From 9a03cf0abc28c06c98c02bb5c36e30ac044b79db Mon Sep 17 00:00:00 2001
From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com>
Date: Mon, 28 Oct 2024 10:37:26 -0600
Subject: [PATCH 01/62] ci: Switch PR checks for linux-64 and osx-64 to GitHub
 Actions (#51720)

* ci: Switch PR checks for linux-64 and osx-64 to GitHub Actions

* try removing pr:none
---
 .github/workflows/PR.yml     | 176 ++++++++++++++++++-----------------
 .github/workflows/master.yml | 155 +++++++++++++++---------------
 azure-pipeline-master.yml    |  12 +--
 azure-pipeline.yml           |  16 ++--
 4 files changed, 180 insertions(+), 179 deletions(-)

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 82f17b7c4a736..53140212f477f 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: |
@@ -149,6 +150,7 @@ 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 +180,20 @@ 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
 
@@ -213,84 +216,85 @@ jobs:
           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..f39c53d4110f9 100644
--- a/azure-pipeline.yml
+++ b/azure-pipeline.yml
@@ -1,10 +1,12 @@
-pr:
-  autoCancel: true
-trigger:
-  branches:
-    exclude:
-      - master
-      - "*"
+# Disable Azure checks in favor of GitHub Actions due to memory issues
+# pr:
+#   autoCancel: true
+trigger: none
+# trigger: 
+  # branches:
+  #   exclude:
+  #     - master
+  #     - "*"
 
 stages:
   - stage: "lint"

From ce97b383168d42ab299c5daf2ddca449579efe38 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:20:41 -0400
Subject: [PATCH 02/62] Update lima to 2.12.0 (#51722)

Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com>
---
 recipes/lima/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml
index 53d51fabd39ef..a5f591870e125 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 }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/PacificBiosciences/barcoding/releases/download/v{{ version }}/lima.tar.gz
-  sha256: a13437bc7a90ab5df3c19eac44384de2a14370d0391586b5aa63a6478f9c2c53
+  sha256: 7e6ac701b8625867bf7486583e741cc86a58e8c91384826613067364229e5627
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx]
   binary_relocation: False
   run_exports:

From 12b3152211b19856b7d8ea7df23b553acbf37ba5 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 12:23:40 -0500
Subject: [PATCH 03/62] Add libgff recipe (#51706)

---
 recipes/libgff/build.sh  | 16 +++++++++++++++
 recipes/libgff/meta.yaml | 42 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 recipes/libgff/build.sh
 create mode 100644 recipes/libgff/meta.yaml

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..ba263c6af5047
--- /dev/null
+++ b/recipes/libgff/meta.yaml
@@ -0,0 +1,42 @@
+{% 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: 0
+  run_exports:
+    - {{ pin_subpackage('libgff', max_pin='x') }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - bzip2
+    - zlib
+    - xz
+
+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

From b81cc99e72efc938cb6ea55d978f2407fa36c8ca Mon Sep 17 00:00:00 2001
From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com>
Date: Mon, 28 Oct 2024 11:56:14 -0600
Subject: [PATCH 04/62] ci: update GHA artifact location (#51728)

* ci: change artifacts path

* use lima for testing artifacts
---
 .github/workflows/PR.yml | 10 ++--------
 recipes/lima/meta.yaml   |  2 +-
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
index 53140212f477f..4bd237d97ddf3 100644
--- a/.github/workflows/PR.yml
+++ b/.github/workflows/PR.yml
@@ -135,14 +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
@@ -214,7 +208,7 @@ jobs:
         with:
           name: osx-packages
           path: |
-            /tmp/artifacts/packages
+            /tmp/artifacts
 
   # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
   # build_and_test-osx-arm64:
diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml
index a5f591870e125..7814a2309053d 100644
--- a/recipes/lima/meta.yaml
+++ b/recipes/lima/meta.yaml
@@ -31,5 +31,5 @@ extra:
     - armintoepfer
     - pb-dseifert
   skip-lints:
-    #repackaged binary
+    #repackaged binary 
     - should_be_noarch_generic

From 1cc8f9a61408e52b3bd477cc0ba3562c0a5626c2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:01:12 -0400
Subject: [PATCH 05/62] Update nextflow to 24.10.0 (#51691)

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/nextflow/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml
index 923a54a387c81..5a044738b8906 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 = "24.10.0" %}
+{% set sha256 = "e848918fb9b85762822c078435d9ff71979a88cccff81ce5babd75d5eee52fe6" %}
 
 package:
   name: nextflow

From bb64e041817581e1e3ca99ee8ce2ab7a91dbf5eb Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Mon, 28 Oct 2024 21:44:44 +0200
Subject: [PATCH 06/62] prodigal-gv: add aarch64/arm64 builds (#51715)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/prodigal-gv/build.sh  |  4 +++-
 recipes/prodigal-gv/meta.yaml | 12 ++++++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

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..e8108dd5a1016 100644
--- a/recipes/prodigal-gv/meta.yaml
+++ b/recipes/prodigal-gv/meta.yaml
@@ -9,7 +9,9 @@ source:
   sha256: 1fb40a8ae204ce2f41a413edb1edf5b8f22c28c2812320e2807ab48f8e8ce795
 
 build:
-  number: 2
+  number: 3
+  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

From d3c925ad5882135bdc9237b8d7efcd613179c0a2 Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Mon, 28 Oct 2024 21:45:08 +0200
Subject: [PATCH 07/62] miniprot: add aarch64/arm64 builds (#51714)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/miniprot/build.sh  | 4 +++-
 recipes/miniprot/meta.yaml | 7 ++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

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

From 58afb95e02935f7de78a11ac2932963146340ee1 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:50:03 -0400
Subject: [PATCH 08/62] Update shortstack to 4.1.1 (#51731)

---
 recipes/shortstack/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 }}

From a83862eff5904e5bc34fd143ebe35b7b141b0008 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:50:27 -0400
Subject: [PATCH 09/62] Update samshee to 0.2.2 (#51703)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/samshee/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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

From 173a4c7ee97109d28ca3d578412cd1d3ba62883a Mon Sep 17 00:00:00 2001
From: stuber <tod.p.stuber@usda.gov>
Date: Mon, 28 Oct 2024 15:17:34 -0500
Subject: [PATCH 10/62] genoflu version 1.05 (#51712)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/genoflu/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml
index bc04110fffc5b..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 = "1.04" %}
-{% set sha256 = "f8dabd01e5f0fe00443b8991bf31dca38aa4d0064a564fb237dc4e9f0f1eec31" %}
+{% set version = "1.05" %}
+{% set sha256 = "af63053347082cd9fcfeab1ea4bff9ce9340ebbef636e509a72c9e7f4c56be3e" %}
 
 package:
   name: {{ name|lower }}

From f2d37e7a9f4855d2cbcaabd39909bff8e97a69c2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:24:13 -0400
Subject: [PATCH 11/62] Update sainsc to 0.2.1 (#51717)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/sainsc/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/sainsc/meta.yaml b/recipes/sainsc/meta.yaml
index b6417121ec76a..874b37831dd12 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 }}
@@ -7,7 +7,7 @@ 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

From afdf6d03210617071271b143f7698b6074c0ca15 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:26:13 -0400
Subject: [PATCH 12/62] Update masurca to 4.1.2 (#51732)

---
 recipes/masurca/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml
index 72f94abe5a0a9..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 }}
@@ -7,12 +7,12 @@ 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: 2
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}

From 1be53314f0edadbf5c0789a81a3306ff70d24e00 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:27:07 -0400
Subject: [PATCH 13/62] Update crabs to 1.0.6 (#51694)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/crabs/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/crabs/meta.yaml b/recipes/crabs/meta.yaml
index 6026b0c0afd56..387177f5b480d 100644
--- a/recipes/crabs/meta.yaml
+++ b/recipes/crabs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "crabs" %}
-{% set version = "1.0.5" %}
-{% set sha256 = "f948244c3b148e7c23b89f7aab68e28149504c60075f1e731e07a05fbd66d8f5" %}
+{% set version = "1.0.6" %}
+{% set sha256 = "8cbb930cd34aab5e7b7edca3403686ce9c15fddaf72fcdb7719a336644c22289" %}
 
 package:
   name: {{ name|lower }}

From 2a57669df53a3ac31cb6ecbd2e50de519833dd42 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:27:47 -0400
Subject: [PATCH 14/62] Update perl-term-table to 0.023 (#51686)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/perl-term-table/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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:

From c82b1bbb9f42093444d376643c12595f43822213 Mon Sep 17 00:00:00 2001
From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:47:32 -0600
Subject: [PATCH 15/62] ci: Update azure-pipeline.yml (#51737)

---
 azure-pipeline.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/azure-pipeline.yml b/azure-pipeline.yml
index f39c53d4110f9..561f68533b7c8 100644
--- a/azure-pipeline.yml
+++ b/azure-pipeline.yml
@@ -1,6 +1,7 @@
 # Disable Azure checks in favor of GitHub Actions due to memory issues
 # pr:
 #   autoCancel: true
+pr: none
 trigger: none
 # trigger: 
   # branches:

From fb974ccb1a2a0ce0ff31e56b9a77b529b615f57f Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:48:17 -0500
Subject: [PATCH 16/62] Update ucsc-wigtobigwig to 472 (#51702)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/ucsc-wigtobigwig/build.sh            |  6 ++---
 recipes/ucsc-wigtobigwig/htmshell.patch      | 11 --------
 recipes/ucsc-wigtobigwig/include.macos.patch | 27 ++++++++++++++++++++
 recipes/ucsc-wigtobigwig/meta.yaml           | 19 +++++++-------
 4 files changed, 39 insertions(+), 24 deletions(-)
 delete mode 100644 recipes/ucsc-wigtobigwig/htmshell.patch
 create mode 100644 recipes/ucsc-wigtobigwig/include.macos.patch

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..33106d75a2610 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 }}"
@@ -11,10 +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: "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:

From b95b804cba00dfab2963a20715346f73322fb785 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:48:43 -0500
Subject: [PATCH 17/62] Update ucsc-bedgraphtobigwig to 472 (#51701)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/ucsc-bedgraphtobigwig/build.sh        |  6 ++---
 .../ucsc-bedgraphtobigwig/include.macos.patch | 27 +++++++++++++++++++
 recipes/ucsc-bedgraphtobigwig/meta.yaml       | 17 ++++++------
 recipes/ucsc-bedgraphtobigwig/patch1.patch    | 19 -------------
 4 files changed, 38 insertions(+), 31 deletions(-)
 create mode 100644 recipes/ucsc-bedgraphtobigwig/include.macos.patch
 delete mode 100644 recipes/ucsc-bedgraphtobigwig/patch1.patch

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..60afbc9e02c53 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 }}"
@@ -11,10 +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"
+  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);
- }
- 

From 43b7efac18d32e89568acd169b6a7e93b67673ec Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:50:56 -0400
Subject: [PATCH 18/62] Update perl-datetime-locale to 1.44 (#51690)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/perl-datetime-locale/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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:

From ff969daf23e6e8488964eed918185b82fa17c949 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:51:52 -0400
Subject: [PATCH 19/62] Update mycotools to 0.32.5 (#51689)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/mycotools/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/mycotools/meta.yaml b/recipes/mycotools/meta.yaml
index 8855520d4f049..caf0051fa4a26 100644
--- a/recipes/mycotools/meta.yaml
+++ b/recipes/mycotools/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mycotools" %}
-{% set version = "0.32.4" %}
+{% 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: 9269affbc752d5c378e0d7f206220c8bedeb96f2064d8783957b07de210c5666 
+  sha256: e886c43b5faffb4d788a23f6016d146724c85ec8c9fc57ab3e0fcc24840c30b7 
 
 build:
   number: 0

From f521ff486c16f9399f3c863333d86752a6b6088d Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:57:47 -0400
Subject: [PATCH 20/62] Update pbskera to 1.3.0 (#51734)

Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com>
---
 recipes/pbskera/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 }}

From 3da52f136e0ffd18ee9e9b8df87ed3f8a3b152a7 Mon Sep 17 00:00:00 2001
From: Jessica Mattick <19544292+jmattick@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:01:22 -0500
Subject: [PATCH 21/62] Update isoseq version 4.2.0 (#51727)

Co-authored-by: Jessica Mattick <jmattick@pacificbiosciences.com>
Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com>
---
 recipes/isoseq/meta.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

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:

From 98e6ec86fec95e415b666b0b61cdd3c52b52d71d Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:01:40 -0500
Subject: [PATCH 22/62] Update staden_io_lib recipe (#51704)

* Update staden_io_lib recipe

* add export m4
---
 recipes/staden_io_lib/build.sh  |  7 ++++++-
 recipes/staden_io_lib/meta.yaml | 13 ++++++++++---
 2 files changed, 16 insertions(+), 4 deletions(-)

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

From 87e99c4687d816e0eddb90581da7e348ce95729b Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:15:21 -0500
Subject: [PATCH 23/62] Move sopa recipe to /recipes (#51657)

* Move sopa recipe to /recipes

* reset build number

* add run_exports
---
 {sopa => recipes/sopa}/meta.yaml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)
 rename {sopa => recipes/sopa}/meta.yaml (79%)

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:

From 714278c5dd438eaff4303b1012df39bd6774f60b Mon Sep 17 00:00:00 2001
From: Chenkai Li <marklck0428@163.com>
Date: Mon, 28 Oct 2024 14:15:32 -0700
Subject: [PATCH 24/62] add ampd-up (#51688)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: mark0428 <Chenkai@ChenkaideMBP.hitronhub.home>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/ampd-up/build.sh  | 13 +++++++++++++
 recipes/ampd-up/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 recipes/ampd-up/build.sh
 create mode 100644 recipes/ampd-up/meta.yaml

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

From b4ecaf292ba3c48ee037de22bba3a1c859c8cd0d Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:16:39 -0400
Subject: [PATCH 25/62] Update hlafreq to 0.0.5 (#51373)

* Update hlafreq to 0.0.5

* Add `setuptools` to host deps

* clean up recipe

---------

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/hlafreq/meta.yaml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

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:

From 4365e36e0e4be9b9dab6041bb5e55319723991c4 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:16:55 -0400
Subject: [PATCH 26/62] Update starfish to 0.3.0 (#51354)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update starfish to 0.3.0

* Add run_exports

* update dependencies

* try switching to ubuntu-22.04

* need more sleep

* Update azure-pipeline.yml

* Update azure-pipeline.yml

* Update azure-pipeline.yml

* Update azure-pipeline.yml

* revert ubuntu images to -latest

---------

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 azure-pipeline.yml         |  2 ++
 recipes/starfish/meta.yaml | 46 +++++++++++++++++++++-----------------
 2 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/azure-pipeline.yml b/azure-pipeline.yml
index 561f68533b7c8..fc2966287e6b3 100644
--- a/azure-pipeline.yml
+++ b/azure-pipeline.yml
@@ -44,6 +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/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"

From 0f8f87a10aee3517ce88f0fa1e0bee812e8eaf64 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:20:35 -0400
Subject: [PATCH 27/62] Update quantms-utils to 0.0.12 (#51357)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update quantms-utils to 0.0.12

* Update meta.yaml

* Update meta.yaml

* dependency added

* remove <4 from host

* add missing deps

---------

Co-authored-by: Yasset Perez-Riverol <ypriverol@gmail.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/quantms-utils/meta.yaml | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

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:

From 0047d85a13b1960b23b31e34fc91c8798c1864d7 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:22:37 -0400
Subject: [PATCH 28/62] Update pbstarphase to 1.0.0 (#51735)

Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com>
---
 recipes/pbstarphase/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 }}

From 8f95ea884c3d32556ade305d4cba1dbc1c0ab798 Mon Sep 17 00:00:00 2001
From: Jessica Mattick <19544292+jmattick@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:24:31 -0500
Subject: [PATCH 29/62] Update pbaa version 1.1.0 (#51724)

Co-authored-by: Jessica Mattick <jmattick@pacificbiosciences.com>
---
 recipes/pbaa/meta.yaml | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

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:

From e76dd9f8da980e011b6ba2a0c05cc5704f9114d5 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:25:08 -0500
Subject: [PATCH 30/62] Update ucsc-pslcdnafilter to 472 (#51700)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update ucsc-pslcdnafilter to 472

* add linux-aarch64 build

* revert linux-aarch64

* revert osx

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/ucsc-pslcdnafilter/build.sh           |  6 ++---
 .../ucsc-pslcdnafilter/include.macos.patch    | 27 +++++++++++++++++++
 recipes/ucsc-pslcdnafilter/meta.yaml          | 19 +++++++------
 3 files changed, 39 insertions(+), 13 deletions(-)
 create mode 100644 recipes/ucsc-pslcdnafilter/include.macos.patch

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

From 77565e2934ba9604c3b44ee27b8850667a9df396 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:26:58 -0400
Subject: [PATCH 31/62] Update fastk to 1.1.0 (#51740)

---
 recipes/fastk/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

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

From 0d4af9eb3eef5d54c034c3c96d78f7a81b24bc5f Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:27:22 -0400
Subject: [PATCH 32/62] Update oakvar to 2.11.24 (#51678)

* Update oakvar to 2.11.22

* Update oakvar to 2.11.24

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/oakvar/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml
index 9ab8356346ac4..6b9359c0a70f9 100644
--- a/recipes/oakvar/meta.yaml
+++ b/recipes/oakvar/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.11.21" %}
-{% set sha256 = "e9a479ada8d64d8c425ebeb9ad217f6a41583ae7a41e4ee1df52851cd71d2d8a" %}
+{% set version = "2.11.24" %}
+{% set sha256 = "72b3f427b66b2bea8a7b36038f6164e3623b6b6d88c945db659fc06c4d6bed3e" %}
 
 package:
   name: {{ name|lower }}

From a3303f245b2587522c249126f10331ae2db2bbb7 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:28:02 -0400
Subject: [PATCH 33/62] Update bioconda-utils to 3.4.1 (#51739)

---
 recipes/bioconda-utils/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 }}

From 8503d46698d617d1c8e85ab3bba2b8e86f18ab86 Mon Sep 17 00:00:00 2001
From: Jessica Mattick <19544292+jmattick@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:35:19 -0500
Subject: [PATCH 34/62] Update lima to v2.12.0 (#51718)

* Update lima to v2.12.0

* Increase build number

---------

Co-authored-by: Jessica Mattick <jmattick@pacificbiosciences.com>
---
 recipes/lima/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml
index 7814a2309053d..f0bf8cdd59581 100644
--- a/recipes/lima/meta.yaml
+++ b/recipes/lima/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 7e6ac701b8625867bf7486583e741cc86a58e8c91384826613067364229e5627
 
 build:
-  number: 0
+  number: 1
   skip: True  # [osx]
   binary_relocation: False
   run_exports:
@@ -31,5 +31,5 @@ extra:
     - armintoepfer
     - pb-dseifert
   skip-lints:
-    #repackaged binary 
+    #repackaged binary
     - should_be_noarch_generic

From 92a95279fd43de8f34f305853ae590c406ee31a2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:37:00 -0400
Subject: [PATCH 35/62] Update merquryfk to 1.1.1 (#51742)

---
 recipes/merquryfk/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

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

From 67754f9f4453da8a90fb7bdfd56c5c7d36ce1729 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:51:04 -0400
Subject: [PATCH 36/62] Update freyja to 1.5.2 (#51511)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update freyja to 1.5.2

* add setuptools to host

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/freyja/meta.yaml | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

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

From 887adfca36c9b79ccb282f51b7885b1283756971 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 18:00:48 -0400
Subject: [PATCH 37/62] Update strangepg to 0.8.11 (#51743)

---
 recipes/strangepg/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml
index 004a6261093a5..f92619717d528 100644
--- a/recipes/strangepg/meta.yaml
+++ b/recipes/strangepg/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "strangepg" %}
-{% set version = "0.8.10" %}
+{% set version = "0.8.11" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: e0cd76903a1f2644d485afde534552344f641bf8d94a5584b2f791e78733c38d
+  sha256: 0178c136787e01069a23accc5af28565982e9e3a1ce2cdc10bfc5fa9a85cf088
 
 build:
   number: 0

From 26895f4904a2a8685539702b7f504dfc4f30d362 Mon Sep 17 00:00:00 2001
From: Moray Smith <65286772+SwiftSeal@users.noreply.github.com>
Date: Mon, 28 Oct 2024 22:01:15 +0000
Subject: [PATCH 38/62] Update Resistify (#51675)

* Update meta.yaml

* Update meta.yaml

* fix pyproject reqs

* move cython

---------

Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/resistify/meta.yaml | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml
index 08e802612190e..125b9325fd10b 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 = "0.5.0" %}
+{% set sha256 = "c23493ec622733fac905afa4c64b6ca3ce79afe44cf358433b0b81f115578e96" %}
 
 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 +48,12 @@ test:
 
 about:
   home: https://github.com/swiftseal/resistify
+  doc_url: "https://github.com/SwiftSeal/resistify/blob/main/README.md"
   license: MIT
+  license_file: 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.
+  

From 0237ba814f8aa9ea6cad5d7e92845e5b442c4cf5 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 18:02:04 -0400
Subject: [PATCH 39/62] Update dapcy to 1.0.1 (#51212)

* Update dapcy to 0.1.2

* clean up recipe

* Update dapcy to 1.0.1

* add setuptools to host

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/dapcy/meta.yaml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

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:

From 65adb89957dde0ae46dc76a65db8493ebe9a0b04 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 18:06:37 -0400
Subject: [PATCH 40/62] Update regenie to 3.6 (#50468)

* Update regenie to 3.4.1

* Update regenie to 3.4.1

* add patch for v3.4.1

* Update regenie to 3.5

* update patch

* fix boost version

* Update regenie to 3.6

---------

Co-authored-by: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
Co-authored-by: Joelle Mbatchou <65199080+joellembatchou@users.noreply.github.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/regenie/meta.yaml                     |   7 +-
 .../0015-update-cmakelist.txt-for-v3.6.patch  | 355 ++++++++++++++++++
 2 files changed, 359 insertions(+), 3 deletions(-)
 create mode 100644 recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch

diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml
index ef14c2e5919c7..e61e5e7317c02 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 = "3.6" %}
+{% set sha256 = "bb935b196da08ef7b37dad9736022030a686ae84539c47c106de6096d4612e09" %}
 
 package:
   name: {{ name|lower }}
@@ -24,7 +24,8 @@ source:
     # - 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/0014-update-cmakelist.txt-for-v3.5.patch
+    - patches/0015-update-cmakelist.txt-for-v3.6.patch
 
 build:
   number: 0
diff --git a/recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch b/recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch
new file mode 100644
index 0000000000000..affa55bdb51bb
--- /dev/null
+++ b/recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch
@@ -0,0 +1,355 @@
+From eac9852f500ba04d75e7f4ad178f365ce690bfa9 Mon Sep 17 00:00:00 2001
+From: Joelle Mbatchou <joelle.mbatchou@regeneron.com>
+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 b874c33..b3b9950 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
+@@ -33,57 +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
+@@ -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 ${CMAKE_PREFIX_PATH}/include)
+ 
+ set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC")
+-add_definitions(-DVERSION_NUMBER="${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")
+@@ -150,7 +124,7 @@ 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
+@@ -160,7 +134,7 @@ 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
+@@ -170,7 +144,7 @@ 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
+@@ -180,12 +154,12 @@ 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
+@@ -209,91 +183,70 @@ 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 "${MKLROOT}/lib/intel64"
+-      "${MKLROOT}/lib" 
+-      REQUIRED)
+-    find_library(MKL_THREAD_LIB libmkl_gnu_thread.a 
+-      HINTS "${MKLROOT}/lib/intel64"
+-      "${MKLROOT}/lib" 
+-      REQUIRED)
+-    find_library(MKL_CORE_LIB libmkl_core.a 
+-      HINTS "${MKLROOT}/lib/intel64"
+-      "${MKLROOT}/lib" 
+-      REQUIRED)
+-    target_link_libraries(regenie PRIVATE "-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"
+-      "${MKLROOT}/lib" 
+-      REQUIRED)
++  target_include_directories(regenie PUBLIC ${MKLROOT}/include/)
++  find_library(MKL_LP64_LIB mkl_intel_lp64 
++    HINTS "${MKLROOT}/lib/intel64" 
++    "${MKLROOT}/lib" 
++    REQUIRED
++    )
++  if("${UNAME_S}" STREQUAL "Linux")
+     find_library(MKL_THREAD_LIB mkl_gnu_thread 
+-      PATHS "${MKLROOT}/lib/intel64"
++      HINTS "${MKLROOT}/lib/intel64" 
+       "${MKLROOT}/lib" 
+-      REQUIRED)
+-    find_library(MKL_CORE_LIB mkl_core 
+-      PATHS "${MKLROOT}/lib/intel64"
++      REQUIRED
++      )
++  elseif("${UNAME_S}" STREQUAL "Darwin")
++    find_library(MKL_THREAD_LIB mkl_intel_thread 
++      HINTS "${MKLROOT}/lib/intel64" 
+       "${MKLROOT}/lib" 
+-      REQUIRED)
+-    target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp)
++      REQUIRED
++      )
++  endif()
++  find_library(MKL_CORE_LIB mkl_core 
++    HINTS "${MKLROOT}/lib/intel64" 
++    "${MKLROOT}/lib" 
++    REQUIRED
++    )
++  if("${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
++    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 ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/)
+ 
+ # Other libraries
+-find_library(ZLIB_LIBRARY libz.a z REQUIRED)
+-find_library(M_LIB m REQUIRED)
+-find_library(DL_LIB dl REQUIRED)
++find_library(ZLIB_LIBRARY z REQUIRED)
++find_library(M_LIB m REQUIRED) 
++find_library(DL_LIB dl REQUIRED) 
+ if("${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}
+-  ${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
+

From 16850dc75dca22256e496fcf7b666eae9c8dde5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Gudy=C5=9B?= <adam.gudys@gmail.com>
Date: Mon, 28 Oct 2024 23:10:15 +0100
Subject: [PATCH 41/62] Update vclust to 1.2.8 (#51692)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update vclust to 1.2.8

* syntax fix

* added pip as dependency

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/vclust/meta.yaml | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

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:

From ce3082833c327a5683caaa4d5ed4c0aa0486ada5 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 17:52:20 -0500
Subject: [PATCH 42/62] Rebuild libgff recipe (#51746)

---
 recipes/libgff/meta.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/recipes/libgff/meta.yaml b/recipes/libgff/meta.yaml
index ba263c6af5047..aeca79f5a22da 100644
--- a/recipes/libgff/meta.yaml
+++ b/recipes/libgff/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('libgff', max_pin='x') }}
 
@@ -21,9 +21,7 @@ requirements:
     - cmake
     - {{ compiler('cxx') }}
   host:
-    - bzip2
     - zlib
-    - xz
 
 test:
   commands:

From 55d5a6b49fc5f6d9128312891de86ffd8ce89101 Mon Sep 17 00:00:00 2001
From: Matty Allan <31744230+matthewfallan@users.noreply.github.com>
Date: Mon, 28 Oct 2024 18:53:02 -0400
Subject: [PATCH 43/62] Update seismic-rna dependencies (#51693)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/seismic-rna/build.sh  |  2 +-
 recipes/seismic-rna/meta.yaml | 12 ++----------
 2 files changed, 3 insertions(+), 11 deletions(-)

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

From 5581f1569345f0bb2c75f18bb1430060e738fec7 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:12:48 -0400
Subject: [PATCH 44/62] Update altamisa to 0.3.0 (#51708)

* Update altamisa to 0.3.0

* Add run_exports

* add run_exports

---------

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/altamisa/meta.yaml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

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

From 95ffd5d1aa759589a71756587bffca3ef120d5ad Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:24:57 -0400
Subject: [PATCH 45/62] Update tirmite to 1.1.5 (#51713)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update tirmite to 1.1.5

* add run_exports

* add hatchling

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/tirmite/meta.yaml | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml
index 4a471678ab4af..364f4e5917a39 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 = "1.1.5" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "82657d6f84f51731cb5f92c33d9e672a61009ecc79a61ba21f6f3fc637b2a25b" %}
+{% set hash_value = "01d2180d073da1786d5236296e51952281c58cb1124aa254345b3d6ab63a1721" %}
 
 package:
   name: '{{ name|lower }}'
@@ -19,14 +19,19 @@ build:
     - 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
+    - python >=3.8
     - pandas >=0.20.3
     - biopython >=1.70
     - pymummer >=0.10.3
@@ -41,9 +46,9 @@ test:
 
 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:

From 817aa0abd88265a5306b57fa607f1533c7871111 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:31:24 -0400
Subject: [PATCH 46/62] Update pybiolib to 1.2.218 (#51749)

---
 recipes/pybiolib/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
index fcbe899863e17..25cbc110e6e5a 100644
--- a/recipes/pybiolib/meta.yaml
+++ b/recipes/pybiolib/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.216" %}
+{% set version = "1.2.218" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 8600ff68710980d26cc0166416383f3020502d62f4a67f54ef863c36f4a8edb2
+  sha256: ea2a905f7dba6c18aec2080ca25f33f1ee0f5bd68855a10532c17799a955c64e
 
 build:
   number: 0

From 79f5213bf4e2883b424daaabe0691431951fa91c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:34:29 -0400
Subject: [PATCH 47/62] Update flippyr to 0.6.0 (#51747)

* Update flippyr to 0.6.0

* add run_exports

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/flippyr/meta.yaml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/recipes/flippyr/meta.yaml b/recipes/flippyr/meta.yaml
index c45b1fd060bad..93b6c77e43075 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 = "0.6.0" %}
+{% set sha256 = "e39da37ecdafe399429213d98761610a93f1bdb1906256a0ea4868bd6271f366" %}
 
 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:

From 21ec5dc8ada1b84e16836b0aa9ed1118007b2ff2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:37:34 -0400
Subject: [PATCH 48/62] Update kaptive to 3.0.0b6 (#51748)

* Update kaptive to 3.0.0b6

* add setuptools to host

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/kaptive/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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

From 341e840a2e44ec0e314a70e3bcc04f8bc7ce078d Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:02:10 -0500
Subject: [PATCH 49/62] Rebuild ucsc-wigtobigwig recipe (#51751)

---
 recipes/ucsc-wigtobigwig/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml
index 33106d75a2610..c9deee8b43399 100644
--- a/recipes/ucsc-wigtobigwig/meta.yaml
+++ b/recipes/ucsc-wigtobigwig/meta.yaml
@@ -15,7 +15,7 @@ source:
     - include.macos.patch  # [osx]
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 

From 3dadfe427d4ab22113befae55aef552bdd14b34c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 20:02:33 -0400
Subject: [PATCH 50/62] Update quota_anchor to 0.0.1a1 (#51585)

* Update quota_anchor to 0.0.1a1

* Update dependencies

* edit tests

* add alive-progress

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/quota_anchor/build.sh  |  3 ++-
 recipes/quota_anchor/meta.yaml | 14 ++++++++------
 2 files changed, 10 insertions(+), 7 deletions(-)

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

From aeb4ad2f744ae8785c4afad050e677df4db514ab Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 28 Oct 2024 19:41:59 -0500
Subject: [PATCH 51/62] Rebuild ucsc-bedgraphtobigwig recipe (#51750)

---
 recipes/ucsc-bedgraphtobigwig/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml
index 60afbc9e02c53..fa8e2af63aaa1 100644
--- a/recipes/ucsc-bedgraphtobigwig/meta.yaml
+++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml
@@ -15,7 +15,7 @@ source:
     - include.macos.patch  # [osx]
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(package, max_pin=None) }}
 

From 24d173920a366f17f4b69f8f72ec45095cebadc3 Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Mon, 28 Oct 2024 21:46:29 -0500
Subject: [PATCH 52/62] Add: deepchopper (#51460)

* Create meta.yaml of deepchopper

* Update meta.yaml of deepchopper

* Create build.sh of deepchopper

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* clean up recipe

* add aarch64/arm64 builds

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml (evaluate do not have latest one)

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update build.sh

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/deepchopper/build.sh  | 20 ++++++++++
 recipes/deepchopper/meta.yaml | 74 +++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+)
 create mode 100644 recipes/deepchopper/build.sh
 create mode 100644 recipes/deepchopper/meta.yaml

diff --git a/recipes/deepchopper/build.sh b/recipes/deepchopper/build.sh
new file mode 100644
index 0000000000000..ba2ee9778318d
--- /dev/null
+++ b/recipes/deepchopper/build.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+# -e = exit on first error
+# -x = print every executed command
+set -ex
+
+# if [ `uname` == Darwin ]; then
+#   export HOME=`mktemp -d`
+# fi
+
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y
+
+export PATH="$HOME/.cargo/bin:$PATH"
+# export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC"
+# export CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER="$CC"
+
+
+maturin build --interpreter python --release
+
+$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv
diff --git a/recipes/deepchopper/meta.yaml b/recipes/deepchopper/meta.yaml
new file mode 100644
index 0000000000000..2e06be86b7c97
--- /dev/null
+++ b/recipes/deepchopper/meta.yaml
@@ -0,0 +1,74 @@
+{% set name = "deepchopper" %}
+{% set version = "1.2.4" %}
+{% set sha256 = "e7f0bfed8c34e011e924bc12e30dec9c58777f1879962b9a2036da29009461e4" %}
+
+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
+
+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

From f83e9c7b5a61fffebb060d7043ecf9bd1af8907c Mon Sep 17 00:00:00 2001
From: Luan Nguyen <125411678+luan-n-nguyen@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:55:43 +1100
Subject: [PATCH 53/62] Update hmftools-{esvee,linx,purple,redux,sage} (#51698)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update hmftools-redux to 1.0_beta.1

* Update hmftools-esvee to 1.0_beta.2

* Update hmftools-purple to 4.1_beta.1

* Update hmftools-linx to 2.0_beta.1

* Added perl GD module to hmftools-linx

* Increment build number for hmftools-linx

* Set perl GD version to  >= 2.76 in hmftools-linx

* Reset build number in hmftools-linx

* Fixed typo in version specification

* Use circos >=0.69.9 in hmftools-linx

* Revert "Use circos >=0.69.9 in hmftools-linx"

This reverts commit 7e8906f4f666ec27caa8e757b2f5a6e0c529144a.

* Also add perl-gd >=2.76 for hmftools-purple

* Update hmftools-esvee to 1.0_beta.3

* Update hmftools-linx to 2.0_beta.3

* Update hmftools-purple to 4.1_beta.4

* Update hmftools-redux to 1.0_beta.2

* Update hmftools-sage to 4.0_beta.2

* Reset build numbers for hmftools esvee, redux and sage

* Increment build numbers for hmftools esvee, redux and sage

* Increment build number for hmftools-esvee

* Increment build number for esvee again

* Increment build number for redux and sage

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/hmftools-esvee/meta.yaml  | 6 +++---
 recipes/hmftools-linx/meta.yaml   | 6 +++---
 recipes/hmftools-purple/meta.yaml | 6 +++---
 recipes/hmftools-redux/meta.yaml  | 6 +++---
 recipes/hmftools-sage/meta.yaml   | 6 +++---
 5 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/recipes/hmftools-esvee/meta.yaml b/recipes/hmftools-esvee/meta.yaml
index 9a11455bde79d..227fec34dfdcd 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 = ".3" %}
+{% set sha256 = "da026c1bec9c8314652f7c3870daa2d8eaddd3dc71ef924d86339c87d084d65a" %}
 
 package:
   name: hmftools-esvee
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 2
+  number: 3
   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-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml
index d979ebdf55c18..dcf946ec3ff8b 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 = ".4" %}
+{% set sha256 = "fef88d9bc349aa6a43c2b90fb6ea9835d50c3bd4d9c622190024bb890a0ae7e9" %}
 
 package:
   name: hmftools-purple
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   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..187be4d48df27 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 = ".2" %}
+{% set sha256 = "a35bce08d84ee1ab00adf1c2fcbe177099924bd2d75e138a5f30d61181d8b9a2" %}
 
 package:
   name: hmftools-redux
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}
 
diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml
index 14d85d65a3c30..2fe25f493e0a8 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 = ".2" %}
+{% set sha256 = "371908a6311f6fc1f43fc450118c1cae19e2966beb4dd5e2586f3db69e0f6d4a" %}
 
 package:
   name: hmftools-sage
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage('hmftools-sage', max_pin="x") }}
 

From 0156829d2bf2d03eee2b99d46e34bf34d0eb7f7f Mon Sep 17 00:00:00 2001
From: Ramiro <ramiro.barrantes@uvm.edu>
Date: Tue, 29 Oct 2024 12:01:25 +0100
Subject: [PATCH 54/62] Initial addition. Works (#51764)

---
 recipes/coptr/meta.yaml | 51 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 recipes/coptr/meta.yaml

diff --git a/recipes/coptr/meta.yaml b/recipes/coptr/meta.yaml
new file mode 100644
index 0000000000000..486605ae42cf5
--- /dev/null
+++ b/recipes/coptr/meta.yaml
@@ -0,0 +1,51 @@
+{% 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 . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+   - {{ pin_subpackage("coptr", max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.6
+    - setuptools >=40.6.0
+    - wheel
+    - pip
+  run:
+    - python >=3.6
+    - numpy >=1.19.1
+    - pysam >=0.16.0.1
+    - scipy >=1.5.2
+    - matplotlib-base >=3.3.2
+
+test:
+  imports:
+    - coptr
+  commands:
+    - pip check
+    - coptr --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/tyjo/coptr
+  summary: Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reads.
+  license: GPL-3.0
+  license_file: COPYING
+
+extra:
+  recipe-maintainers:
+    - ramirobarrantes

From b858773e6c93442d0dd812dfafc2b6d381415c10 Mon Sep 17 00:00:00 2001
From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com>
Date: Tue, 29 Oct 2024 05:36:12 -0700
Subject: [PATCH 55/62] Update nextclade to 3.9.1 (#51763)

Co-authored-by: nextstrain-bot <nextstrainbot@nextstrain.org>
---
 recipes/nextclade/meta.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

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

From 7201e2de558963497e454b63fbf3384ffeb413a5 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:37:37 +0100
Subject: [PATCH 56/62] Add cell2cell (#51744)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* meta.yaml created by greyskull

* update meta.yaml

* update meta

* Update recipes/cell2cell/meta.yaml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Update recipes/cell2cell/meta.yaml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* update meta

* update meta

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/cell2cell/meta.yaml | 62 +++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 recipes/cell2cell/meta.yaml

diff --git a/recipes/cell2cell/meta.yaml b/recipes/cell2cell/meta.yaml
new file mode 100644
index 0000000000000..0db26e51ae700
--- /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: 0
+  run_exports:
+    - {{ pin_subpackage("cell2cell", max_pin="x.x.x") }}
+
+requirements:
+  build:
+    - {{ compiler("cxx") }}
+
+  host:
+    - python <=3.8
+    - cython
+    - pip
+  run:
+    - python <=3.8
+    - 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

From 0307b27b66717b66f2657be62b5668863dcaf8c3 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 29 Oct 2024 08:37:54 -0400
Subject: [PATCH 57/62] Update galaxy-objectstore to 24.1.3 (#51758)

---
 recipes/galaxy-objectstore/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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:

From 1d9feaeec90c1982bc95fb90fc6f3e62bb285926 Mon Sep 17 00:00:00 2001
From: Jeroen Van Goey <j.vangoey@instadeep.com>
Date: Tue, 29 Oct 2024 14:38:10 +0200
Subject: [PATCH 58/62] Update pyopenms to 3.2.0 (#51753)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* bump version

* add eigen to build,host,run

* bump eigen version

* Bump eigen >= 3.4.0

* exchange to eigen3 package

* Try upstream fix of openms to find eigen -> update checksum

* fix eigen to 3.3.4

* fix eigen to 3.3.5

* Relax eigen version pin

* Update conda_build_config.yaml

* Update conda_build_config.yaml

* Update packages in pyopenms recipe

* Remove duplicated eigen dependency and remove trailing spaces

* Update recipes/pyopenms/meta.yaml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Update recipes/pyopenms/meta.yaml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Move eigen to host section

---------

Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/pyopenms/build_failure.linux-64.yaml | 104 -------------------
 recipes/pyopenms/conda_build_config.yaml     |   5 +-
 recipes/pyopenms/meta.yaml                   |  19 ++--
 3 files changed, 15 insertions(+), 113 deletions(-)
 delete mode 100644 recipes/pyopenms/build_failure.linux-64.yaml

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
index adf8945de603d..dd7f1933d9e4e 100644
--- a/recipes/pyopenms/conda_build_config.yaml
+++ b/recipes/pyopenms/conda_build_config.yaml
@@ -2,14 +2,17 @@ python:
   - 3.9.*
   - 3.10.*
   - 3.11.*
+  - 3.12.*
 python_impl:
   - cpython
   - cpython
   - cpython
+  - cpython
 numpy:
   - 1.23.*
   - 1.23.*
-  - 1.23.*  
+  - 1.23.*
+  - 1.26.*
 zip_keys:
   - python
   - python_impl
diff --git a/recipes/pyopenms/meta.yaml b/recipes/pyopenms/meta.yaml
index a3376b5a32f13..f156ccddb0a36 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  }}
@@ -11,8 +11,8 @@ 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:
@@ -26,14 +26,15 @@ 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
+    - qt-main >=5.15.8
     - python {{ python }}
     - cython >=0.25.2
     - autowrap >=0.22.10
@@ -44,13 +45,15 @@ requirements:
     - 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
+    - qt-main >=5.15.8
+    - eigen >=3.3.4
     - python {{ python }}
     - numpy {{ numpy }}
     - pandas

From 34d08b052ed8a8565a3e8b3266a04eea2dd81b96 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Tue, 29 Oct 2024 13:38:56 +0100
Subject: [PATCH 59/62] add Corneto (#51745)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* meta.yaml created by greyskull

* update meta.yaml

* Update recipes/corneto/meta.yaml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* SPDX identifier

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/corneto/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 recipes/corneto/meta.yaml

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

From 8902c7601b320dbfeed8e93b2381b1d4f7cae24a Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 29 Oct 2024 08:40:23 -0400
Subject: [PATCH 60/62] Update pgscatalog.core to 0.3.3 (#51761)

---
 recipes/pgscatalog.core/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/pgscatalog.core/meta.yaml b/recipes/pgscatalog.core/meta.yaml
index 9db0cfa331250..c7a45cf48520e 100644
--- a/recipes/pgscatalog.core/meta.yaml
+++ b/recipes/pgscatalog.core/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pgscatalog.core" %}
-{% set version = "0.3.2" %}
+{% 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: a91d1d20692af7473ca55a3a40c96b43cb65890fe3f1516a394e52c0fa515f34
+  sha256: 5b2851860e3dda29ec4863701cf2acb9e1007549960b24e1dcdfec4258f6792f
 
 build:
   entry_points:

From 3dab52f5f6531b98ebb45f8ab14487e64e7f6b38 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 29 Oct 2024 08:40:29 -0400
Subject: [PATCH 61/62] Update pybiolib to 1.2.221 (#51755)

---
 recipes/pybiolib/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
index 25cbc110e6e5a..bb70bf88a32f9 100644
--- a/recipes/pybiolib/meta.yaml
+++ b/recipes/pybiolib/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.218" %}
+{% set version = "1.2.221" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: ea2a905f7dba6c18aec2080ca25f33f1ee0f5bd68855a10532c17799a955c64e
+  sha256: cba8e863eec447c4290e0a103657d9d8d83fccb79a7088e0f5b15176574da263
 
 build:
   number: 0

From 2914659a8cb171f35ddda3cf9db533cbc80cb4cb Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 29 Oct 2024 09:56:45 -0400
Subject: [PATCH 62/62] Update galaxy-schema to 24.1.3 (#51756)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update galaxy-schema to 24.1.3

* Update meta.yaml

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/galaxy-schema/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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 }}