ncbi-{{ version }}.tar.gz  
+  sha256: 78bef363451506dd36e29d3cd126840bf67eb6b3eafa6b541076da632c2a43dc  
+
+build:  
+  noarch: python  
+  number: 0  
+  script: "{{ PYTHON }} -m pip install . -vv"  
+  entry_points:  
+    - searchncbi=search_ncbi.cli:main  
+  run_exports:  
+    - {{ pin_subpackage("search_ncbi", max_pin="x.x") }}
+
+requirements:  
+  host:  
+    - python >=3.7  
+    - pip  
+    - setuptools
+  run:  
+    - python >=3.7  
+    - biopython >=1.78  
+    - pandas >=1.3.0  
+    - tqdm >=4.66.3  
+    - xmltodict >=0.13.0
+    - requests >=2.32.0
+    - setuptools
+
+test: 
+  commands:
+    - searchncbi --help
+
+about:  
+  home: https://github.com/Bluetea577/search_ncbi  
+  summary: A package for searching and processing NCBI data  
+  license: MIT  
+  license_family: MIT  
+
+extra:  
+  recipe-maintainers:  
+    - Bluetea577
diff --git a/recipes/seismic-rna/build.sh b/recipes/seismic-rna/build.sh
index 9b50c3a0078a9..d5b201ec86981 100644
--- a/recipes/seismic-rna/build.sh
+++ b/recipes/seismic-rna/build.sh
@@ -3,6 +3,6 @@
 # DO NOT RUN THIS SCRIPT YOURSELF!
 # It should only be run by conda build.
 
-set -euxo pipefail
+set -eux -o pipefail
 
 $PYTHON -m pip install --no-dependencies $PWD
\ No newline at end of file
diff --git a/recipes/seismic-rna/meta.yaml b/recipes/seismic-rna/meta.yaml
index 4dd421e1aef29..b0cac5d5585c1 100644
--- a/recipes/seismic-rna/meta.yaml
+++ b/recipes/seismic-rna/meta.yaml
@@ -3,7 +3,6 @@
 package:
   name: seismic-rna
   version: 0.21.1
-
 about:
   home: https://github.com/rouskinlab/seismic-rna
   license: GPL-3.0-only
@@ -11,33 +10,27 @@ about:
   license_file: LICENSE
   license_url: https://www.gnu.org/licenses/gpl-3.0.html
   summary: SEISMIC-RNA software by the Rouskin Lab
-  
 source:
   url: https://github.com/rouskinlab/seismic-rna/archive/refs/tags/v0.21.1.tar.gz
   sha256: 8cad84303ff0e98cbab5da6fc5e921780100cdd9ed799496cc772f85470a25e4
-  
 build:
   noarch: python
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("seismic-rna", max_pin="x.x") }}
-    
 requirements:
   build:
     - python >=3.10
-    - pip
     - hatch >=1.12
   run:
     - python >=3.10
     - bowtie2 >=2.5.4
-    - fastqc >=0.12.1
+    - fastp >=0.23.0
     - rnastructure >=6.4
     - samtools >=1.20
-    - matplotlib-base >=3.9
     - brotli-python >=1.0
     - python-kaleido >=0.2.1
     - click >=8.1
-    - cutadapt >=4.8
     - fastqsplitter >=1.2
     - numpy >=1.26,<1.27
     - numba >=0.60
@@ -45,7 +38,6 @@ requirements:
     - plotly >=5.23
     - pyyaml >=6.0
     - scipy >=1.13
-
 test:
   imports:
     - seismicrna
diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml
index be624c6675928..e2fee90b517d4 100644
--- a/recipes/sentieon/meta.yaml
+++ b/recipes/sentieon/meta.yaml
@@ -4,14 +4,14 @@ package:
   name: sentieon
   version: {{ version }}
 source:
-  - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz # [linux64]
-    sha256: d51d1a192aa9fd3108f4baa5e1d0784ea80af6734fcc1a27a57e15779f43fcf1 # [linux64]
-    patches: # [linux64]
+  - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz
+    sha256: d51d1a192aa9fd3108f4baa5e1d0784ea80af6734fcc1a27a57e15779f43fcf1
+    patches:
       # Fix driver scripts so they resolves location including symlinks
-      - sentieon_symlinks.patch # [linux64]
+      - sentieon_symlinks.patch
 
 build:
-  number: 0
+  number: 1
   skip: True # [not linux64]
   binary_relocation: false
   run_exports:
@@ -41,5 +41,6 @@ about:
   summary: Accelerated performance bioinformatics tools for mapping and variant calling
 
 extra:
-  skip-lints:
-      - should_be_noarch_generic # Supports Linux64 only
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml
index 538a6f2093241..9994fb9779923 100644
--- a/recipes/seqkit/meta.yaml
+++ b/recipes/seqkit/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.8.2" %}
+{% set version = "2.9.0" %}
 
 package:
   name: seqkit
@@ -6,19 +6,19 @@ package:
 
 source:
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx]
-  md5: 03b13956b7e3ef1678db591a79eb68ed # [osx]
+  md5: 50fff73601f3094d664031e5c00674f5 # [osx]
 
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_arm64.tar.gz # [arm64]
-  md5: 0b2716f39c3974a5c3e310bcbd4076eb # [arm64]
+  md5: cf1b7c4b74664f04d3cc361e9c5370a1 # [arm64]
 
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux]
-  md5: 67220b508f3f81c2c8697e6534eed440 # [linux]
+  md5: 83e359c186dee6b49cd4df362d0b6d5a # [linux]
 
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_arm64.tar.gz # [aarch64]
-  md5: b83b021850c9447cfc8e0d5751b7be99 # [aarch64]
+  md5: 7a81adcd79553e10552456060c2b17ba # [aarch64]
 
 build:
-  number: 1
+  number: 0
   skip: False
   run_exports:
     - {{ pin_subpackage("seqkit", max_pin="x.x") }}
diff --git a/recipes/seqscreen/meta.yaml b/recipes/seqscreen/meta.yaml
index 9c8cbdf6eb2a8..c1d9692c33137 100644
--- a/recipes/seqscreen/meta.yaml
+++ b/recipes/seqscreen/meta.yaml
@@ -10,7 +10,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("seqscreen", max_pin="x.x") }}
 requirements:
@@ -20,7 +20,7 @@ requirements:
     - scikit-learn
     - jinja2
     - biopython
-    - nextflow 21.10.6
+    - nextflow >=22.0.0,<22.11
     - blast >=2.10
     - diamond >=2.0.15
     - centrifuge-core
@@ -36,10 +36,10 @@ requirements:
     - samtools >=1.15.1
     - ete3 >=3.1.2
     - minimap2 >=2.24
-    - ncbi-datasets-cli 13.20.1
+    - ncbi-datasets-cli >=13.20.1
     - pandas >=1.4.3
-    - bwa 0.7.17
-    - pyfasta 0.5.2
+    - bwa >=0.7.17
+    - pyfasta >=0.5.2
 
 test:
   commands:
diff --git a/recipes/seqspec/meta.yaml b/recipes/seqspec/meta.yaml
index c4a928dfcb61f..60296907ebdc4 100644
--- a/recipes/seqspec/meta.yaml
+++ b/recipes/seqspec/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "seqspec" %}
-{% set version = "0.3.0" %}
+{% set version = "0.3.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/seqspec-{{ version }}.tar.gz
-  sha256: d9e6c283daaca06f58f1090c0c7dcfecf646b9658e62aa873a4e85fef56c56c9
+  sha256: 1c71201e3913526542f4fe7dfcbc866a295976e983dc91c7f53efb655797b3c2
 
 build:
   run_exports:
diff --git a/recipes/sfold/build.sh b/recipes/sfold/build.sh
index 0584640650b30..b86e125258d17 100755
--- a/recipes/sfold/build.sh
+++ b/recipes/sfold/build.sh
@@ -13,4 +13,12 @@ cp -r STarMir ${SFOLD_DIR}
 
 # modify the sfoldenv file
 cp sfoldenv ${SFOLD_DIR}/sfoldenv
-sed -i "s|SFOLDDIR=.*|SFOLDDIR=${SFOLD_DIR}|g" ${SFOLD_DIR}/sfoldenv
\ No newline at end of file
+sed -i.bak "s|SFOLDDIR=.*|SFOLDDIR=${SFOLD_DIR}|g" ${SFOLD_DIR}/sfoldenv
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/STarMir/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/STarMir/starmir-param/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/bin/*.pl
+
+rm -rf ${SFOLD_DIR}/*.bak
+rm -rf ${SFOLD_DIR}/STarMir/*.bak
+rm -rf ${SFOLD_DIR}/STarMir/starmir-param/*.bak
+rm -rf ${SFOLD_DIR}/bin/*.bak
diff --git a/recipes/sfold/meta.yaml b/recipes/sfold/meta.yaml
index 98dce74f72249..b6509c09158c3 100644
--- a/recipes/sfold/meta.yaml
+++ b/recipes/sfold/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: c25e4d8cf055e13c523ef59f68c8847b66584e36359ce4fb9dc675a97f1a2939
 
 build:
-  number: 1
+  number: 3
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage('sfold', max_pin='x') }}
diff --git a/recipes/sgdemux/meta.yaml b/recipes/sgdemux/meta.yaml
index 6846b7a29256c..7f412931f8a6c 100644
--- a/recipes/sgdemux/meta.yaml
+++ b/recipes/sgdemux/meta.yaml
@@ -1,3 +1,4 @@
+{% set name = "sgdemux" %}
 {% set version = "1.2.0" %}
 
 package:
@@ -5,8 +6,9 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
-
+  number: 3
+  run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}'
+  
 source:
   url: https://github.com/Singular-Genomics/singular-demux/archive/refs/tags/v{{ version }}.tar.gz
   sha256: aa7b61b04e40bdd0dba91cfa57874203745506521e17139bbcfa4d36a5811dc5
@@ -35,3 +37,6 @@ about:
 extra:
   recipe-maintainers:
     - nh13
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml
index f473cd67cc6e1..bd23e0850fed5 100644
--- a/recipes/shortstack/meta.yaml
+++ b/recipes/shortstack/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ShortStack" %}
-{% set version = "4.1.0" %}
-{% set sha256 = "f138672d1f564cdd9dffe384bc84ca01bbd67b8e76a9d9f030b47a0e478f3fe1" %}
+{% set version = "4.1.1" %}
+{% set sha256 = "24f0c259f3adce25637a7586bd8c7dae59f32df4d6fb2c974b57ad5506da2158" %}
 
 package:
   name: {{ name|lower }}
diff --git a/recipes/sigprofilermatrixgenerator/meta.yaml b/recipes/sigprofilermatrixgenerator/meta.yaml
index a1960b918d439..a1774cd036abe 100644
--- a/recipes/sigprofilermatrixgenerator/meta.yaml
+++ b/recipes/sigprofilermatrixgenerator/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "SigProfilerMatrixGenerator" %}
-{% set version = "1.2.30" %}
+{% set version = "1.2.31" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerMatrixGenerator-{{ version }}.tar.gz
-  sha256: 55453304c565acacc62bce77592f8c44a14bca367df33585825f06893e315280
+  sha256: 632621178fc6c572d0953c24bff7a1079e55311ea870ee02ecb90468a894a5d2
 
 build:
   entry_points:
diff --git a/recipes/smudgeplot/0001-Makefile.patch b/recipes/smudgeplot/0001-Makefile.patch
new file mode 100644
index 0000000000000..0ae20a2f5ec9c
--- /dev/null
+++ b/recipes/smudgeplot/0001-Makefile.patch
@@ -0,0 +1,13 @@
+diff --git a/Makefile b/Makefile
+index ad29043..4dff5ca 100644
+--- a/Makefile
++++ b/Makefile
+@@ -15,7 +15,7 @@ $(INSTALL_PREFIX)/bin/% : exec/%
+ 	install -C $< $(INSTALL_PREFIX)/bin
+ 
+ exec/hetmers: src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/libfastk.h src_ploidyplot/matrix.c src_ploidyplot/matrix.h
+-	gcc $(CFLAGS) -o $@ src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/matrix.c -lpthread -lm
++	$(CC) $(CFLAGS) -o $@ src_ploidyplot/PloidyPlot.c src_ploidyplot/libfastk.c src_ploidyplot/matrix.c -lpthread -lm
+ 
+ 
+ .PHONY : clean
diff --git a/recipes/smudgeplot/build.sh b/recipes/smudgeplot/build.sh
index 7dd1d9fd55b4a..78424b59ac005 100644
--- a/recipes/smudgeplot/build.sh
+++ b/recipes/smudgeplot/build.sh
@@ -1,10 +1,13 @@
 #!/bin/bash
 
+export CPATH="${PREFIX}/include"
+
 mkdir -p $PREFIX/bin
 
-# Install the current codebase as an R package
-Rscript install.R
+make -s INSTALL_PREFIX="${PREFIX}" CC="${CC}" -j"${CPU_COUNT}"
 
 # Install executables
 install -C exec/smudgeplot.py $PREFIX/bin
+install -C exec/hetmers $PREFIX/bin
 install -C exec/smudgeplot_plot.R $PREFIX/bin
+install -C exec/centrality_plot.R $PREFIX/bin
diff --git a/recipes/smudgeplot/meta.yaml b/recipes/smudgeplot/meta.yaml
index 9d41489cad4f2..4bff036cc65bd 100644
--- a/recipes/smudgeplot/meta.yaml
+++ b/recipes/smudgeplot/meta.yaml
@@ -1,17 +1,19 @@
-{% set version = "0.3.0" %}
+{% set version = "0.4.0" %}
 
 package:
   name: smudgeplot
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('smudgeplot', max_pin="x.x") }}
 
 source:
   url: https://github.com/KamilSJaron/smudgeplot/archive/v{{ version }}.tar.gz
-  sha256: b95b61e517de8f33c49910825a5c68e9a0d1e27cc33463939ef4c994e61dda92
+  sha256: 61ca437e29830a415e6f18f39d5d1fd994d20ea4a9bd46d1ab5fdcc52fa4008d
+  patches:
+    - 0001-Makefile.patch
 
 requirements:
   build:
@@ -31,10 +33,11 @@ requirements:
     - r-argparse
     - numpy
     - scipy
+    - pandas
 
 test:
   commands:
-    - smudgeplot.py --version 2>&1 | grep 'Running'
+    - "smudgeplot.py --version 2>&1"
 
 about:
   home: https://github.com/KamilSJaron/smudgeplot
diff --git a/recipes/snakedeploy/meta.yaml b/recipes/snakedeploy/meta.yaml
index d1bd0b783bd98..a65bb502853f4 100644
--- a/recipes/snakedeploy/meta.yaml
+++ b/recipes/snakedeploy/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.10.2" %}
+{% set version = "0.10.3" %}
 
 package:
   name: snakedeploy
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/s/snakedeploy/snakedeploy-{{ version }}.tar.gz
-  sha256: 88203f7622551cb08da9ad73b2697a7e64e0b0094b533652a7d74fb39a936102
+  sha256: 821be1954f32d75530771f9c3fb39915068ad0987bfe3d2fc7e7f9b35b95ff78
 
 build:
   number: 0
diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml
index 5130d754bac38..700e7526b5919 100644
--- a/recipes/snakemake-executor-plugin-slurm/meta.yaml
+++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snakemake-executor-plugin-slurm" %}
-{% set version = "0.11.1" %}
+{% set version = "0.11.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz
-  sha256: 293a951dcf829400bf6197705d6c602faed95aaaae9ad0d661d23b0184074134
+  sha256: fca29038d78387c237afb4ec2b04638e6128d2456940dd7b96ac4205f319d7f3
 
 build:
   noarch: python
diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml
index 1cfda1fb4b20d..417adf4f21c71 100644
--- a/recipes/snakemake/meta.yaml
+++ b/recipes/snakemake/meta.yaml
@@ -1,7 +1,7 @@
 # Attention: when upgrading the version, please compare below dependencies with
 # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg
 {% set name = "snakemake" %}
-{% set version = "8.24.0" %}
+{% set version = "8.25.3" %}
 
 package:
   name: {{ name }}
@@ -9,7 +9,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz
-  sha256: 4445f33e4e23ae9025bbc5aef46b868d8b615ef463544659674db8aabf40bcd4
+  sha256: b05262fbb25b8b463ea45f92789c39935a775c02b072be8a42e6cd262ed86c21
 
 build:
   number: 0
@@ -85,7 +85,7 @@ outputs:
         - setuptools
       run:
         # Keep in sync with snakemake/setup.cfg 
-        - python >=3.11,<3.13
+        - python >=3.11,<3.13 # we restrict to <3.13 because Python can have breaking changes in minor version bumps
         - appdirs
         - immutables
         - configargparse
@@ -99,15 +99,15 @@ outputs:
         - nbformat
         - packaging
         - psutil
-        - pulp >=2.3.1,<2.9
+        - pulp >=2.3.1,<2.10
         - pyyaml
-        - requests >=2.8.1
+        - requests >=2.8.1,<3.0
         - reretry
         - smart_open >=4.0,<8.0
         - snakemake-interface-executor-plugins >=9.3.2,<10.0.0
         - snakemake-interface-common >=1.17.0,<2.0
         - snakemake-interface-storage-plugins >=3.2.3,<4.0
-        - snakemake-interface-report-plugins >=1.0.0,<2.0.0
+        - snakemake-interface-report-plugins >=1.1.0,<2.0.0
         - tabulate
         - throttler
         - wrapt
diff --git a/recipes/snapatac2/build.sh b/recipes/snapatac2/build.sh
index e2ff247a81a4f..b9259f5b409d3 100644
--- a/recipes/snapatac2/build.sh
+++ b/recipes/snapatac2/build.sh
@@ -1,17 +1,11 @@
 #!/bin/bash -ex
 
-# Use a custom temporary directory as home on macOS.
-# (not sure why this is useful, but people use it in bioconda recipes)
-if [ `uname` == Darwin ]; then
-	export HOME=`mktemp -d`
-fi
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 # Build the package using maturin - should produce *.whl files.
 maturin build -m snapatac2-python/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip
 
 # Install *.whl files using pip
-${PYTHON} -m pip install snapatac2-python/target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
+${PYTHON} -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
 
 cd ${SRC_DIR}/snapatac2-python/ && cargo clean && rm -rf ${BUILD_PREFIX}/.cargo
diff --git a/recipes/snapatac2/build_failure.linux-64.yaml b/recipes/snapatac2/build_failure.linux-64.yaml
deleted file mode 100644
index 192d0da24c090..0000000000000
--- a/recipes/snapatac2/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-recipe_sha: 0020e1f18882dacb116e05fb00a1e435b21713b2e0a803ece479d299f8c00347  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: disk space
-reason: GitHub Actions runs out of space trying to build all python versions.
\ No newline at end of file
diff --git a/recipes/snapatac2/build_failure.osx-64.yaml b/recipes/snapatac2/build_failure.osx-64.yaml
deleted file mode 100644
index 4a6f367e00bb0..0000000000000
--- a/recipes/snapatac2/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 0020e1f18882dacb116e05fb00a1e435b21713b2e0a803ece479d299f8c00347  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-    = note: ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libproc_macro-d9904b6b430ac650.rlib(proc_macro-d9904b6b430ac650.proc_macro.f7284eae513ccf25-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib(core-1638dc700d175798.core.b1c2fc210f4dfff9-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib(alloc-0ff05b9b25b786cc.alloc.9242d371e396bc4c-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib(hashbrown-0e3ea0ec18336be2.hashbrown.febebf65344cb99d-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib(rustc_demangle-37f4c48e230f618e.rustc_demangle.9fdffeb2b56169d1-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib(gimli-de95e5c2a2ace281.gimli.72653df79598dcb2-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib(object-0e1339b212cc7409.object.e3756fe3fb577255-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib(memchr-925e672b3deb429c.memchr.4dc4a05d80618598-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib(addr2line-e92d517a950bccd8.addr2line.7eb29e6a0a38fefd-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib(panic_unwind-8ce93eee8bf4c86e.panic_unwind.a3b8ea81b157ee45-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib(compiler_builtins-7f42af62722c8f43.compiler_builtins.19fed66cffb9e9f5-cgu.089.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9)
-            Undefined symbols for architecture x86_64:
-              "_getentropy", referenced from:
-                  std::sys::pal::unix::rand::hashmap_random_keys::hcc27ed0e9fd421d6 in libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o)
-            ld: symbol(s) not found for architecture x86_64
-            clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
-
-
-  error: could not compile serde_derive (lib) due to 1 previous error
-   maturin failed
-    Caused by: Failed to build a native library through cargo
-    Caused by: Cargo build finished with "exit status: 101": env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.11-64bit" PYO3_PYTHON="/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python" PYTHON_SYS_EXECUTABLE="/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python" "cargo" "rustc" "--features" "pyo3/extension-module" "--target" "x86_64-apple-darwin" "--message-format" "json-render-diagnostics" "--manifest-path" "/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work/snapatac2-python/Cargo.toml" "--release" "--lib" "--" "-C" "link-arg=-undefined" "-C" "link-arg=dynamic_lookup" "-C" "link-args=-Wl,-install_name,@rpath/snapatac2._snapatac2.cpython-311-darwin.so" "-C" "link-arg=-s"
-  Extracting download
-  Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/snapatac2/cargo.toml.patch
-  Traceback (most recent call last):
-  Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/snapatac2/cargo.toml.patch with args:
-    File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
-  ['-Np1', '-i', '/tmp/tmpdjpsa4y_/cargo.toml.patch.native', '--binary']
-  Patch analysis gives:
-  [[ RA-MD1LOVE ]] - [[                                                        cargo.toml.patch ]]
-
-  Key:
-
-  R :: Reversible                       A :: Applicable
-  Y :: Build-prefix patch in use        M :: Minimal, non-amalgamated
-  D :: Dry-runnable                     N :: Patch level (1 is preferred)
-  L :: Patch level not-ambiguous        O :: Patch applies without offsets
-  V :: Patch applies without fuzz       E :: Patch applies without emitting to stderr
-
-  source tree in: /opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work
-      sys.exit(execute())
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
-  export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/_build_env
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-  INFO: activate_clang_osx-64.sh made the following environmental changes:
-  AR=x86_64-apple-darwin13.4.0-ar
-      packages_from_this = build(
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-      utils.check_call_env(
-  AS=x86_64-apple-darwin13.4.0-as
-  CC=x86_64-apple-darwin13.4.0-clang
-  CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-  CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/snapatac2-2.6.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
-  CLANG=x86_64-apple-darwin13.4.0-clang
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-  CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
-  CMAKE_PREFIX_PATH=:$PREFIX
-  CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
-  CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
-    File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1717630619008/work/conda_build.sh']' returned non-zero exit status 1.
-  DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/snapatac2-2.6.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  HOST=x86_64-apple-darwin13.4.0
-  INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
-  LD=x86_64-apple-darwin13.4.0-ld
-  LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
-  LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
-  LIBTOOL=x86_64-apple-darwin13.4.0-libtool
-  LIPO=x86_64-apple-darwin13.4.0-lipo
-  MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
-  NM=x86_64-apple-darwin13.4.0-nm
-  NMEDIT=x86_64-apple-darwin13.4.0-nmedit
-  OBJC=x86_64-apple-darwin13.4.0-clang
-  OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  OTOOL=x86_64-apple-darwin13.4.0-otool
-  PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
-  RANLIB=x86_64-apple-darwin13.4.0-ranlib
-  REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
-  SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
-  SEGEDIT=x86_64-apple-darwin13.4.0-segedit
-  SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
-  SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
-  SIZE=x86_64-apple-darwin13.4.0-size
-  STRINGS=x86_64-apple-darwin13.4.0-strings
-  STRIP=x86_64-apple-darwin13.4.0-strip
-  _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
-  ac_cv_func_malloc_0_nonnull=yes
-  ac_cv_func_realloc_0_nonnull=yes
-  build_alias=x86_64-apple-darwin13.4.0
-  host_alias=x86_64-apple-darwin13.4.0
-# Last 100 lines of the build log.
diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml
index 8989a9d16459f..04b6501a2c45d 100644
--- a/recipes/snapatac2/meta.yaml
+++ b/recipes/snapatac2/meta.yaml
@@ -1,19 +1,20 @@
 {% set name = "snapatac2" %}
-{% set version = "2.6.4" %}
-{% set sha256 = "6ce80ae2c67f0ae05efed2b785b25e4d13fcc9d58697291b7d578a628b74bd05" %}
+{% set version = "2.7.1" %}
+{% set sha256 = "18c206153112fbf9ca97c690d6d8d1e51cb5d125739ead6e8a3aece8f01cbd66" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snapatac2-{{ version }}.tar.gz
+  url: https://github.com/kaizhang/SnapATAC2/archive/refs/tags/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
     - cargo.toml.patch
+    - pyproject.toml.patch
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 39 or py > 312]
   run_exports:
     - {{ pin_subpackage('snapatac2', max_pin="x") }}
@@ -32,44 +33,43 @@ requirements:
   run:
     - python
     - anndata
-    - harmonypy >=0.0.9
     - python-igraph >=0.10.3
     - multiprocess
     - macs3
     - natsort
     - numpy >=1.16.0
     - pandas >=1.0,<2.1.2
-    - plotly >=5.6.0
-    - polars >=0.20.0
+    - plotly >=5.19.0
+    - polars >=1.0
     - pooch >=1.6.0
     - pyarrow
     - pyfaidx >=0.7.0,<0.8.0
     - python-kaleido
     - rustworkx
-    - scanorama >=1.7.3
-    - scanpy
     - scipy >=1.4
     - scikit-learn >=1.0
-    - scvi-tools >=1.0
     - tqdm >=4.62
     - typing_extensions
-    - umap-learn >=0.5.0
-    - xgboost >=1.4
+    - typeguard >=4.0
 
 test:
   imports:
     - snapatac2
 
 about:
-  home: https://github.com/kaizhang/SnapATAC2
-  summary: "SnapATAC2: Single-cell epigenomics analysis pipeline"
+  home: "https://github.com/kaizhang/SnapATAC2"
+  summary: "SnapATAC2: Single-cell epigenomics analysis pipeline."
   license: MIT
   license_family: MIT
-  license_file: LICENSE
-  doc_url: https://kzhang.org/SnapATAC2/
-  dev_url: https://github.com/kaizhang/SnapATAC2
+  license_file: snapatac2-python/LICENSE
+  doc_url: "https://kzhang.org/SnapATAC2"
+  dev_url: "https://github.com/kaizhang/SnapATAC2"
 
 extra:
   identifiers:
     - biotools:snapatac
     - doi:10.1038/s41592-023-02139-9
+    - usegalaxy-eu:snapatac2_preprocessing
+    - usegalaxy-eu:snapatac2_clustering
+    - usegalaxy-eu:snapatac2_peaks_and_motif
+    - usegalaxy-eu:snapatac2_plotting
diff --git a/recipes/snapatac2/pyproject.toml.patch b/recipes/snapatac2/pyproject.toml.patch
new file mode 100644
index 0000000000000..920d2e5eb30fb
--- /dev/null
+++ b/recipes/snapatac2/pyproject.toml.patch
@@ -0,0 +1,13 @@
+diff --git a/snapatac2-python/pyproject.toml b/snapatac2-python/pyproject.toml
+index 15d7b75..82f9c43 100644
+--- a/snapatac2-python/pyproject.toml
++++ b/snapatac2-python/pyproject.toml
+@@ -6,6 +6,8 @@ build-backend = "maturin"
+ features = ["pyo3/extension-module"]
+ python-source = "python"
+ module-name = "snapatac2._snapatac2"
++strip = true
++profile = "release"
+ 
+ [project]
+ name = "snapatac2"
diff --git a/recipes/sniffles/meta.yaml b/recipes/sniffles/meta.yaml
index 445120497e1c0..bf2b788e117fb 100644
--- a/recipes/sniffles/meta.yaml
+++ b/recipes/sniffles/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "2.4" %}
-{% set sha256 = "e3c2f552105cd5f5941d6291b9ee9dbfe634ad19b5e7a64fa26b9e2daa6547d4" %}
+{% set version = "2.5.2" %}
+{% set sha256 = "b041580091a87d8c180303a1cb8ca513864ad1b41e64928fc0e04a59fdf5a80f" %}
 
 package:
   name: sniffles
@@ -12,18 +12,18 @@ source:
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage('sniffles', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3.10
+    - python ==3.10.15
     - pip
   run:
-    - python >=3.10
+    - python ==3.10.15
     - pysam >=0.21.0
-    - edlib >=1.3.9
+    - python-edlib >=1.3.9
     - psutil >=5.9.4
 
 test:
@@ -31,11 +31,18 @@ test:
     - sniffles --help
 
 about:
-  home: https://github.com/fritzsedlazeck/Sniffles
+  home: "https://github.com/fritzsedlazeck/Sniffles"
   license: MIT
   license_file: LICENSE
   license_family: MIT
-  summary: Sniffles is a structural variation caller using third generation sequencing
-    (PacBio or Oxford Nanopore)
-  doc_url: https://github.com/fritzsedlazeck/Sniffles/wiki
-  dev_url: https://github.com/fritzsedlazeck/Sniffles
+  summary: "Sniffles is a structural variation caller using third generation sequencing
+    (PacBio or Oxford Nanopore)."
+  doc_url: "https://github.com/fritzsedlazeck/Sniffles/wiki"
+  dev_url: "https://github.com/fritzsedlazeck/Sniffles"
+
+extra:
+  identifiers:
+    - doi:10.1038/s41587-023-02024-y
+    - doi:10.1038/s41592-018-0001-7
+    - biotools:sniffles
+    - usegalaxy-eu:sniffles
diff --git a/recipes/snipe/meta.yaml b/recipes/snipe/meta.yaml
index 8bc801c964004..a5b3dfc5fc2b5 100644
--- a/recipes/snipe/meta.yaml
+++ b/recipes/snipe/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snipe" %}
-{% set version = "0.1.4" %}
+{% set version = "0.1.6" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/snipe-bio/snipe/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 18f49da162e426dede11a8836b77a347e94bb618a1f0ae9eb8ae967960c81b16
+  sha256: 6847a51dbfca18442681f7981483401741a9860c0399f3f2592bb3894227afb8
 
 build:
   number: 0
diff --git a/recipes/snipit/meta.yaml b/recipes/snipit/meta.yaml
index 6145586560291..1f1ae926cc1a6 100644
--- a/recipes/snipit/meta.yaml
+++ b/recipes/snipit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snipit" %}
-{% set version = "1.2" %}
+{% set version = "1.6" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 92e4395a23ef5e55ae753868723daa3e68d5803a10db6ae27fc6722a99bcc708
+  sha256: 4d3080926bebfd3eeb52e98a35e69bbd66a99e3752dbf436c8d5ccb428bfdb10
 
 build:
   number: 0
diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml
index 42b89cd854fde..e0dc1cbf8c992 100644
--- a/recipes/snippy/meta.yaml
+++ b/recipes/snippy/meta.yaml
@@ -12,7 +12,7 @@ source:
   sha256: '{{ sha256 }}'
 
 build:
-  number: 4
+  number: 5
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
@@ -22,7 +22,7 @@ requirements:
     - perl
     - perl-bioperl >=1.7.2
     - bwa >=0.7.17
-    - samtools >=1.10
+    - samtools >=1.10,<=1.20
     - bcftools >=1.10
     - bedtools >=2.28.0
     - parallel >=20170422
diff --git a/recipes/snk-cli/meta.yaml b/recipes/snk-cli/meta.yaml
index 9e1434504395f..809eeffb36f15 100644
--- a/recipes/snk-cli/meta.yaml
+++ b/recipes/snk-cli/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snk-cli" %}
-{% set version = "0.5.5" %}
+{% set version = "0.7.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,14 +7,14 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name | replace("-","_") }}-{{ version }}.tar.gz
-  sha256: 5ba6a88aca3473751152cdcd22b0cdc31b0f4034d9eabf859a3dfc6dcc4a487f
+  sha256: eec5fb4411e54a97927586f2cf0018219513a6ef8de1e38ec0741a642521c299
 
 build:
   run_exports:
     - {{ pin_subpackage('snk-cli', max_pin="x.x") }}
   noarch: python
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 0
+  number: 1
 
 requirements:
   host:
@@ -31,6 +31,7 @@ requirements:
     - ascii-art >=5.9,<6.dev0
     - makefun >=1.15,<2.dev0
     - datrie >=0.8.2
+    - graphviz >=2.38.0
 
 test:
   imports:
diff --git a/recipes/snk/meta.yaml b/recipes/snk/meta.yaml
index 26dfad0f59b98..29c191526db9c 100644
--- a/recipes/snk/meta.yaml
+++ b/recipes/snk/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snk" %}
-{% set version = "0.30.1" %}
+{% set version = "0.31.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name | replace("-","_") }}-{{ version }}.tar.gz
-  sha256: 6bb3ed373c94ed4d9764b3ced41aecddc112c373400925f1166d52b5e5ca7c90
+  sha256: 5190498c3a5e7969fbd11f1c10b401a1ade314e3737858f23bc72ac20ea655e5
 
 build:
   run_exports:
@@ -15,7 +15,7 @@ build:
   entry_points:
     - snk = snk.main:app
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   number: 0
 
 requirements:
@@ -27,7 +27,7 @@ requirements:
   run:
     - python >=3.8
     - gitpython >=3.1.0,<3.2.dev0
-    - snk-cli >=0.5.2
+    - snk-cli >=0.7.0
     - git
 
 test:
@@ -50,5 +50,3 @@ about:
 extra:
   recipe-maintainers:
     - Wytamma
-
-
diff --git a/recipes/snpick/meta.yaml b/recipes/snpick/meta.yaml
new file mode 100644
index 0000000000000..9af6c924cbf13
--- /dev/null
+++ b/recipes/snpick/meta.yaml
@@ -0,0 +1,70 @@
+{% set name = "snpick" %}
+{% set version = "1.0.0" %}
+{% set sha256 = "6a5ae16a65c92c90ecf710c4d53afa0e3a76b7a43554c52e48cda843f7e20744" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://github.com/PathoGenOmics-Lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz"
+  sha256: "{{ sha256 }}"
+
+build:
+  number: 0
+  script: |
+    set -xe
+    export LANG=C.UTF-8
+    export LC_ALL=C.UTF-8
+    export RUST_BACKTRACE=1
+    export OPENSSL_NO_VENDOR=1
+    export OPENSSL_DIR=$PREFIX
+    export OPENSSL_INCLUDE_DIR=$PREFIX/include
+    export OPENSSL_LIB_DIR=$PREFIX/lib
+    export LIBCLANG_PATH=$PREFIX/lib
+    export CPLUS_INCLUDE_PATH=$PREFIX/include
+    cargo install --locked --verbose --root "${PREFIX}" --path .
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('rust') }}
+    - pkg-config
+  host:
+    - openssl
+    - zlib
+    - xz
+    - bzip2
+  run:
+    - {{ pin_compatible('openssl') }}
+    - {{ pin_compatible('zlib') }}
+    - {{ pin_compatible('xz') }}
+    - {{ pin_compatible('bzip2') }}
+
+test:
+  commands:
+    - snpick --help
+    - snpick --version
+
+about:
+  home: "https://github.com/PathoGenOmics-Lab/snpick"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
+  license_file: LICENSE
+  summary: "A fast and memory-efficient tool for SNP extraction from genomic alignments."
+  description: |
+    snpick is a Rust-based tool designed for extracting SNPs efficiently from large genomic alignments, with minimal RAM usage and high performance. It outputs variable sites in alignment files and provides VCF generation.
+  doc_url: "https://github.com/PathoGenOmics-Lab/snpick"
+  dev_url: "https://github.com/PathoGenOmics-Lab/snpick"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - PathoGenOmics-Lab
+  categories:
+    - Genomics
+    - Variant Analysis
+    - SNP Extraction
diff --git a/sopa/meta.yaml b/recipes/sopa/meta.yaml
similarity index 79%
rename from sopa/meta.yaml
rename to recipes/sopa/meta.yaml
index cbe346742649b..2b6e6a30ed5d1 100644
--- a/sopa/meta.yaml
+++ b/recipes/sopa/meta.yaml
@@ -13,8 +13,10 @@ build:
   entry_points:
     - sopa = sopa.main:app
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   number: 0
+  run_exports:
+    - {{ pin_subpackage('sopa', max_pin="x") }}
 
 requirements:
   host:
@@ -28,8 +30,7 @@ requirements:
     - scanpy >=1.9.8
     - botocore 1.34.19
     - typer >=0.9.0
-    - setuptools >=69.2.0
-    - flake8 <8.0.0,>=7.0.0
+    - flake8 >=7.0.0,<8.0.0
   run_constrained:
     - cellpose >=3.0.5
     - opencv >=4.8.0.76
@@ -37,7 +38,7 @@ requirements:
     - toml >=0.10.2
     - loompy >=3.0.7
     - tangram-sc >=1.0.4
-    - snakemake >=7.32.4,<8.0.0,<8.1.3
+    - snakemake-minimal >=7.32.4,<8.0.0,<8.1.3
     - pulp >=2.3.1,<3.0.0,<2.8
     - tiffslide >=2.3.1,<3.0.0
     - black >=22.8.0,<23.0.0
@@ -54,16 +55,15 @@ test:
   imports:
     - sopa
   commands:
-    - pip check
     - sopa --help
-  requires:
-    - pip
 
 about:
   home: https://gustaveroussy.github.io/sopa
-  summary: Spatial-omics pipeline and analysis
+  summary: "Spatial-omics pipeline and analysis."
   license: BSD-3-Clause
+  license_family: BSD
   license_file: LICENSE
+  dev_url: https://gustaveroussy.github.io/sopa
 
 extra:
   recipe-maintainers:
diff --git a/recipes/spaln/meta.yaml b/recipes/spaln/meta.yaml
index 897fbab3335c3..c2a7d7c8260ab 100644
--- a/recipes/spaln/meta.yaml
+++ b/recipes/spaln/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "spaln" %}
-{% set version = "3.0.6" %}
-{% set sha256 = "0b627609b69e0e1487cbb75ff564cfe3816c24da8552acbaf50bf19bce1c6490" %}
+{% set version = "3.0.6b" %}
+{% set sha256 = "8e496ef6d02696543f4a5e31922f464555eff9b8405da366587ba7bea27b4e76" %}
 
 package:
   name: {{ name|lower }}
@@ -41,7 +41,7 @@ test:
 
 about:
   home: https://github.com/ogotoh/spaln
-  doc_url: "https://github.com/ogotoh/spaln/blob/master/README.md"
+  doc_url: "https://github.com/ogotoh/spaln/blob/ver.{{ version }}/README.md"
   dev_url: https://github.com/ogotoh/spaln
   license: "GPL-2.0-or-later"
   license_family: GPL
diff --git a/recipes/spring/Makefile.patch b/recipes/spring/Makefile.patch
new file mode 100644
index 0000000000000..68c4e799d9dd8
--- /dev/null
+++ b/recipes/spring/Makefile.patch
@@ -0,0 +1,23 @@
+diff --git a/src/libbsc/bsc.h b/src/libbsc/bsc.h
+index 25230dc..caca189 100644
+--- a/src/libbsc/bsc.h
++++ b/src/libbsc/bsc.h
+@@ -48,6 +48,7 @@ preprocessor macro LIBBSC_SORT_TRANSFORM_SUPPORT at compile time.
+ #ifndef SPRING_LIBBSC_BSC_H_
+ #define SPRING_LIBBSC_BSC_H_
+ 
++#include <cstdint>
+ #include "params.h"
+ 
+ namespace spring {
+diff --git a/src/util.h b/src/util.h
+index 30bad68..a72a0b6 100644
+--- a/src/util.h
++++ b/src/util.h
+@@ -17,6 +17,7 @@ limitations under the License.
+ 
+ #include <fstream>
+ #include <string>
++#include <cstdint>
+ 
+ namespace spring {
\ No newline at end of file
diff --git a/recipes/spring/build.sh b/recipes/spring/build.sh
index 08e68971964f4..684be7536d398 100644
--- a/recipes/spring/build.sh
+++ b/recipes/spring/build.sh
@@ -8,6 +8,10 @@ export CXXPATH=${PREFIX}/include
 export CFLAGS="$CFLAGS -I$PREFIX/include"
 export CXXFLAGS="$CFLAGS -I$PREFIX/include"
 export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
-cmake -Dspring_optimize_for_portability=ON ..
+if [ $(arch) == "aarch64" ]; then
+   cmake ..
+  else
+      cmake -Dspring_optimize_for_portability=ON ..
+fi
 make
 cp spring $PREFIX/bin
diff --git a/recipes/spring/meta.yaml b/recipes/spring/meta.yaml
index 3025d74de5bd1..8dac430b3ae51 100644
--- a/recipes/spring/meta.yaml
+++ b/recipes/spring/meta.yaml
@@ -5,8 +5,10 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
+  number: 3
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('spring', max_pin="x") }}
 
 source:
   url: https://github.com/shubhamchandak94/Spring/archive/v{{ version }}.tar.gz
@@ -26,5 +28,9 @@ about:
   home: https://github.com/shubhamchandak94/Spring
   license: Free for non-commercial use
   license_file: license.pdf
-  summary: Spring is a compression tool for Fastq files
+  summary: "Spring is a compression tool for Fastq files."
+  dev_url: https://github.com/shubhamchandak94/Spring
 
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml
index 6b95c234d852a..b1f2a2bcc8252 100644
--- a/recipes/squirrel/meta.yaml
+++ b/recipes/squirrel/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.11" %}
+{% set version = "1.0.12" %}
 {% set name = "squirrel" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 2d3a4e1a3227372f32ffb6d97005efb08839b53e71f1b6e3d844fe8327835fe5
+  sha256: a99eb37903d553c0bee2f2e0bc5104035fac6644f3115a7986619abf6a29297c
 
 build:
   number: 0
diff --git a/recipes/srahunter/meta.yaml b/recipes/srahunter/meta.yaml
index 2f3de29f283d5..e6e025cebedc2 100644
--- a/recipes/srahunter/meta.yaml
+++ b/recipes/srahunter/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "srahunter" %}
-{% set version = "0.0.3" %}
+{% set version = "0.0.6" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url:    https://github.com/GitEnricoNeko/srahunter/archive/refs/tags/{{version}}.tar.gz
-  sha256: f8efc31a28f84bbf62aa4b9b5b78703273ed3b6fdc29a36edc9f835838e6dd2b
+  sha256: da29cc06f8ae42506ef587a5e69ab5a4ec07fee42880f6612086fcd680531810
 build:
   entry_points:
     - srahunter=scripts.cli:main
diff --git a/recipes/staden_io_lib/build.sh b/recipes/staden_io_lib/build.sh
index 61d759975fa98..c7ca1b7910795 100644
--- a/recipes/staden_io_lib/build.sh
+++ b/recipes/staden_io_lib/build.sh
@@ -1,5 +1,10 @@
 #!/bin/bash
 
+export M4="${BUILD_PREFIX}/bin/m4"
+
+autoreconf -if
 ./configure --prefix=${PREFIX} --with-libdeflate=${PREFIX}
-make
+make -j"${CPU_COUNT}"
 make install
+
+cp -f io_lib_config.h ${PREFIX}/include/io_lib/
diff --git a/recipes/staden_io_lib/meta.yaml b/recipes/staden_io_lib/meta.yaml
index aceb5b5700ad2..78bbf9e7e9ff7 100644
--- a/recipes/staden_io_lib/meta.yaml
+++ b/recipes/staden_io_lib/meta.yaml
@@ -14,7 +14,7 @@ source:
     - config.patch
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('staden_io_lib', max_pin='x.x') }}
 
@@ -22,6 +22,9 @@ requirements:
   build:
     - make
     - {{ compiler('c') }}
+    - autoconf
+    - automake
+    - libtool ==2.4.6
   host:
     - bzip2
     - zlib
@@ -35,11 +38,15 @@ test:
 
 about:
   home: https://github.com/jkbonfield/io_lib/
-  license: BSD
+  license: BSD-3-Clause
+  license_family: BSD
   license_file: COPYRIGHT
-  summary: 'Staden io_lib is a library of file reading and writing code e.g. for SAM/BAM/CRAM'
+  summary: 'Staden io_lib is a library of file reading and writing code e.g. for SAM/BAM/CRAM.'
+  dev_url: https://github.com/jkbonfield/io_lib
 
 extra:
   additional-platforms:
     - linux-aarch64
     - osx-arm64
+  identifiers:
+    - biotools:staden_io_lib
diff --git a/recipes/starfish/meta.yaml b/recipes/starfish/meta.yaml
index fb523d58069c0..b7c292b10bdca 100644
--- a/recipes/starfish/meta.yaml
+++ b/recipes/starfish/meta.yaml
@@ -1,51 +1,57 @@
-{% set version = "0.2.2" %}
+{% set name = "starfish" %}
+{% set version = "0.3.0" %}
 
 package:
-  name: starfish
+  name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://github.com/spacetx/starfish/archive/{{ version }}.tar.gz
-  sha256: 3183465443420ca068a2235ee754c4d02e787d69784349713b74ecf3f83b82fd
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/starfish-{{ version }}.tar.gz
+  sha256: 29152eaa81d396ccc32695e9b1a0271e4f89851cf1f8f13687566b1d03fdd58a
 
 build:
   number: 0
+  run_exports:
+    - {{ pin_subpackage("starfish", max_pin="x.x") }}
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
 
 requirements:
   host:
-    - python >=3.6
+    - python >=3.9,<3.12
     - pip
   run:
-    - python >=3.6
+    - python >=3.9,<3.12
     - click
-    - dataclasses
+    - docutils <0.21
     - h5py
-    - jsonschema
-    - matplotlib-base
-    - numpy !=1.13.0
-    - pandas >=0.23.4
+    - jsonschema <4.18
+    - matplotlib-base <3.8
+    - mistune ==0.8.4
+    - numpy <1.25
     - regional
     - read-roi
     - semantic_version
-    - scikit-image >=0.14.0,!=0.16.0.*,!= 0.16.1.*,!=0.16.2.*,!= 0.17.1.*,!=0.17.2.*
+    - scikit-image ==0.21
     - scikit-learn
-    - scipy
-    - showit >=1.1.4
-    - slicedimage ==4.1.1
+    - seaborn-base
+    - showit
+    - slicedimage
     - sympy
     - tqdm
     - trackpy
     - validators
-    - xarray >=0.14.1
-    - ipywidgets
+    - xarray <2023.09
 
 test:
   imports:
     - starfish
 
 about:
-  home: https://github.com/spacetx/starfish
+  home: "https://github.com/spacetx/starfish"
   license: MIT
-  summary: standardized analysis pipeline for image-based transcriptomics
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Standardized analysis pipeline for image-based transcriptomics."
+  dev_url: "https://github.com/spacetx/starfish"
+  doc_url: "https://spacetx-starfish.readthedocs.io/en/latest"
diff --git a/recipes/steamboat/meta.yaml b/recipes/steamboat/meta.yaml
new file mode 100644
index 0000000000000..c605ef5021979
--- /dev/null
+++ b/recipes/steamboat/meta.yaml
@@ -0,0 +1,49 @@
+{% set name = "steamboat" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/steamboat-binf/steamboat_binf-{{ version }}.tar.gz
+  sha256: dfade01e251d5bbfb117378b9abeaf7231e0fc7a37fc7e37be0933ac9185981c
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv .
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.9
+    - pip
+    - poetry-core
+  run:
+    - biopython
+    - executor
+    - pigz
+    - python >=3.9
+    - pyyaml
+    - rich-click >=1.6.0
+
+test:
+  imports:
+    - steamboat
+  commands:
+    - pip check
+    - gisaid-batch --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/rpetit3/steamboat-py
+  summary: A collection of tools/scripts for microbial bioinformatics
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - rpetit3
diff --git a/recipes/strainge/build_failure.linux-64.yaml b/recipes/strainge/build_failure.linux-64.yaml
deleted file mode 100644
index aff92ef2abc4c..0000000000000
--- a/recipes/strainge/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 8d421a84b249ede354ec5b8b84c06165e973405ca4cf7997724b3633e681d5b8  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |2-
-
-    [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip.
-    [1;35mfull command[0m: [34m/opt/conda/conda-bld/strainge_1717901108313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python /opt/conda/conda-bld/strainge_1717901108313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmps55ogjs_[0m
-    [1;35mcwd[0m: /opt/conda/conda-bld/strainge_1717901108313/work
-    Preparing metadata (pyproject.toml): finished with status 'error'
-  [1;31merror[0m: [1mmetadata-generation-failed[0m
-
-  [31m[0m Encountered error while generating package metadata.
-  [31m>[0m See above for output.
-
-  [1;35mnote[0m: This is an issue with the package mentioned above, not pip.
-  [1;36mhint[0m: See above for details.
-  Exception information:
-  Traceback (most recent call last):
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata
-      distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir)
-                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel
-      return super().prepare_metadata_for_build_wheel(
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel
-      return self._call_hook('prepare_metadata_for_build_wheel', {
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook
-      self._subprocess_runner(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner
-      call_subprocess(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess
-      raise error
-  pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1
-
-  The above exception was the direct cause of the following exception:
-
-  Traceback (most recent call last):
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
-      status = run_func(*args)
-               ^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
-      return func(self, options, args)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run
-      requirement_set = resolver.resolve(
-                        ^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve
-      collected = self.factory.collect_root_requirements(root_reqs)
-                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements
-      reqs = list(
-             ^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req
-      cand = self._make_base_candidate_from_link(
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link
-      self._link_candidate_cache[link] = LinkCandidate(
-                                         ^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__
-      super().__init__(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__
-      self.dist = self._prepare()
-                  ^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare
-      dist = self._prepare_distribution()
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution
-      return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement
-      return self._prepare_linked_requirement(req, parallel_builds)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement
-      dist = _get_prepared_distribution(
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution
-      abstract_dist.prepare_distribution_metadata(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata
-      self.req.prepare_metadata()
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata
-      self.metadata_directory = generate_metadata(
-                                ^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata
-      raise MetadataGenerationFailed(package_details=details) from error
-  pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed
-  Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-dk_u9tdk'
-  Removed build tracker: '/tmp/pip-build-tracker-dk_u9tdk'
-  Traceback (most recent call last):
-    File "/opt/conda/bin/conda-build", line 11, in <module>
-      sys.exit(execute())
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
-      api.build(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
-      return build_tree(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
-      packages_from_this = build(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
-      utils.check_call_env(
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
-      return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
-    File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
-      raise subprocess.CalledProcessError(proc.returncode, _args)
-  subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strainge_1717901108313/work/conda_build.sh']' returned non-zero exit status 1.
-# Last 100 lines of the build log.
diff --git a/recipes/strainge/build_failure.osx-64.yaml b/recipes/strainge/build_failure.osx-64.yaml
deleted file mode 100644
index 16a4be15fc58e..0000000000000
--- a/recipes/strainge/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,104 +0,0 @@
-recipe_sha: 8d421a84b249ede354ec5b8b84c06165e973405ca4cf7997724b3633e681d5b8  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-log: |-
-  SIZE=x86_64-apple-darwin13.4.0-size
-  STRINGS=x86_64-apple-darwin13.4.0-strings
-  STRIP=x86_64-apple-darwin13.4.0-strip
-  _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
-  ac_cv_func_malloc_0_nonnull=yes
-  ac_cv_func_realloc_0_nonnull=yes
-  build_alias=x86_64-apple-darwin13.4.0
-  host_alias=x86_64-apple-darwin13.4.0
-  INFO: activate_clangxx_osx-64.sh made the following environmental changes:
-  CLANGXX=x86_64-apple-darwin13.4.0-clang
-  CXX=x86_64-apple-darwin13.4.0-clang
-  CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strainge-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-  DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strainge-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-  Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12)
-  Non-user install because user site-packages disabled
-  Ignoring indexes: https://pypi.org/simple
-  Created temporary directory: /private/tmp/pip-build-tracker-ka0pkz1f
-  Initialized build tracking at /private/tmp/pip-build-tracker-ka0pkz1f
-  Created build tracker: /private/tmp/pip-build-tracker-ka0pkz1f
-  Entered build tracker: /private/tmp/pip-build-tracker-ka0pkz1f
-  Created temporary directory: /private/tmp/pip-install-y6nw1c6k
-  Created temporary directory: /private/tmp/pip-ephem-wheel-cache-vyuojn_m
-  Processing $SRC_DIR
-    Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-ka0pkz1f'
-    Created temporary directory: /private/tmp/pip-modern-metadata-tvd9hhrw
-    Preparing metadata (pyproject.toml): started
-    Preparing metadata (pyproject.toml): finished with status 'error'
-  Exception information:
-  Traceback (most recent call last):
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata
-      distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir)
-                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel
-      return super().prepare_metadata_for_build_wheel(
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel
-      return self._call_hook('prepare_metadata_for_build_wheel', {
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook
-      self._subprocess_runner(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner
-      call_subprocess(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess
-      raise error
-  pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1
-
-  The above exception was the direct cause of the following exception:
-
-  Traceback (most recent call last):
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
-      status = run_func(*args)
-               ^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
-      return func(self, options, args)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run
-      requirement_set = resolver.resolve(
-                        ^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve
-      collected = self.factory.collect_root_requirements(root_reqs)
-                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements
-      reqs = list(
-             ^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req
-      cand = self._make_base_candidate_from_link(
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link
-      self._link_candidate_cache[link] = LinkCandidate(
-                                         ^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__
-      super().__init__(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__
-      self.dist = self._prepare()
-                  ^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare
-      dist = self._prepare_distribution()
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution
-      return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement
-      return self._prepare_linked_requirement(req, parallel_builds)
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement
-      dist = _get_prepared_distribution(
-             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution
-      abstract_dist.prepare_distribution_metadata(
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata
-      self.req.prepare_metadata()
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata
-      self.metadata_directory = generate_metadata(
-                                ^^^^^^^^^^^^^^^^^^
-    File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata
-      raise MetadataGenerationFailed(package_details=details) from error
-  pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed
-  Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-ka0pkz1f'
-  Removed build tracker: '/private/tmp/pip-build-tracker-ka0pkz1f'
-# Last 100 lines of the build log.
diff --git a/recipes/strainge/meta.yaml b/recipes/strainge/meta.yaml
index 87bd9aeccfa3d..c89ccefaae546 100644
--- a/recipes/strainge/meta.yaml
+++ b/recipes/strainge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "strainge" %}
-{% set version = "1.3.8" %}
+{% set version = "1.3.9" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,16 +7,16 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: d93f1d5fea0f13519cdf19e6b0914c8ef5ce07778d653b74db267e92643e4bd1
+  sha256: a056798fdadf9cb9d12675cb421508c0605e637f4a5baf468eca32922ed30d08
 
 build:
-  number: 1
-  skip: true  # [py<38]
+  number: 0
+  skip: True  # [py < 38]
   entry_points:
     - strainge=strainge.cli.main:strainge_cli
     - straingst=strainge.cli.main:straingst_cli
     - straingr=strainge.cli.main:straingr_cli
-  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  script: {{ PYTHON }} -m pip install . --no-build-isolation --no-cache-dir --no-deps -vvv
   run_exports:
     - {{ pin_subpackage("strainge", max_pin="x") }}
 
@@ -28,11 +28,12 @@ requirements:
     - pip
     - pybind11 >=2.2
     - numpy
+    - toml
+    - versioneer
     - zlib
   run:
     - python
-    - numpy
-    - pybind11 >=2.2
+    - {{ pin_compatible('numpy') }}
     - h5py
     - intervaltree
     - matplotlib-base
@@ -57,6 +58,7 @@ about:
   license_family: BSD
   license_file: LICENSE
   summary: "Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains."
+  dev_url: https://github.com/broadinstitute/strainge
 
 extra:
   recipe-maintainers:
diff --git a/recipes/strainy/meta.yaml b/recipes/strainy/meta.yaml
index 9653b9a4f9738..4a12d82f26861 100644
--- a/recipes/strainy/meta.yaml
+++ b/recipes/strainy/meta.yaml
@@ -1,33 +1,33 @@
 {% set version = "1.2" %}
 {% set name = "strainy" %}
 
-
 package:
    name: strainy
    version: {{ version }}
 
-
 source:
    url: https://github.com/katerinakazantseva/strainy/archive/refs/tags/{{ version }}.tar.gz
    sha256: 6ea476eb4a3dcbe1f1af10d2e73982b1aa57aedeedd2b688043a480052655d24
 
-
 build:
-  number: 0
+  number: 1
   noarch: python
-  script: {{ PYTHON }} -m pip install -vv .
+  script: {{ PYTHON }} -m pip install -vvv . --no-deps --no-build-isolation --no-cache-dir
+  entry_points:
+    - strainy = strainy.main:main
   run_exports:
     - {{ pin_subpackage("strainy", max_pin="x") }}  
 
-
 requirements:
   host:
-  - python
+  - python >=3.8
+  - pip
+  - setuptools
   run:
   - python >=3.8
   - samtools >=1.14
   - bcftools >=1.14
-  - minimap2
+  - minimap2 >=2.28
   - pygraphviz
   - matplotlib-base
   - biopython
@@ -41,7 +41,6 @@ requirements:
   - scipy >=1.8,<1.13
   - flye
 
-
 test:
    commands:
    - strainy -h
@@ -51,4 +50,4 @@ about:
    license: GPL-3.0-or-later
    license_family: GPL3
    license_file: LICENSE
-   summary: Assembly-based metagenomic strain phasing using long reads
+   summary: "Assembly-based metagenomic strain phasing using long reads."
diff --git a/recipes/strangepg/build.sh b/recipes/strangepg/build.sh
index 3040da4a94b98..b120ae649490a 100644
--- a/recipes/strangepg/build.sh
+++ b/recipes/strangepg/build.sh
@@ -2,6 +2,8 @@
 
 set -xe
 
-export CFLAGS="$CFLAGS -I${PREFIX}/include"
-export LDFLAGS="$LDFLAGS -ldl -lpthread"
-make -j ${CPU_COUNT} install
+export C_INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDLIBS="-ldl -lpthread"
+
+make CC="${CC}" PREFIX="${PREFIX}" -j ${CPU_COUNT} install
diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml
index 723f9b69e7bb2..1be6b9d623d57 100644
--- a/recipes/strangepg/meta.yaml
+++ b/recipes/strangepg/meta.yaml
@@ -1,25 +1,20 @@
 {% set name = "strangepg" %}
-{% set version = "0.8.9" %}
+{% set version = "0.8.14" %}
+{% set ref = "1e666b80f464f9e898e8fce1e42f96eaf10953be" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 882db3467cec22f348b8129b5730590c47fa388dbc123c972528a0a65315b5bd
+  url: https://github.com/qwx9/{{ name }}/archive/{{ ref }}.tar.gz
+  sha256: 23b154d12ea00326e57083c4a4907f80132fdbc0c7310bfc6b5bad5b53d26a63
 
 build:
   number: 0
-  skip: True # [not linux]
+  skip: True  # [not linux]
   run_exports:
-    - {{ pin_subpackage('strangepg', max_pin=None) }}
-  ignore_run_exports:
-    - libxcb
-    - xorg-libxau
-    - xorg-libxdmcp
-    - xorg-libxext
-    - xorg-libxfixes
+    - {{ pin_subpackage('strangepg', max_pin='x.x') }}
 
 requirements:
   build:
@@ -55,10 +50,9 @@ about:
   license: MIT
   license_family: MIT
   license_file: LICENSE
+  dev-url: https://github.com/qwx9/{{ name }}
 
 extra:
-  additional-platforms:
-    - linux-aarch64
   recipe-maintainers:
     - qwx9
   container:
diff --git a/recipes/strangepg/run_test.sh b/recipes/strangepg/run_test.sh
index 0093b29f85b73..31a5f72a4ef42 100644
--- a/recipes/strangepg/run_test.sh
+++ b/recipes/strangepg/run_test.sh
@@ -3,4 +3,3 @@
 
 strangepg -h 2>/dev/null
 strangepg /dev/mordor 2>/dev/null || [[ $? == 1 ]]
-echo | strawk -f cmd/main.awk
diff --git a/recipes/stranger/meta.yaml b/recipes/stranger/meta.yaml
index cddbaa9d4f343..bd6fd9d48f89f 100644
--- a/recipes/stranger/meta.yaml
+++ b/recipes/stranger/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: f27c705b53e27098907f6ff8710ee817408baf75ea26720423bfbf1a2383f013
 
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - stranger = stranger.__main__:base_command
@@ -30,6 +30,7 @@ requirements:
     - coloredlogs
     - python >=3.6.0
     - pyyaml
+    - setuptools
 
 test:
   imports:
@@ -46,5 +47,5 @@ about:
   license: MIT
   license_family: MIT
   summary: "Annotate VCF files with str variants"
-  doc_url: "https://github.com/moonso/stranger"
-  dev_url: "https://github.com/moonso/stranger"
+  doc_url: "https://github.com/Clinical-Genomics/stranger"
+  dev_url: "https://github.com/Clinical-Genomics/stranger"
diff --git a/recipes/svision-pro/meta.yaml b/recipes/svision-pro/meta.yaml
new file mode 100644
index 0000000000000..923e70cc358ee
--- /dev/null
+++ b/recipes/svision-pro/meta.yaml
@@ -0,0 +1,53 @@
+{% set name = "SVision-pro" %}
+{% set version = "2.1" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/songbowang125/{{ name }}/archive/v{{ version }}.tar.gz
+  sha256: c642bee23cfad1796929b97c93aff50d10ba25ac1b484b2a1bef210fcb75e151
+
+build:
+  number: 0
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+  run_exports:
+    - {{ pin_subpackage('svision-pro', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.7.9
+    - pip
+    - setuptools
+  run:
+    - python >=3.7.9
+    - pytorch ==1.10.1
+    - numpy ==1.21.6
+    - pysam >=0.20.0
+    - scipy  ==1.7.3
+    - pillow ==9.2.0
+    - py-opencv >=4.5.3
+
+test:
+  commands:
+    - SVision-pro --help
+
+about:
+  home: "https://github.com/songbowang125/SVision-pro"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
+  license_file: LICENSE
+  dev_url: "https://github.com/songbowang125/SVision-pro"
+  doc_url: "https://github.com/songbowang125/SVision-pro/blob/v{{ version }}/README.md"
+  summary: 'Neural-network-based long-read SV caller.'
+  description: |
+    A neural-network-based instance segmentation framework that represents genome-to-genome-level sequencing differences visually and discovers SV comparatively between genomes without any prerequisite for inference models.
+
+extra:
+  recipe-maintainers:
+    - tdido
+  # needed for libGL.so
+  container:
+    extended-base: True
diff --git a/recipes/svtopo/build.sh b/recipes/svtopo/build.sh
new file mode 100644
index 0000000000000..21eb517ceb41e
--- /dev/null
+++ b/recipes/svtopo/build.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+mkdir -p "${PREFIX}"/bin
+
+cp svtopo "${PREFIX}"/bin/
diff --git a/recipes/svtopo/meta.yaml b/recipes/svtopo/meta.yaml
new file mode 100644
index 0000000000000..ecce2aaf487e2
--- /dev/null
+++ b/recipes/svtopo/meta.yaml
@@ -0,0 +1,39 @@
+{% set name = "svtopo" %}
+{% set version = "0.1.3" %}
+{% set shasum = "621e3e3e6b903deb2ad36846dfe8e23af6dbb9c418dea46a4490c16160bcfb26" %}
+
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/PacificBiosciences/HiFi-SVTopo/releases/download/v{{ version }}/svtopo_v{{ version }}-x86_64-unknown-linux-gnu.tar.gz
+  sha256: {{ shasum}}
+
+build:
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('svtopo', max_pin="x.x") }}
+
+requirements:
+  run:
+    - svtopovz =={{ version}}
+
+test:
+  commands:
+    - svtopo --version
+    - svtopo --help
+
+about:
+  home: https://github.com/PacificBiosciences/HiFi-SVTopo
+  license: "Pacific Biosciences Software License Agreement"
+  summary: "Complex structural variant visualization for HiFi sequencing data: extraction tool"
+
+extra:
+  recipe-maintainers:
+    - jbelyeu
+  skip-lints:
+    - should_use_compilers
+    - should_be_noarch_generic
diff --git a/recipes/svtopovz/meta.yaml b/recipes/svtopovz/meta.yaml
new file mode 100644
index 0000000000000..5b49d9802f4a5
--- /dev/null
+++ b/recipes/svtopovz/meta.yaml
@@ -0,0 +1,47 @@
+{% set name = "svtopovz" %}
+{% set version = "0.1.3" %}
+{% set shasum = "2a8878a46b60678af98581aacec9aaf8225030204043c9992c17c6e709d9449b" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/PacificBiosciences/HiFi-SVTopo/archive/v{{ version }}.tar.gz 
+  sha256: {{ shasum }}
+
+build:
+  noarch: python
+  number: 0
+  script: "{{ PYTHON }} -m pip install HiFi-SVTopoVz/ --no-deps --no-build-isolation --no-cache-dir"
+  entry_points:
+    - svtopovz = svtopovz.__main__:main
+  run_exports:
+    - {{ pin_subpackage('svtopovz', max_pin="x.x") }}
+
+requirements:
+  host:
+    - pip
+    - python >=3.10
+    - cython >=3.0.10
+    - setuptools
+  run:
+    - python >=3.10
+    - matplotlib-base >=3.8.4
+    - numpy ==1.26.4
+    - scikit-image >=0.24.0
+
+test:
+  commands:
+    - svtopovz --version
+    - svtopovz --help
+
+about:
+  home: https://github.com/PacificBiosciences/HiFi-SVTopo
+  license: "Pacific Biosciences Software License Agreement"
+  summary: "Complex structural variant visualization for HiFi sequencing data: plotting tool."
+  dev_url: https://github.com/PacificBiosciences/HiFi-SVTopo
+
+extra:
+  recipe-maintainers:
+    - jbelyeu
diff --git a/recipes/sylph/build.sh b/recipes/sylph/build.sh
index 3662f6efb60db..bdab29de4ab9e 100644
--- a/recipes/sylph/build.sh
+++ b/recipes/sylph/build.sh
@@ -1,8 +1,4 @@
 #!/bin/bash -euo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX
diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml
index 06ecabc04a199..b6e2318d12140 100644
--- a/recipes/sylph/meta.yaml
+++ b/recipes/sylph/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.6.1" %}
+{% set version = "0.7.0" %}
 
 package:
   name: sylph
@@ -11,12 +11,12 @@ build:
 
 source:
   url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz
-  sha256: 9f384ecf33d5eed57e518c1cc238ffb5ac68948dcf921731ba77ccbd02b57bdb
+  sha256: 8d0dd0c4b64de9b4c7402f6a44a019b2f54aae0626308a6b8831b3239640b609
 
 requirements:
   build:
     - {{ compiler("cxx") }}
-    - rust >=1.61
+    - {{ compiler("rust") }}
     - make
     - cmake >=3.12
 
@@ -27,10 +27,11 @@ test:
 about:
   home: https://github.com/bluenote-1577/sylph
   license: MIT
+  license_family: MIT
   summary: sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI.  
   license_file: LICENSE
+  dev_url: https://github.com/bluenote-1577/sylph
 
 extra:
   recipe-maintainers:
     - bluenote-1577
-    
diff --git a/recipes/table2asn/build.sh b/recipes/table2asn/build.sh
index 6e0c82f01b182..3e7c35737880e 100644
--- a/recipes/table2asn/build.sh
+++ b/recipes/table2asn/build.sh
@@ -3,10 +3,10 @@
 gunzip *table2asn.gz
 mkdir -p ${PREFIX}/bin
 
-if [ `uname` == Darwin ]; then
-	cp mac.table2asn ${PREFIX}/bin/table2asn
+if [[ `uname` == Darwin ]]; then
+	cp -f mac.table2asn ${PREFIX}/bin/table2asn
 	else
-	cp *.table2asn ${PREFIX}/bin/table2asn
+	cp -f *.table2asn ${PREFIX}/bin/table2asn
 fi
 
 chmod 0755 "${PREFIX}/bin/table2asn"
@@ -15,7 +15,7 @@ chmod 0755 "${PREFIX}/bin/table2asn"
 
 # patchelf to modify the RPATH of table2asn's libbz libraries; refer to:
 # https://github.com/bioconda/bioconda-recipes/pull/38770#issuecomment-1473627378
-if [ `uname` == Darwin ]; then
+if [[ `uname` == Darwin ]]; then
 	install_name_tool -change libbz2.1.dylib libbz2.1.0.dylib "${PREFIX}/bin/table2asn"
 	install_name_tool -add_rpath "${PREFIX}/lib" "${PREFIX}/bin/table2asn"
 	else
diff --git a/recipes/table2asn/meta.yaml b/recipes/table2asn/meta.yaml
index 9787dc6a10cc7..b337b71f5de5c 100644
--- a/recipes/table2asn/meta.yaml
+++ b/recipes/table2asn/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "table2asn" %}
-{% set version = "1.28.1111" %}
-{% set sha256 = "626116210fea6b1426092e370c32c7f766a6cc98857c4202712eb7b265da23cb" %}
-{% set release_date = "2024-06-18" %}
+{% set version = "1.28.1179" %}
+{% set sha256 = "7cdb95ccd7e025a54ad093f00c7d63f95ad2a4b0b433287657cb6a45e5125be7" %}
+{% set release_date = "2024-10-23" %}
 
 package:
   name: {{ name }}
@@ -9,7 +9,7 @@ package:
 
 source:
 - url: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/{{ release_date }}/by_program/{{ name }}/mac.{{ name }}.gz  # [osx]
-  sha256: 1b3ce05a1d3ef5afaa38c9b5c5a520b74d27aea9b516513ec647576e3a98bb32   # [osx]
+  sha256: ccb439c328f40ef82dae12f84a5ad4f0ccd442b7e8dbef83bcbebe81efb85781   # [osx]
 - url: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/{{ release_date }}/by_program/{{ name }}/linux64.{{ name }}.gz  # [linux]
   sha256: {{ sha256 }}  # [linux]
 
diff --git a/recipes/tantan/meta.yaml b/recipes/tantan/meta.yaml
index 4f30f88e14745..5ddf8f7da345d 100644
--- a/recipes/tantan/meta.yaml
+++ b/recipes/tantan/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "tantan" %}
-{% set version = "50" %}
+{% set version = "51" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://gitlab.com/mcfrith/tantan/-/archive/{{ version }}/tantan-{{ version }}.tar.gz
-  sha256: a239e9fb3c059ed9eb4c25a29b3c44a2ef1c1b492a9780874f429de7ae8b5407
+  sha256: f25db9441409d526becfb10df7a610c10d0e5f163d58b21535e4f045bcfc118f
 
 build:
   number: 0
@@ -27,13 +27,13 @@ test:
     - "tantan -h"
 
 about:
-  home: https://gitlab.com/mcfrith/tantan
+  home: "https://gitlab.com/mcfrith/tantan"
   license: "GPL-3.0-or-later"
   license_family: GPL3
   license_file: "COPYING.txt"
   summary: "tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences."
-  dev_url: https://gitlab.com/mcfrith/tantan
-  doc_url: https://gitlab.com/mcfrith/tantan/-/blob/main/README.rst
+  dev_url: "https://gitlab.com/mcfrith/tantan"
+  doc_url: "https://gitlab.com/mcfrith/tantan/-/blob/main/README.rst"
 
 extra:
   identifiers:
diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml
index f1f47d02d7e8c..dd38d454a0249 100644
--- a/recipes/taxonkit/meta.yaml
+++ b/recipes/taxonkit/meta.yaml
@@ -1,23 +1,23 @@
-{% set version = "0.17.0" %}
+{% set version = "0.18.0" %}
 
 package:
   name: taxonkit
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('taxonkit', max_pin='x.x') }}
 
 source:
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx]
-    md5: 5c12cfac4939f966824eda8eb774cf9b # [osx]
+    md5: 2417d0b8a08210690498b98279c16ae0 # [osx]
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_arm64.tar.gz # [arm64]
-    md5: 4077cb27d588cd0c3ed174e80d9a54af # [arm64]
+    md5: 045a509947edf27345889db901291059 # [arm64]
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux and x86_64]
-    md5: bfedc8dbfc2db63460ed31843fc5f3c3 # [linux and x86_64]
+    md5: 5df8f74847a4b5968be787d78d6fc9a7 # [linux and x86_64]
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_arm64.tar.gz # [linux and aarch64]
-    md5: d0af9a15d225005705d8af63db6a970d # [linux and aarch64]
+    md5: 451aeaede731780d167b6771ca6d1f0e # [linux and aarch64]
 
 test:
   commands:
diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml
index 0d2dcc79dbf30..ef798cef8199e 100644
--- a/recipes/tb-profiler/meta.yaml
+++ b/recipes/tb-profiler/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "tb-profiler" %}
-{% set version = "6.3.0" %}
-{% set sha256 = "45f3f104a3dd0f2fe07b315e3dc4ab1f0e35be095180363ecc65d41842972140" %}
+{% set version = "6.4.1" %}
+{% set sha256 = "1f325cfc32f3276b52e3e2b5078cce8492b495361799938e4540e1f0dc5d7938" %}
 
 package:
   name: {{name}}
@@ -12,13 +12,14 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('tb-profiler', max_pin="x") }}
 
 requirements:
   host:
     - python >=3.8
+    - setuptools
     - pip
     - gatk4
     - samtools >=1.10
@@ -28,11 +29,9 @@ requirements:
     - python >=3.8
     - git
     - jinja2
-    - pathogen-profiler =4.3.0
+    - pathogen-profiler =4.5.1
     - filelock
     - docxtpl
-    - iqtree
-    # - usher
     - joblib
     - tqdm
     - pysam
diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml
index 288843e270285..8ec2478fa2848 100644
--- a/recipes/teloclip/meta.yaml
+++ b/recipes/teloclip/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "teloclip" %}
-{% set version = "0.0.4" %}
+{% set version = "0.1.0" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 7f9919c1aa5d3d9f8e21c3a49bc3edccb7d9ef1c4ad0686761a9a9f623999ade
+  sha256: da2cc882b0e31db76de2cf485601ce26f28b2b95a3056d754c288d87fb9a83df
 
 build:
   run_exports:
@@ -17,16 +17,16 @@ build:
   entry_points:
     - teloclip=teloclip.app:main
     - teloclip-extract=teloclip.app_extract:main
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
 
 requirements:
   host:
-    - python >=3
+    - python >=3.8
     - pip
-    - setuptools
-    - setuptools-scm
+    - hatchling
+    - hatch-vcs
   run:
-    - python >=3
+    - python >=3.8
 
 test:
   imports:
@@ -36,14 +36,13 @@ test:
     - teloclip-extract --help
 
 about:
-  home: https://github.com/Adamtaranto/teloclip
-  license: MIT License
+  home: "https://github.com/Adamtaranto/teloclip"
+  license: MIT
   license_family: MIT
-  license_file: ''
-  summary: A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
-  description: ''
-  doc_url: ''
-  dev_url: ''
+  license_file: 'LICENSE'
+  summary: "A tool for the recovery of unassembled telomeres from soft-clipped read alignments."
+  doc_url: 'https://github.com/Adamtaranto/teloclip/blob/{{ version }}/README.md'
+  dev_url: 'https://github.com/Adamtaranto/teloclip'
 
 extra:
   recipe-maintainers: 
diff --git a/recipes/teloscope/build.sh b/recipes/teloscope/build.sh
new file mode 100644
index 0000000000000..f264af8576ce4
--- /dev/null
+++ b/recipes/teloscope/build.sh
@@ -0,0 +1,8 @@
+#!/bin/sh
+set -xe
+export LIBRARY_PATH="${PREFIX}/lib:$LIBRARY_PATH"
+export CXXFLAGS="-g -Wall -I$PREFIX/include -O3  -I$SRC_DIR/include -I$SRC_DIR/include/zlib -std=gnu++17 -lstdc++"
+make -j ${CPU_COUNT} CXX=$CXX
+mkdir -p $PREFIX/bin/
+cp build/bin/teloscope $PREFIX/bin/
+chmod +x $PREFIX/bin/teloscope
diff --git a/recipes/teloscope/meta.yaml b/recipes/teloscope/meta.yaml
new file mode 100644
index 0000000000000..b8d7346a1e3a0
--- /dev/null
+++ b/recipes/teloscope/meta.yaml
@@ -0,0 +1,39 @@
+{% set name = "teloscope" %}
+{% set version = "0.0.3" %}
+package:
+  name: {{ name }}
+  version: {{ version }}
+source:
+  url: https://github.com/vgl-hub/teloscope/releases/download/v{{version}}/teloscope.v{{version}}-with_submodules.zip
+  sha256: 73267c978e8175f53f2fef034f110d3c98dd15ea5b0e0b2814c65b34207bc499
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('teloscope', max_pin="x") }}
+requirements:
+  build:
+    - make
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+test:
+  commands:
+    - teloscope -h | grep "teloscope"
+about:
+  home: https://github.com/vgl-hub/teloscope
+  license_familiy: MIT
+  license: MIT
+  summary: A telomere annotation tools for genome assemblies
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - biotools:teloscope
+    - usegalaxy-eu:teloscope
+  container:
+    # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
+    extended-base: true
+  skip-lints:
+    - uses_vcs_url
+    - missing_hash
diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml
index 1451e942c5aca..1d9c74e0bf53f 100644
--- a/recipes/thapbi-pict/meta.yaml
+++ b/recipes/thapbi-pict/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "thapbi-pict" %}
-{% set version = "1.0.16" %}
+{% set version = "1.0.17" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,33 +7,34 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz
-  sha256: 85cf6d180db38166bb7ccd14af8c3813e2b3fa0d5026cac76bce8867492563f7
+  sha256: 030f27b94f5390de58f1e5b227d7fd1de50e7a6b01bb0fafd2b4320bee7c87f8
 
 build:
   noarch: python
   number: 0
   entry_points:
     - thapbi_pict = thapbi_pict.__main__:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   host:
     - pip
-    - python >=3.8
+    - python >=3.10
+    - setuptools
   run:
     # Python
     - biom-format >=2.1.14
-    - biopython >=1.82
-    - cutadapt >=4.0
-    - matplotlib-base >=3.7
-    - networkx >=2.4,!=2.8.3,!=2.8.4
-    - pydot <3
-    - python >=3.8
-    - rapidfuzz >=2.4.0
-    - sqlalchemy >=2.0
-    - xlsxwriter
+    - biopython >=1.84
+    - cutadapt >=4.9
+    - matplotlib-base >=3.9.2
+    - networkx >=3.4.2
+    - pydot >=3.0.1
+    - python >=3.10
+    - rapidfuzz >=3.10.1
+    - sqlalchemy >=2.0.36
+    - xlsxwriter >=3.2
     # Command line
     - blast
     - flash >=1.2.11
diff --git a/recipes/tiberius/build.sh b/recipes/tiberius/build.sh
index 7db29bf46afdf..ab969c31efbb0 100644
--- a/recipes/tiberius/build.sh
+++ b/recipes/tiberius/build.sh
@@ -4,4 +4,5 @@ mkdir -p ${PREFIX}/bin
 cp -R $SRC_DIR/bin/* ${PREFIX}/bin/
 chmod +x ${PREFIX}/bin/tiberius.py
 ln -s ${PREFIX}/bin/tiberius.py ${PREFIX}/bin/tiberius
-sed -i '1s|^|#!/usr/bin/env python3\n|' ${PREFIX}/bin/tiberius
\ No newline at end of file
+sed -i.bak '1s|^|#!/usr/bin/env python3\n|' ${PREFIX}/bin/tiberius
+rm -rf ${PREFIX}/bin/*.bak
diff --git a/recipes/tiberius/meta.yaml b/recipes/tiberius/meta.yaml
index 74d57de25be23..659c156ca5bcc 100644
--- a/recipes/tiberius/meta.yaml
+++ b/recipes/tiberius/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.0" %}
+{% set version = "1.1.1" %}
 {% set name = "tiberius" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/Gaius-Augustus/Tiberius/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 05fc993a72a1881bac2ec85ae412d2a186daf9d5a2bebb60237c8437b3a68da0
+  sha256: ce753ac94351f1f82b922cad6761d0109af097582a7e51359bac230aeadd5a06
 
 build:
   number: 0
@@ -17,7 +17,7 @@ build:
 
 requirements:
   host:
-    - python
+    - python >=3.7
     - pip
   run:
     - python >=3.7
@@ -38,6 +38,8 @@ test:
 about:
   home: https://github.com/Gaius-Augustus/Tiberius
   license: MIT
+  license_family: MIT
   license_file: LICENSE
   summary: |
-   Tiberius is a programme for quantifying and analysing genetic sequence data.
\ No newline at end of file
+   Tiberius is a programme for quantifying and analysing genetic sequence data.
+  dev_url: https://github.com/Gaius-Augustus/Tiberius
diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml
index fb3f66a5b43af..445569cc5722f 100644
--- a/recipes/tides-ml/meta.yaml
+++ b/recipes/tides-ml/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "tides-ml" %}
-{% set version = "1.3.4" %}
+{% set version = "1.3.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,14 +7,14 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz
-  sha256: 6b4680a6b1ba98c7bc7db8530ff85f547f57892137ca233a32cdade367435d96
+  sha256: f655bdddeb2d097c287657183b8032753623a42aa07248469145f2d6d8bf19e2
 
 build:
   entry_points:
     - tides = tides.tides:main
   noarch: python
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
diff --git a/recipes/tinscan/build.sh b/recipes/tinscan/build.sh
deleted file mode 100644
index 04547dc83fe20..0000000000000
--- a/recipes/tinscan/build.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt
\ No newline at end of file
diff --git a/recipes/tinscan/meta.yaml b/recipes/tinscan/meta.yaml
index 09101a5711553..2cccea9a9820f 100644
--- a/recipes/tinscan/meta.yaml
+++ b/recipes/tinscan/meta.yaml
@@ -1,31 +1,38 @@
+{% set name = "tinscan" %}
+{% set version = "0.2.1" %}
+
 package:
-  name: tinscan
-  version: "0.2.0"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://pypi.python.org/packages/c9/99/d6e16cb82532feb854e9e4fd403567d6c3fa462ff3a506685cfa4d545ba3/tinscan-0.2.0.tar.gz
-  md5: 3e420a6dd9ac68563324cc8dad0d2612
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/tinscan-{{ version }}.tar.gz
+  sha256: e3ca443aeff3bc0f94050e5d46c0f79db65f20e7f13ab440b5963a8a4ed06c48
 
 build:
   noarch: python
-  number: 2
+  number: 0
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   entry_points:
-    - tinscan-prep=tinscan.run_prep:main
-    - tinscan-align=tinscan.run_align:main
-    - tinscan-find=tinscan.run_scan:main
+    - tinscan-prep = tinscan.run_prep:main
+    - tinscan-align = tinscan.run_align:main
+    - tinscan-find = tinscan.run_scan:main
+  run_exports:
+    - {{ pin_subpackage('tinscan', max_pin="x.x") }}
 
 requirements:
   host:
-    - python >=3
+    - python >=3.8
     - pip
+    - hatchling
+    - hatch-vcs
   run:
-    - python >=3
+    - python >=3.8
     - biopython >=1.70
 
 test:
   imports:
     - tinscan
-
   commands:
     - tinscan-prep --help
     - tinscan-align --help
@@ -33,6 +40,8 @@ test:
 
 about:
   home: https://github.com/Adamtaranto/TE-insertion-scanner
-  license: MIT License
+  license: MIT
   summary: 'Find alignment signatures characteristic of transposon insertion sites.'
   license_family: MIT
+  dev_url: https://github.com/Adamtaranto/TE-insertion-scanner
+  doc_url: https://github.com/Adamtaranto/TE-insertion-scanner/blob/{{ version }}/README.md
diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml
index 4a471678ab4af..21ba1c785ed09 100644
--- a/recipes/tirmite/meta.yaml
+++ b/recipes/tirmite/meta.yaml
@@ -1,8 +1,8 @@
 {% set name = "tirmite" %}
-{% set version = "1.1.4" %}
+{% set version = "1.1.6" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "82657d6f84f51731cb5f92c33d9e672a61009ecc79a61ba21f6f3fc637b2a25b" %}
+{% set hash_value = "9267c94ec12db1c385a5fd6aca8b85d88005ee69ebf42b5e8dd92418454ae26e" %}
 
 package:
   name: '{{ name|lower }}'
@@ -17,17 +17,21 @@ build:
   number: 0
   entry_points:
     - tirmite=tirmite.cmd_tirmite:main
-    - tsplit-LTR=tirmite.cmd_LTR:main
     - tsplit-TIR=tirmite.cmd_TIR:main
-  script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_subpackage('tirmite', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3
+    - python >=3.8
     - pip
+    - setuptools
+    - hatchling
+    - hatch-vcs
   run:
-    - python >=3
-    - pandas >=0.20.3
+    - python >=3.8
+    - pandas >=0.23.4
     - biopython >=1.70
     - pymummer >=0.10.3
 
@@ -36,14 +40,13 @@ test:
     - tirmite
   commands:
     - tirmite --help
-    - tsplit-LTR --help
     - tsplit-TIR --help
 
 about:
   home: https://github.com/Adamtaranto/TIRmite
-  license: MIT License
+  license: MIT
   license_family: MIT
-  summary: Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
+  summary: "Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons."
   description: "Build profile Hidden Markov Models for Terminal Inverted repeat families (TIR-pHMMs) and map to genomic sequences for annotation of MITES and complete DNA-Transposons with variable internal sequence composition."
 
 extra:
diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml
index ae769341e2447..c988db6a743e4 100644
--- a/recipes/tissuumaps/meta.yaml
+++ b/recipes/tissuumaps/meta.yaml
@@ -4,7 +4,7 @@
 # - add pyqt6 (or possibly pyqt>=6) dependency
 # Until then, only the "tissuumaps_server" script is available, not "tissuumaps"
 
-{% set version = "3.2.1.10" %}
+{% set version = "3.2.1.11" %}
 
 package:
   name: tissuumaps
@@ -12,7 +12,7 @@ package:
 
 source:
   url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 126537079ea9fef743b0d2575d4e6cafac1351c465de7bbf0b0ec2b080748e34
+  sha256: 3a2e81c2e37415a6ed7e32b95b7923cef55450b5b3f2cd77fa9f2d7b12542bda
 
 build:
   number: 0
diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml
index 9c1e48fd450d3..3a54f7c34eada 100644
--- a/recipes/treeswift/meta.yaml
+++ b/recipes/treeswift/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.1.44" %}
+{% set version = "1.1.45" %}
 
 package:
   name: "treeswift"
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz
-  sha256: c023c8130e29f124cdd3d98d3b29e168a4f150df29dc6a243524e2875d22b799
+  sha256: 3bd1db3a45dbd443051a4f9ecafc99a8e38b23b47a28333878c1eef6e8f67e7e
 
 build:
   noarch: python
diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml
index bb87d98169589..4c3e0712059bf 100644
--- a/recipes/trgt/meta.yaml
+++ b/recipes/trgt/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "trgt" %}
-{% set version = "1.2.0" %}
-{% set trgt_sha256 = "5dec0943d3400fd1677236fa35737e5a442a486fac55188029c3c9164edb3d23" %}
+{% set version = "1.3.0" %}
+{% set trgt_sha256 = "25d1e7a67c13cde0ab196ef8061a048f58c5c8b70c4ab9acd31613a6dab8ef1d" %}
 
 package:
   name: {{ name }}
diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml
index cf9d3fb5e9a6f..8f4af88b5cc12 100644
--- a/recipes/trtools/meta.yaml
+++ b/recipes/trtools/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "trtools" %}
-{% set version = "6.0.2" %}
+{% set version = "6.1.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 7bdb476951a4ec748df20058a31da3d1def14554cd9a67f85d3c61bf63f8f303
+  sha256: 3a177cf19060945eff4044f16d5ebdc66364e72a8a3c9bd725086ba10003df96
 
 build:
   noarch: python
@@ -20,6 +20,7 @@ build:
     - associaTR=trtools.associaTR:run
     - prancSTR = trtools.prancSTR:run
     - simTR = trtools.simTR:run
+    - annotaTR = trtools.annotaTR:run
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   number: 0
   run_exports:
@@ -32,7 +33,7 @@ requirements:
     - pip >=20.3
   run:
     - python >=3.7.1,<4.0
-    - cyvcf2 >=0.30.4
+    - cyvcf2 >=0.30.27
     - matplotlib-base >=3.1.2
     - numpy >=1.17.3
     - pandas >=1.2.0
@@ -42,6 +43,7 @@ requirements:
     - statsmodels >=0.10.2
     - pyfaidx >=0.5.6
     - ART >=2016.06.05
+    - pgenlib >=0.90.1
 
 test:
   imports:
@@ -54,6 +56,7 @@ test:
     - trtools.statSTR
     - trtools.prancSTR
     - trtools.simTR
+    - trtools.annotaTR
     - trtools.utils
   requires:
     - bcftools
@@ -69,6 +72,7 @@ test:
     - qcSTR --help
     - prancSTR --help
     - simTR --help
+    - annotaTR --help
 
 about:
   home: https://github.com/gymreklab/TRTools
@@ -86,3 +90,6 @@ extra:
   identifiers:
     - biotools:trtools
     - doi:10.1093/bioinformatics/btaa736
+  additional-platforms:
+    - osx-arm64
+    - linux-aarch64
diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
new file mode 100755
index 0000000000000..b5970e094f4eb
--- /dev/null
+++ b/recipes/tttrlib/build.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+mkdir b2 && cd b2
+
+if [[ "${target_platform}" == osx-* ]]; then
+  # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
+  export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+  export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+  export CONFIG_ARGS=""
+fi
+
+cmake -S .. -B . \
+  -DCMAKE_CXX_COMPILER="${CXX}" \
+  -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+  -DBUILD_PYTHON_INTERFACE=ON \
+  -DCMAKE_BUILD_TYPE=Release \
+  -DBUILD_LIBRARY=ON \
+  -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
+  -DPython_ROOT_DIR="${PREFIX}/bin" \
+  -DBUILD_PYTHON_DOCS=ON \
+  -DBoost_USE_STATIC_LIBS=OFF \
+  -DWITH_AVX=OFF \
+  -G Ninja \
+  "${CONFIG_ARGS}"
+
+# On some platforms (notably aarch64 with Drone) builds can fail due to
+# running out of memory. If this happens, try the build again; if it
+# still fails, restrict to one core.
+ninja install -k 0 || ninja install -k 0 || ninja install -j ${CPU_COUNT}
+
+# Copy programs to bin
+chmod 0755 $SRC_DIR/bin/*
+cp -f $SRC_DIR/bin/* $PREFIX/bin
diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
new file mode 100644
index 0000000000000..daf00affe224d
--- /dev/null
+++ b/recipes/tttrlib/meta.yaml
@@ -0,0 +1,72 @@
+{% set name = "tttrlib" %}
+{% set version = "0.25.1" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: a224214e50d7a202ef1d264c64641ab0b26f29bf756a96659489847953b698a6
+
+build:
+  number: 0
+  run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}'
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - pkg-config
+    - cmake
+    - ninja
+    - make
+  host:
+    - swig <4.3.0
+    - doxygen
+    - llvm-openmp   # [osx]
+    - libgomp   # [linux]
+    - boost-cpp
+    - hdf5
+    - python
+    - pip
+    - numpy
+  run:
+    - python
+    - llvm-openmp   # [osx]
+    - libgomp   # [linux]
+    - boost-cpp
+    - tqdm
+    - click
+    - click-didyoumean
+    - numpy
+    - scikit-image
+    - matplotlib-base
+    - hdf5
+
+test:
+  imports:
+    - tttrlib
+  commands:
+    - tttrlib --help
+
+about:
+  home: https://github.com/fluorescence-tools/tttrlib
+  summary: 'A file format agnostic library for time-resolved imaging and spectroscopic data.'
+  description: |
+    tttrlib is a simple, fast, libray to read, write and process
+    time-resolved imaging and spectroscopic data. For speed, it 
+    is written in C++ and wrapped for Python via SWIG.
+  license: BSD-3-Clause
+  license_family: BSD
+  license_file: LICENSE.txt
+  doc_url: https://tttrlib.readthedocs.io
+  dev_url: https://github.com/fluorescence-tools/tttrlib
+
+extra:
+  recipe-maintainers:
+    - tpeulen
+    - khemmen
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/ucsc-bedgraphtobigwig/build.sh b/recipes/ucsc-bedgraphtobigwig/build.sh
index 5d7368f71bdd2..8632d226c6629 100644
--- a/recipes/ucsc-bedgraphtobigwig/build.sh
+++ b/recipes/ucsc-bedgraphtobigwig/build.sh
@@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
 (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
@@ -17,5 +17,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/bedGraphToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/bedGraphToBigWig "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/bedGraphToBigWig"
+chmod 0755 bin/bedGraphToBigWig
+mv bin/bedGraphToBigWig "${PREFIX}/bin"
diff --git a/recipes/ucsc-bedgraphtobigwig/include.macos.patch b/recipes/ucsc-bedgraphtobigwig/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-bedgraphtobigwig/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml
index ea2f56db02e67..fa8e2af63aaa1 100644
--- a/recipes/ucsc-bedgraphtobigwig/meta.yaml
+++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-bedgraphtobigwig" %}
 {% set program = "bedGraphToBigWig" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,11 +11,11 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 
@@ -28,14 +28,13 @@ requirements:
     - libuuid
     - mysql-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,11 +42,11 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "Varies; see http://genome.ucsc.edu/license"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see https://genome.ucsc.edu/license"
   summary: "Convert a bedGraph file to bigWig format."
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
diff --git a/recipes/ucsc-bedgraphtobigwig/patch1.patch b/recipes/ucsc-bedgraphtobigwig/patch1.patch
deleted file mode 100644
index 483b0342a43da..0000000000000
--- a/recipes/ucsc-bedgraphtobigwig/patch1.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- userApps/kent/src/lib/htmshell.c.old	2022-10-28 08:32:08.344445121 +0000
-+++ userApps/kent/src/lib/htmshell.c	2022-10-28 08:32:31.708262420 +0000
-@@ -711,11 +711,11 @@
- puts("Status: 400\r");
- puts("Content-Type: text/plain; charset=UTF-8\r");
- puts("\r");
--if (format != NULL && args != NULL)
--    {
--    vfprintf(stdout, format, args);
--    fprintf(stdout, "\n");
--    }
-+if (format != NULL)
-+    {
-+    vfprintf(stdout, format, args);
-+    fprintf(stdout, "\n");
-+    }
- exit(-1);
- }
- 
diff --git a/recipes/ucsc-blat/build.sh b/recipes/ucsc-blat/build.sh
index abeab8ea7afd6..5b6ca8d4ff08d 100644
--- a/recipes/ucsc-blat/build.sh
+++ b/recipes/ucsc-blat/build.sh
@@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
 (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
@@ -17,5 +17,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/blat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/blat "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/blat"
+chmod 0755 bin/blat
+mv bin/blat "${PREFIX}/bin"
diff --git a/recipes/ucsc-blat/include.macos.patch b/recipes/ucsc-blat/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-blat/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-blat/meta.yaml b/recipes/ucsc-blat/meta.yaml
index 3a050f884b74b..ae226831c18f2 100644
--- a/recipes/ucsc-blat/meta.yaml
+++ b/recipes/ucsc-blat/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-blat" %}
 {% set program = "blat" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,10 +11,10 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
   number: 0
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
@@ -28,14 +28,13 @@ requirements:
     - libuuid
     - mysql-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,11 +42,11 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "Varies; see http://genome.ucsc.edu/license"
-  summary: "Standalone BLAT v. 36x2 fast sequence search command line tool"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see https://genome.ucsc.edu/license"
+  summary: "Standalone BLAT v. 39x1 fast sequence search command line tool."
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
diff --git a/recipes/ucsc-fatotwobit/build.sh b/recipes/ucsc-fatotwobit/build.sh
index 47d1b7225bb5c..370675dc11e50 100644
--- a/recipes/ucsc-fatotwobit/build.sh
+++ b/recipes/ucsc-fatotwobit/build.sh
@@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 
 mkdir -p "${BINDIR}"
@@ -24,5 +24,5 @@ fi
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/faToTwoBit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/faToTwoBit "${PREFIX}/bin"
+cp -f bin/faToTwoBit "${PREFIX}/bin"
 chmod 0755 "${PREFIX}/bin/faToTwoBit"
diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml
index 0a74ff24cf3fc..c129b57df25c7 100644
--- a/recipes/ucsc-fatotwobit/meta.yaml
+++ b/recipes/ucsc-fatotwobit/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-fatotwobit" %}
 {% set program = "faToTwoBit" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -15,7 +15,7 @@ source:
     - include.macos.patch  # [osx]
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 
@@ -47,9 +47,9 @@ test:
 about:
   home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
   license: "Varies; see http://genome.ucsc.edu/license"
-  summary: "Convert DNA from fasta to 2bit format"
+  summary: "Convert DNA from fasta to 2bit format."
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
diff --git a/recipes/ucsc-pslcdnafilter/build.sh b/recipes/ucsc-pslcdnafilter/build.sh
index 6f9c17e7cba0b..0d01ae296724e 100644
--- a/recipes/ucsc-pslcdnafilter/build.sh
+++ b/recipes/ucsc-pslcdnafilter/build.sh
@@ -8,7 +8,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export BINDIR=$(pwd)/bin
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
@@ -18,5 +18,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/pslCDnaFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/pslCDnaFilter "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/pslCDnaFilter"
+chmod 0755 bin/pslCDnaFilter
+mv bin/pslCDnaFilter "${PREFIX}/bin"
diff --git a/recipes/ucsc-pslcdnafilter/include.macos.patch b/recipes/ucsc-pslcdnafilter/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-pslcdnafilter/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml
index 58d533a67e4ff..bb1f6757f31f7 100644
--- a/recipes/ucsc-pslcdnafilter/meta.yaml
+++ b/recipes/ucsc-pslcdnafilter/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-pslcdnafilter" %}
 {% set program = "pslCDnaFilter" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,11 +11,12 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
   number: 0
+  skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 
@@ -28,14 +29,13 @@ requirements:
     - libuuid
     - mysql-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,8 +43,8 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "Varies; see http://genome.ucsc.edu/license"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see https://genome.ucsc.edu/license"
   summary: "
 Filter cDNA alignments in psl format.  Filtering criteria are
 comparative, selecting near best in genome alignments for each given
@@ -52,10 +52,9 @@ cDNA and non-comparative, based only on the quality of an individual
 alignment.
 "
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
     - biotools:UCSC_Genome_Browser_Utilities
     - doi:10.1093/bib/bbs038
-  
\ No newline at end of file
diff --git a/recipes/ucsc-twobitinfo/build.sh b/recipes/ucsc-twobitinfo/build.sh
index 510984dbad870..2fde6d85012b6 100644
--- a/recipes/ucsc-twobitinfo/build.sh
+++ b/recipes/ucsc-twobitinfo/build.sh
@@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
 (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
@@ -17,5 +17,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/twoBitInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/twoBitInfo "${PREFIX}/bin"
+cp -f bin/twoBitInfo "${PREFIX}/bin"
 chmod 0755 "${PREFIX}/bin/twoBitInfo"
diff --git a/recipes/ucsc-twobitinfo/include.macos.patch b/recipes/ucsc-twobitinfo/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-twobitinfo/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml
index f02d59ed3bbbe..efd408cb42f7b 100644
--- a/recipes/ucsc-twobitinfo/meta.yaml
+++ b/recipes/ucsc-twobitinfo/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-twobitinfo" %}
 {% set program = "twoBitInfo" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,10 +11,10 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
   number: 0
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
@@ -24,18 +24,17 @@ requirements:
     - make
     - {{ compiler('c') }}
   host:
+    - clangdev # [osx]
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,11 +42,11 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
   license: "Varies; see http://genome.ucsc.edu/license"
-  summary: "get information about sequences in a .2bit file"
+  summary: "Get information about sequences in a .2bit file."
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
diff --git a/recipes/ucsc-twobittofa/build.sh b/recipes/ucsc-twobittofa/build.sh
index 1db3e3360894c..4f4e6626c5163 100644
--- a/recipes/ucsc-twobittofa/build.sh
+++ b/recipes/ucsc-twobittofa/build.sh
@@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
 (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
@@ -17,5 +17,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/twoBitToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/twoBitToFa "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/twoBitToFa"
+chmod 0755 bin/twoBitToFa
+mv bin/twoBitToFa "${PREFIX}/bin"
diff --git a/recipes/ucsc-twobittofa/htmshell.patch b/recipes/ucsc-twobittofa/htmshell.patch
deleted file mode 100644
index 1e6f87375ed01..0000000000000
--- a/recipes/ucsc-twobittofa/htmshell.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- kent/src/lib/htmshell.c	2024-03-27 10:56:44.493892141 +0200
-+++ kent/src/lib/htmshell.c	2024-03-27 10:57:01.073792396 +0200
-@@ -713,7 +713,7 @@
- puts("Status: 400\r");
- puts("Content-Type: text/plain; charset=UTF-8\r");
- puts("\r");
--if (format != NULL && args != NULL)
-+if (format != NULL)
-     {
-     vfprintf(stdout, format, args);
-     fprintf(stdout, "\n");
diff --git a/recipes/ucsc-twobittofa/include.macos.patch b/recipes/ucsc-twobittofa/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-twobittofa/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml
index 6c74d0cff77f5..b7543b173d7f9 100644
--- a/recipes/ucsc-twobittofa/meta.yaml
+++ b/recipes/ucsc-twobittofa/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-twobittofa" %}
 {% set program = "twoBitToFa" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,10 +11,10 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
   number: 0
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
@@ -28,14 +28,13 @@ requirements:
     - libuuid
     - mysql-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,11 +42,11 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
   license: "Varies; see http://genome.ucsc.edu/license"
-  summary: "Convert all or part of .2bit file to fasta"
+  summary: "Convert all or part of .2bit file to fasta."
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/v{{ version }}_base/README"
 
 extra:
   identifiers:
diff --git a/recipes/ucsc-wigtobigwig/build.sh b/recipes/ucsc-wigtobigwig/build.sh
index 113f9a2031ecb..2d32f36cdfac3 100644
--- a/recipes/ucsc-wigtobigwig/build.sh
+++ b/recipes/ucsc-wigtobigwig/build.sh
@@ -9,7 +9,7 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
 (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
@@ -17,5 +17,5 @@ mkdir -p "${BINDIR}"
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/wigToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/wigToBigWig "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/wigToBigWig"
+chmod 0755 bin/wigToBigWig
+mv bin/wigToBigWig "${PREFIX}/bin"
diff --git a/recipes/ucsc-wigtobigwig/htmshell.patch b/recipes/ucsc-wigtobigwig/htmshell.patch
deleted file mode 100644
index 1e6f87375ed01..0000000000000
--- a/recipes/ucsc-wigtobigwig/htmshell.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- kent/src/lib/htmshell.c	2024-03-27 10:56:44.493892141 +0200
-+++ kent/src/lib/htmshell.c	2024-03-27 10:57:01.073792396 +0200
-@@ -713,7 +713,7 @@
- puts("Status: 400\r");
- puts("Content-Type: text/plain; charset=UTF-8\r");
- puts("\r");
--if (format != NULL && args != NULL)
-+if (format != NULL)
-     {
-     vfprintf(stdout, format, args);
-     fprintf(stdout, "\n");
diff --git a/recipes/ucsc-wigtobigwig/include.macos.patch b/recipes/ucsc-wigtobigwig/include.macos.patch
new file mode 100644
index 0000000000000..979f87005a72e
--- /dev/null
+++ b/recipes/ucsc-wigtobigwig/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml
index ac2226d78ed5d..c9deee8b43399 100644
--- a/recipes/ucsc-wigtobigwig/meta.yaml
+++ b/recipes/ucsc-wigtobigwig/meta.yaml
@@ -1,7 +1,7 @@
 {% set package = "ucsc-wigtobigwig" %}
 {% set program = "wigToBigWig" %}
-{% set version = "469" %}
-{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %}
+{% set version = "472" %}
+{% set sha256 = "26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2" %}
 
 package:
   name: "{{ package }}"
@@ -11,11 +11,11 @@ source:
   url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz"
   sha256: "{{ sha256 }}"
   patches:
-    - "include.patch"
+    - include.patch  # [linux]
+    - include.macos.patch  # [osx]
 
 build:
-  skip: True  # [osx]
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 
@@ -28,14 +28,13 @@ requirements:
     - libuuid
     - mysql-connector-c
     - libopenssl-static
+    - clangdev  # [osx]
     - zlib
-
   run:
     - libpng
     - libuuid
     - mysql-connector-c
     - libopenssl-static
-    - zlib
 
 test:
   commands:
@@ -43,11 +42,11 @@ test:
     - test -x ${PREFIX}/bin/{{ program }}
 
 about:
-  home: "https://hgdownload.cse.ucsc.edu/admin/exe/"
-  license: "Varies; see http://genome.ucsc.edu/license"
-  summary: "Convert ascii format wig file (in fixedStep, variableStep"
+  home: "https://hgdownload.cse.ucsc.edu/admin/exe"
+  license: "Varies; see https://genome.ucsc.edu/license"
+  summary: "Convert ascii format wig file (in fixedStep, variableStep)."
   dev_url: "https://github.com/ucscGenomeBrowser/kent"
-  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README"
+  doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README"
 
 extra:
   identifiers:
diff --git a/recipes/unikseq/meta.yaml b/recipes/unikseq/meta.yaml
index 6eee8a084f202..097d8f6d62ea2 100644
--- a/recipes/unikseq/meta.yaml
+++ b/recipes/unikseq/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.3.5" %}
+{% set version = "2.0.0" %}
 
 package:
   name: unikseq
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/bcgsc/unikseq/releases/download/v{{ version }}/unikseq-{{ version }}.tar.gz
-  sha256: 9b497384ce023a06fd79353c2488455f1517f10e575c86f1f5df1e21463d09e8
+  sha256: 5682d54e15ca41662f958c402c13328f9f19a6dd6a13043e4198679b10a6acb0
   patches:
     - unikseq-bloom.patch
     - unikseq-write-bloom.patch
diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml
index 6baa90f445ec8..4f0542b85b1b0 100644
--- a/recipes/varfish-cli/meta.yaml
+++ b/recipes/varfish-cli/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.6.3" %}
-{% set sha256 = "7a7344b3d88b8ac303f0a54f7709fa528fe1555dd6e935c45e6ec452d955871d" %}
+{% set version = "0.6.4" %}
+{% set sha256 = "229fbfb2798f5703fc2023b24034e05a6af7356681de0c0fa902f68fe80f1490" %}
 
 package:
   name: varfish-cli
@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: python
-  number: 2
+  number: 0
   script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv
   entry_points:
     - varfish-cli = varfish_cli.__main__:main
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3
     - pip
+    - setuptools
   run:
     - python >=3.9
     - attrs
diff --git a/recipes/vclust/meta.yaml b/recipes/vclust/meta.yaml
index 71cf91dc7c40d..4d36cd6f02789 100644
--- a/recipes/vclust/meta.yaml
+++ b/recipes/vclust/meta.yaml
@@ -1,14 +1,19 @@
-{% set version = "1.2.7" %}
+{% set version = "1.2.8" %}
 
-{% set system = "x64_linux" %}       # [linux and x86_64]
-{% set system = "x64_mac" %}         # [osx and x86_64]
-{% set system = "arm64_linux" %}     # [linux and aarch64]
-{% set system = "arm64_mac" %}       # [osx and arm64]
+{% set system = "manylinux2014_x86_64" %}      # [linux and x86_64]
+{% set system = "manylinux2014_aarch64" %}     # [linux and aarch64]
+{% set system = "macosx_10_9_x86_64" %}        # [osx and x86_64]
+{% set system = "macosx_11_0_arm64" %}         # [osx and arm64]
 
-{% set sha256 = "5f750bd1bfc8448d127ea8a566860bc10c58c768a79d3d9a814243d64c1f16cf" %}  # [linux and x86_64]
-{% set sha256 = "077a44e14e429a526868ca16364c62b800eeade9aa7df184fdda8f93e053c356" %}  # [osx and x86_64]
-{% set sha256 = "9b2b410607d26ec05b1bdc42329b73285e4a862c93f67aff6c157b10b02e3383" %}  # [linux and aarch64]
-{% set sha256 = "b917c5af92e806b4244a62a32063c81bc9de3eae3760498444398fe7c5a7f623" %}  # [osx and arm64]
+{% set site = "https://files.pythonhosted.org/packages/70/b3/a7dc474d515f511564ba31f4cae44a23f7badc687151a254d54d2ad1936b" %}     # [linux and x86_64]
+{% set site = "https://files.pythonhosted.org/packages/5c/f4/09e3be13268d857ea9cb227e5324cbb23bd7cdb47efa48fb9cf591619727" %}     # [linux and aarch64]
+{% set site = "https://files.pythonhosted.org/packages/52/26/a349c6911bee8b14ec3a1919ab416c759768ec81a41566f2fc42399303f5" %}     # [osx and x86_64]
+{% set site = "https://files.pythonhosted.org/packages/0e/a8/d35b83baff04e299b3600b91b3f4f5df9aa08210381198ee5ab814e6881c" %}     # [osx and arm64]
+
+{% set sha256 = "fcc62e88de1d87bca792ed08845f0876ac4647ac80d6bbdc66585600684a9659" %}  # [linux and x86_64]
+{% set sha256 = "f77df5fae8771d15cb99f8862b780237a2df3903243ba2cf4fa7dbece995f349" %}  # [linux and aarch64]
+{% set sha256 = "a5f381652b92c83dd22b111faa42e37f0ae564e579d586e2e1164cd2e968fbf3" %}  # [osx and x86_64]
+{% set sha256 = "8c70fd4b684c233743c98b5dc1004ad0a4c1c9ad793278a2337a26962dfe1ad6" %}  # [osx and arm64]
 
 
 package:
@@ -20,17 +25,16 @@ build:
   run_exports:
     - {{ pin_subpackage('vclust', max_pin='x') }}
   script: |
-    mkdir -p ${PREFIX}/bin
-    cp -r vclust.py bin ${PREFIX}/bin/
-    chmod +x ${PREFIX}/bin/vclust.py
+    {{ PYTHON }} -m pip install vclust-{{ version }}-py3-none-{{ system }}.whl
 
 source:
-  url: https://github.com/refresh-bio/vclust/releases/download/v{{ version }}/vclust-v{{ version }}-{{ system }}.tar.gz
+  url: {{ site }}/vclust-{{ version }}-py3-none-{{ system }}.whl
   sha256: {{ sha256 }}
 
 requirements:
   host:
     - python >=3.7
+    - pip
   run:
     - python >=3.7
 
@@ -42,8 +46,8 @@ about:
 
 test:
   commands:
-    - vclust.py --help
-    - vclust.py info
+    - vclust --help
+    - vclust info
 
 extra:
   additional-platforms:
diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml
index 9ec0557e1bc67..a9174ae4e5e91 100644
--- a/recipes/vg/meta.yaml
+++ b/recipes/vg/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "vg" %}
-{% set version = "1.59.0" %}
+{% set version = "1.61.0" %}
 
 package:
   name: {{ name }}
@@ -7,9 +7,9 @@ package:
 
 source:
   - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg       # [linux and x86_64]
-    sha256: a2270237c8541867ac345ad924c1641881bc9fd60be157a6d3d29fa910aacfc2    # [linux and x86_64]
+    sha256: dfdc9f14c70aa68f05dcfdb8a9938f235f89353ce0f88076fc29a4ad92c3c7cf    # [linux and x86_64]
   - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg-arm64 # [linux and aarch64]
-    sha256: e0df4e81e0c7b3ac1c7f3fc7a7bc8421416256bf2bc4a1ca2b87feebaf40d4d0    # [linux and aarch64]
+    sha256: 835bdb1354e45dc1ad7e991adda92a327da2e24a09f6e2a53cad3a926510a2ac    # [linux and aarch64]
 
 build:
   number: 0
diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml
index 6b485917f485d..ee07000da75ec 100644
--- a/recipes/virheat/meta.yaml
+++ b/recipes/virheat/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "virheat" %}
-{% set version = "0.7.1" %}
+{% set version = "0.7.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,13 +7,13 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz
-  sha256: 142b62f05dfe91b9d04a8fe3e7b27d0d20e502dbfa3163d839666262143f67d6
+  sha256: 35ce98dd10af4d2519195c6351321b6f5f26d699ad662c0c5e75f7cec00c3dd1
 
 build:
   entry_points:
     - virheat = virheat.command:main
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps -vvv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
   run_exports:
     - {{ pin_subpackage('virheat', max_pin="x.x") }}
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.9
     - pip
+    - setuptools
   run:
     - python >=3.9
     - matplotlib-base >=3.5.1,<=3.8.0
@@ -32,10 +33,7 @@ test:
   imports:
     - virheat
   commands:
-    - pip check
     - virheat --help
-  requires:
-    - pip
 
 about:
   home: https://github.com/jonas-fuchs/virHEAT
diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml
index f3b2d947ad235..eda5656e50341 100644
--- a/recipes/vsearch/meta.yaml
+++ b/recipes/vsearch/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "2.29.0" %}
-{% set sha256 = "2c5bd0d9b3c2ec8eecd1af06ae11611138d87fdfecfa423ae791d52dccd27e63" %}
+{% set version = "2.29.1" %}
+{% set sha256 = "a36f175c4eddf1c7ce7030561de52c20d36ddc5ed1f498ee4853c6808f7375bb" %}
 
 package:
   name: vsearch
diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml
index c38a49f2cc743..2fc7c8f32250f 100644
--- a/recipes/yacht/meta.yaml
+++ b/recipes/yacht/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.2.3" %}
+{% set version = "1.3.0" %}
 
 package:
   name: yacht
@@ -6,19 +6,22 @@ package:
 
 source:
   url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version  }}/yacht-{{ version  }}.tar.gz
-  sha256: 93adb23ad4f143d48c9f0ea661fe2283ff42e9c51e073a05460596ecabc65214
+  sha256: 68d272daeb70ed7390aa2d468934dc4bf0aa9a021f99fe99847b8a664e8ac8cf
 
 build:
   number: 0
-  noarch: python
-  skip: True  # [win or osx]
-  script: "{{ PYTHON  }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
+  skip: True  # [osx]
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
-    - {{ pin_subpackage('yacht', max_pin="x") }}
+    - {{ pin_subpackage('yacht') }}
 
 requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make                        # Ensures that Make is available (for Unix)
+
   host:
-    - python >3.6
+    - python >3.6,<3.12
     - pip
     - pandas
     - pytaxonkit
@@ -27,16 +30,16 @@ requirements:
     - loguru
     - tqdm
     - biom-format
-    - numpy
+    - numpy >=1.22.4
     - setuptools
     - requests
+
   run:
-    - python >3.6
+    - python >3.6,<3.12
     - sourmash >=4.8.3,<5
-    - rust
     - scipy
     - requests
-    - numpy
+    - numpy >=1.22.4
     - pandas
     - scikit-learn
     - codecov
@@ -51,7 +54,6 @@ requirements:
     - ruff
     - sourmash_plugin_branchwater
 
-
 test:
   commands:
     - yacht --help
@@ -67,19 +69,20 @@ about:
 
 extra:
   skip-lints:
-    - should_not_be_noarch_skip
     - should_use_compilers
+    - should_be_noarch_generic
   identifiers:
-    - doi:10.1101/2023.04.18.537298
+    - doi:10.1093/bioinformatics/btae047
   recipe-maintainers:
+    - chunyuma
     - dkoslicki
   authors:
     - dkoslicki
     - chunyuma
+    - mahmudhera
     - sew347
     - mlupei
     - mfl15
     - ShaopengLiu1
     - raquellewei
     - mohsenht
-  
diff --git a/recipes/zamp/meta.yaml b/recipes/zamp/meta.yaml
index 15dc951847f5f..bb8a79067fb0d 100644
--- a/recipes/zamp/meta.yaml
+++ b/recipes/zamp/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 366d1a1bdff60e1a8100298608f20ab2294ef476a1da1bee9c1975641c495f6e
 
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - zamp=zamp.__main__:main
@@ -25,7 +25,7 @@ requirements:
     - setuptools
   run:
     - python >=3.11
-    - snakemake-minimal >=8.0.0
+    - snakemake-minimal >=8.0.0,<=8.24.1
     - Click >=8.1.3
     - attrmap >=0.0.7
     - snaketool-utils >=0.0.5
diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml
index cdfd987fa4d37..11a5536b94524 100644
--- a/recipes/zdb/meta.yaml
+++ b/recipes/zdb/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.3.3" %}
+{% set version = "1.3.4" %}
 
 package:
   name: zdb
@@ -11,8 +11,8 @@ build:
     - {{ pin_subpackage('zdb', max_pin="x.x") }}
 
 source:
-  url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.3.tar.gz
-  sha256: 9f5e29d3730740c2e60fb275db709916ef54d3a2c3e4cf54ae448e9add14bb49
+  url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.4.tar.gz
+  sha256: 6b9bb6433c05a1343794cc17e274dd58d202cc3a14a7f87b159fd381a8890e61
 
 requirements:
   run:
diff --git a/recipes/zol/build.sh b/recipes/zol/build.sh
index 048162828ed7d..4c06ecd4976bd 100644
--- a/recipes/zol/build.sh
+++ b/recipes/zol/build.sh
@@ -1,23 +1,15 @@
 #!/bin/bash
 
+set -xe
+
 $PYTHON -m pip install . --ignore-installed --no-deps -vv
 
 mkdir -p ${PREFIX}/bin
 
-# (re)-compile RBH/InParanoid-esque programs written in C++
-${CXX} -std=c++11 -o zol/orthologs/runRBH zol/orthologs/runRBH.cpp
-${CXX} -std=c++11 -o zol/orthologs/splitDiamondResults zol/orthologs/splitDiamondResults.cpp
-${CXX} -std=c++11 -o zol/splitDiamondResultsForFai zol/splitDiamondResultsForFai.cpp
-
-cp zol/orthologs/runRBH ${PREFIX}/bin/
-cp zol/orthologs/splitDiamondResults ${PREFIX}/bin/
-cp zol/splitDiamondResultsForFai ${PREFIX}/bin/
-cp zol/clusterHeatmap.R ${PREFIX}/bin/
-cp zol/plotTinyAAI.R ${PREFIX}/bin/
-cp zol/plotSegments.R ${PREFIX}/bin/
-cp zol/njTree.R ${PREFIX}/bin/
-cp zol/phyloHeatmap.R ${PREFIX}/bin/
-cp zol/salt_gc_vs_ribo_aai.R ${PREFIX}/bin/
+export LDFLAGS=
+${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/runRBH src/zol/orthologs/runRBH.cpp
+${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResults src/zol/orthologs/splitDiamondResults.cpp
+${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResultsForFai src/zol/splitDiamondResultsForFai.cpp
 
 chmod +x ${PREFIX}/bin/runRBH
 chmod +x ${PREFIX}/bin/splitDiamondResults
diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml
index ac3066121d731..d9994831effb8 100644
--- a/recipes/zol/meta.yaml
+++ b/recipes/zol/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "zol" %}
-{% set version = "1.4.12" %}
+{% set version = "1.5.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: cb02a98c7257a9d7ef089bc585637aa9ee5671c6b3a65dbaed6c0dd2331b651b
+  sha256: fa8f23071c519daf9cfc2c3ca96121d8119dbc55c2359c3901f8ed2081583ddb
 
 build:
   number: 0
@@ -26,7 +26,8 @@ requirements:
     - python >=3.10
     - r-base 
     - biopython 
-    - muscle >=5.0
+    - muscle >=5.0,<=5.1 [osx]
+    - muscle >=5.0 [not osx]
     - mcl
     - pal2nal >=14.1
     - hmmer >=3.0.0
@@ -52,10 +53,15 @@ requirements:
     - slclust
     - trimal
     - gzip
-    - miniprot =0.7
+    - miniprot =0.13 # [x86_64]
+    - miniprot >=0.13 # [aarch64]
     - bioconductor-ggtree
     - ete3
     - codoff
+    - gravis
+    - colour
+    - rich-argparse
+    - tqdm
 
 test:
   commands:
@@ -70,5 +76,7 @@ about:
   dev_url: https://github.com/Kalan-Lab/zol
   
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - raufs