From e88111c28141e3320603647ab3a955d5362e46f6 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:16:01 -0400
Subject: [PATCH 01/16] Update squirrel to 1.0.11 (#51402)

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

diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml
index 31fe86f18b49b0..6b95c234d852a1 100644
--- a/recipes/squirrel/meta.yaml
+++ b/recipes/squirrel/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.10" %}
+{% set version = "1.0.11" %}
 {% set name = "squirrel" %}
 
 package:
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz
-  sha256: f59e433906b995004f4e266235b0cfd58d80a08fd63c776d86c1846c8565254e
+  sha256: 2d3a4e1a3227372f32ffb6d97005efb08839b53e71f1b6e3d844fe8327835fe5
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: python -m pip install --no-deps --ignore-installed .
   run_exports:

From 0f996fdc3af0b95e4c4584d6c34b105611270bb1 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:47:22 -0400
Subject: [PATCH 02/16] Update gencove to 2.23.0 (#51404)

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

diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml
index 3e73bdf53321c9..113e485ce3f40c 100644
--- a/recipes/gencove/meta.yaml
+++ b/recipes/gencove/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.21.0" %}
-{% set sha256 = "805be8b0c0f3e8d189bca16a805649e9594d455c0fa183ecd856ee3208287258" %}
+{% set version = "2.23.0" %}
+{% set sha256 = "edb1a4855f88d87c41902745d6f823142747005a29932700afcabc0c216f16e9" %}
 
 package:
   name: {{ name }}

From 984d92aae10ae0b084f8cf420883405ac10957c7 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:47:32 -0400
Subject: [PATCH 03/16] Update metabolights-utils to 1.2.1 (#51403)

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

diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml
index 2cdc8e5417f948..b235bec50bcfe5 100644
--- a/recipes/metabolights-utils/meta.yaml
+++ b/recipes/metabolights-utils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "metabolights-utils" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
-  sha256: 4e8c7eb7fd06243389dfe13545ee517a76606ceaaa46d3e55a961dc333572fcf
+  sha256: 2db0e90df0540f87820955de31f8ec7bf9cbc6a0f669632c252c1f5908b31c9d
 
 build:
   entry_points:

From cd4fabacf80f23c069035b76dd62c5c85a34ec18 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:47:49 -0400
Subject: [PATCH 04/16] Update seqwish to 0.7.11 (#51408)

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

diff --git a/recipes/seqwish/meta.yaml b/recipes/seqwish/meta.yaml
index 04cdcf32616b4d..b494ce3617d030 100644
--- a/recipes/seqwish/meta.yaml
+++ b/recipes/seqwish/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "seqwish" %}
-{% set version = "0.7.10" %}
+{% set version = "0.7.11" %}
 
 package:
   name: "{{ name }}"
@@ -7,13 +7,13 @@ package:
 
 source:
   url: https://github.com/ekg/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 133b32c9c99caf44eba955b74bae338681da78300e4b21269e07475f88c88b29
+  sha256: 9cbf51990787a93c58a1ee04239608785beb7e8a38efeb02929121b3c8c4a103
 
 build:
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x.x') }}
-  number: 1
+  number: 0
 
 requirements:
   build:

From 60b837ad0c5d631c09c958032d74cb7c1e2b2e2a Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:11:18 -0400
Subject: [PATCH 05/16] Update smoothxg to 0.8.0 (#51407)

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

diff --git a/recipes/smoothxg/meta.yaml b/recipes/smoothxg/meta.yaml
index b0382f7fd18a9b..5357d1b2094b61 100644
--- a/recipes/smoothxg/meta.yaml
+++ b/recipes/smoothxg/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "smoothxg" %}
-{% set version = "0.7.4" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 6c15c1156ac3e1a29cdb4db20f46e1b22382b22640beaa7ec8e0d76564dc53ca
+  sha256: b2b1402971c2e5cf85b318ab98583bf33f78cee33c4bcd8faa140624a76e84be
   patches:
     - CMakeLists.patch
 

From 6f2e6da82a5ccb9f1645a32e81614c4def968a90 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 18:45:50 -0400
Subject: [PATCH 06/16] Update easypqp to 0.1.50 (#51406)

* Update easypqp to 0.1.50

* add setuptools to host

---------

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

diff --git a/recipes/easypqp/meta.yaml b/recipes/easypqp/meta.yaml
index d4de88853b7832..51573537911189 100644
--- a/recipes/easypqp/meta.yaml
+++ b/recipes/easypqp/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "easypqp" %}
-{% set version = "0.1.49" %}
-{% set sha256 = "96fffd59e617de0007f1fbe88ab223d605a7d4a4e94a7b4f4d4a94b4016e327c" %}
+{% set version = "0.1.50" %}
+{% set sha256 = "d3ebc1c7cbe61f081c5ab71e76e7130aa7fae955895ffe8f719363b29870a000" %}
 
 package:
   name: {{ name|lower }}
@@ -23,6 +23,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - numba

From fbddd31780b12770e06a3425261c4e583b77373d Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 18:49:23 -0400
Subject: [PATCH 07/16] Update seqfu to 1.22.3 (#51410)

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

diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml
index 9dfcd4bb28b7fc..7fc4118201e171 100644
--- a/recipes/seqfu/meta.yaml
+++ b/recipes/seqfu/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "seqfu" %}
-{% set version = "1.22.2" %}
-{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %}
+{% set version = "1.22.3" %}
+{% set sha256 = "65c1090cafe0e760e68d15d450bccfd57c0a03d553fdabca26e2191f566fef62" %}
 
 package:
   name: {{ name }}

From 0e18054bf7f998b7ee726371430c288811116592 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 19:33:40 -0400
Subject: [PATCH 08/16] Update afpdb to 0.2.3 (#51413)

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

diff --git a/recipes/afpdb/meta.yaml b/recipes/afpdb/meta.yaml
index 0bfcfd3e0e7e6c..9d64f383ab285c 100644
--- a/recipes/afpdb/meta.yaml
+++ b/recipes/afpdb/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "afpdb" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98
+  sha256: aad8f90092630dce86254227bc94e4f42a28598a6ccf69f07d0e619bc88c0ae8
 
 build:
   number: 0

From 9697ab390aa54d400a2aac3af7edd69818b61bd8 Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <natasha.pavlovikj@yahoo.com>
Date: Tue, 15 Oct 2024 18:47:48 -0500
Subject: [PATCH 09/16] Pin gsl to 2.5 for rmats (#51411)

* Pin gsl to 2.5 for rmats

* Fix pinning
---
 recipes/rmats/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml
index 4ae4f2d4d6aa7f..6f36f750e10057 100644
--- a/recipes/rmats/meta.yaml
+++ b/recipes/rmats/meta.yaml
@@ -10,7 +10,7 @@ source:
   url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz
 
 build:
-  number: 2
+  number: 3
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -26,14 +26,14 @@ requirements:
     - python
     - cython
     - numpy
-    - gsl
+    - gsl 2.5
     - zlib
     - libblas
     - liblapack
   run:
     - python
     - numpy
-    - gsl
+    - gsl 2.5
     - zlib
     - star >=2.5
 
@@ -50,4 +50,4 @@ about:
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64

From 11c494da6c8ab87ac11bbcccd45e7ca8d2aee64a Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 15 Oct 2024 18:57:54 -0500
Subject: [PATCH 10/16] Update rseqc to v5.0.4 (#51414)

---
 recipes/rseqc/meta.yaml | 38 ++++++++++++++++++--------------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml
index 063aa6d4133ecc..da1b56e67a473a 100644
--- a/recipes/rseqc/meta.yaml
+++ b/recipes/rseqc/meta.yaml
@@ -1,55 +1,53 @@
-{% set name = "RSeQC" %}
-{% set version = "5.0.3" %}
+{% set name = "rseqc" %}
+{% set version = "5.0.4" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 869f542e08f50c8874280d58e4f5565857b0aebac66a8eceef3f23016175061e
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/rseqc-{{ version }}.tar.gz
+  sha256: b7f3996f3de0b0b0a09eec949281a8f3e665a20827fcb3cbbd7546b94574a088
 
 build:
-  number: 3
-  skip: True  # [py2k]
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv"
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
 requirements:
-  build:
-    - {{ compiler('c') }}
   host:
     - pip
-    - python
-    - cython >=0.12
-    - nose
+    - python >=3.5
+    - setuptools
   run:
     - bx-python
     - numpy
     - pybigwig
     - pysam
-    - python
-    - r-base
-    - pandas
+    - python >=3.5
+    - logomaker
 
 test:
   imports:
     - qcmodule
     - qcmodule.SAM
+    - psyco_full
   commands:
     - read_distribution.py 2>&1 | grep Usage > /dev/null
     - geneBody_coverage.py 2>&1 | grep Usage > /dev/null
 
 about:
-  home: http://rseqc.sourceforge.net/
-  license: GNU General Public License v2 (GPLv2)
-  summary: 'RNA-seq QC Package'
+  home: "https://rseqc.sourceforge.net"
+  license: "GPL-2.0-or-later"
+  summary: 'QC package for RNA-seq data.'
   license_family: GPL2
+  license_file: LICENSE
+  dev_url: "https://rseqc.sourceforge.net"
+  doc_url: "https://rseqc.sourceforge.net/#usage-information"
 
 extra:
-  additional-platforms:
-    - linux-aarch64
   identifiers:
     - biotools:rseqc
     - doi:10.1093/bioinformatics/bts356

From bf5e1112a8eb8b20e3c10954efb537c1e9f1253a Mon Sep 17 00:00:00 2001
From: Maarten Kooyman <maarten-k@users.noreply.github.com>
Date: Wed, 16 Oct 2024 02:07:32 +0200
Subject: [PATCH 11/16] Update snakemake: remove toposort as dependency
 (#51412)

* remove toposort as depency

Since this replaced by a graphlib

* Updated build number
---
 recipes/snakemake/meta.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml
index 56ad5ea17cf056..90ae273ce9c1da 100644
--- a/recipes/snakemake/meta.yaml
+++ b/recipes/snakemake/meta.yaml
@@ -12,7 +12,7 @@ source:
   sha256: 5c4348f55256eb62b2af10c64b0422ca08206193aef725b6412372a7804ef54b
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage("snakemake", max_pin="x") }}
@@ -110,7 +110,6 @@ outputs:
         - snakemake-interface-report-plugins >=1.0.0,<2.0.0
         - tabulate
         - throttler
-        - toposort >=1.10,<2.0
         - wrapt
         - yte >=1.5.1,<2.0
         - dpath >=2.1.6,<3.0.0

From c19109241fcd63d1289ee8dc1f6560cd63bbefd1 Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Wed, 16 Oct 2024 04:50:45 +0300
Subject: [PATCH 12/16] devider: add aarch64/arm64 builds (#51370)

* devider: add aarch64/arm64 builds

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* devider: add a patch for better ARM64 support

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* devider: add clangdev host dependency for linux-aarch64

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Do not build osx-arm64. It tries to build an unrelated recipe

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 recipes/devider/build.sh              | 19 +++++++++++++++----
 recipes/devider/devider-aarch64.patch | 14 ++++++++++++++
 recipes/devider/meta.yaml             |  8 +++++++-
 3 files changed, 36 insertions(+), 5 deletions(-)
 create mode 100644 recipes/devider/devider-aarch64.patch

diff --git a/recipes/devider/build.sh b/recipes/devider/build.sh
index 17d5db214e9a0a..e3d6bbba51363a 100644
--- a/recipes/devider/build.sh
+++ b/recipes/devider/build.sh
@@ -1,10 +1,21 @@
-#!/bin/bash -euo
+#!/bin/bash
+
+set -xeuo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
 # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+export CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
 cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
-RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path .
+
+case $(uname -m) in
+    aarch64 | arm64)
+        FEATURES="--features neon --no-default-features"
+        ;;
+    *)
+        FEATURES=""
+        ;;
+esac
+
+RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . ${FEATURES}
 cp scripts/* $PREFIX/bin
diff --git a/recipes/devider/devider-aarch64.patch b/recipes/devider/devider-aarch64.patch
new file mode 100644
index 00000000000000..6c2478c0cccfab
--- /dev/null
+++ b/recipes/devider/devider-aarch64.patch
@@ -0,0 +1,14 @@
+--- Cargo.toml.orig	2024-10-14 10:59:48.140000000 +0000
++++ Cargo.toml	2024-10-14 11:03:33.120000000 +0000
+@@ -13,9 +13,9 @@
+ rayon="1.7"
+ rand="0.8"
+ rand_core="0.6"
+-rust-htslib= { version = "0.44", default-features = false }
++rust-htslib= { version = "0.47", default-features = false }
+ clap = { version = "=4.2.0", features = ["derive"] }
+-block-aligner = { version = "0.4", default-features = false }
++block-aligner = { version = "0.5", default-features = false }
+ debruijn = "0.3"
+ simple_logger="4"
+ log="0.4"
diff --git a/recipes/devider/meta.yaml b/recipes/devider/meta.yaml
index b9ea2b34e8c0da..90c59b51251240 100644
--- a/recipes/devider/meta.yaml
+++ b/recipes/devider/meta.yaml
@@ -7,9 +7,11 @@ package:
 source:
   url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz
   sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce
+  patches:
+    - devider-aarch64.patch # [aarch64]
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('devider', max_pin="x.x") }}
 
@@ -20,6 +22,8 @@ requirements:
     - cargo-bundle-licenses
     - make
     - cmake >=3.12
+  host:
+    - clangdev >=16,<17 # [linux and aarch64]
   run:
     - python 
     - samtools
@@ -43,5 +47,7 @@ about:
   summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - bluenote-1577

From 50260364a6ee09e0437bacd09aff4180bc68dd89 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 22:54:28 -0400
Subject: [PATCH 13/16] Update odgi to 0.9.0 (#51405)

* Update odgi to 0.9.0

* clean up recipe

* do not build on aarch64/arm64

* add python back to host

* revert to skipping osx

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/odgi/build.sh  | 39 ++++++++++++++++++++++-----------------
 recipes/odgi/meta.yaml | 31 +++++++++++++++++++------------
 recipes/odgi/patch     | 12 ------------
 3 files changed, 41 insertions(+), 41 deletions(-)
 delete mode 100644 recipes/odgi/patch

diff --git a/recipes/odgi/build.sh b/recipes/odgi/build.sh
index cd4b51ac50228a..8d97950684e857 100644
--- a/recipes/odgi/build.sh
+++ b/recipes/odgi/build.sh
@@ -1,20 +1,25 @@
 #!/bin/bash
-export LIBRARY_PATH=${PREFIX}/lib
-export LD_LIBRARY_PATH=${PREFIX}/lib
-export CPATH=${PREFIX}/include
-export C_INCLUDE_PATH=${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${PREFIX}/include
-export CPP_INCLUDE_PATH=${PREFIX}/include
-export CXX_INCLUDE_PATH=${PREFIX}/include
-#cmake -H. -Bbuild -DPYTHON_EXECUTABLE:FILEPATH=$PYTHON -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast -Og'
-cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast'
-cmake --build build
+
 mkdir -p $PREFIX/bin
-mv bin/* $PREFIX/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Generic \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-march=sandybridge -Ofast' \
+	"${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
+
 PYVER=`python -c 'import sys; print(str(sys.version_info[0])+"."+str(sys.version_info[1]))'`
-mkdir -p $PREFIX/lib/python$PYVER/site-packages
-cp lib/*cpython* $PREFIX/lib/python$PYVER/site-packages
-cp lib/* $PREFIX/lib
-#set -x
-#python -c "import sys; sys.path.append('./lib'); import odgi_ffi"
-#python -c "import sys; sys.path.append('./lib'); import odgi"
+mkdir -p "${PREFIX}/lib/python${PYVER}/site-packages"
+cp -rf lib/*cpython* "${PREFIX}/lib/python${PYVER}/site-packages"
+cp -rf lib/* "${PREFIX}/lib"
diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml
index f75494a207e1fb..4de1264118239f 100644
--- a/recipes/odgi/meta.yaml
+++ b/recipes/odgi/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "odgi" %}
-{% set version = "0.8.6" %}
+{% set version = "0.9.0" %}
 
 package:
   name: "{{ name }}"
@@ -7,32 +7,31 @@ package:
 
 source:
   url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: a6db190b782608082b14b42c660389aa18010791de1e2d07e29f7f61d8787754
-  patches:
-    - patch
+  sha256: 73b181c371e619b5e3e5ee87649cb8de82b054e492dcd128d93cec42be062f2f
 
 build:
-  skip: True  # [osx or py27]
-  number: 2
+  skip: True  # [osx]
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
     - cmake
     - make
   host:
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - zlib
-    - python
     - jemalloc
+    - python
     - pybind11
   run:
     - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - python
+    - jemalloc
     - pybind11
 
 test:
@@ -40,11 +39,19 @@ test:
     - odgi test
 
 about:
-  home: https://github.com/pangenome/odgi
+  home: "https://github.com/pangenome/odgi"
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: An optimized dynamic genome/graph implementation
+  summary: "An optimized dynamic genome/graph implementation."
+  dev_url: "https://github.com/pangenome/odgi"
+  doc_url: "https://github.com/pangenome/odgi/blob/v{{ version }}/README.md"
 
 extra:
   recipe-maintainers:
     - AndreaGuarracino
+  identifiers:
+    - doi:10.1093/bioinformatics/btac308
+    - biotools:odgi
+    - usegalaxy-eu:odgi_viz
+    - usegalaxy-eu:odgi_build
diff --git a/recipes/odgi/patch b/recipes/odgi/patch
deleted file mode 100644
index f5e417a8ecd377..00000000000000
--- a/recipes/odgi/patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/pythonmodule.cpp b/src/pythonmodule.cpp
-index 6a7942b..e38b12b 100644
---- a/src/pythonmodule.cpp
-+++ b/src/pythonmodule.cpp
-@@ -5,6 +5,7 @@
- #include <pybind11/pybind11.h>
- #include <pybind11/functional.h>
- #include <pybind11/iostream.h>
-+#include <pybind11/stl.h>
- 
- namespace py = pybind11;
- 

From a4d30f95120075923ac0e3a230489994f54c2dac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ond=C5=99ej=20Sladk=C3=BD?=
 <127035311+OndrejSladky@users.noreply.github.com>
Date: Wed, 16 Oct 2024 06:03:57 +0200
Subject: [PATCH 14/16] Add FMSI (#51277)

* Initial version of adding FMSI to bioconda.

* Corrected LICENSE.

* FMSI recipe: do not build SDSL but have it as dependency.

* clean up recipe

* clean up recipe

* clean up recipe

* try patching makefile

* add patches section

* edit chmod command

* do not build on aarch64/arm64

* add D_LIBCPP_DISABLE_AVAILABILITY

* linux-aarch64 build

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/fmsi/0001-Makefile.patch | 29 +++++++++++++++++++
 recipes/fmsi/0002-version.patch  |  7 +++++
 recipes/fmsi/build.sh            | 20 +++++++++++++
 recipes/fmsi/meta.yaml           | 49 ++++++++++++++++++++++++++++++++
 4 files changed, 105 insertions(+)
 create mode 100644 recipes/fmsi/0001-Makefile.patch
 create mode 100644 recipes/fmsi/0002-version.patch
 create mode 100644 recipes/fmsi/build.sh
 create mode 100644 recipes/fmsi/meta.yaml

diff --git a/recipes/fmsi/0001-Makefile.patch b/recipes/fmsi/0001-Makefile.patch
new file mode 100644
index 00000000000000..517f6b2a3cc197
--- /dev/null
+++ b/recipes/fmsi/0001-Makefile.patch
@@ -0,0 +1,29 @@
+diff --git a/src/Makefile b/src/Makefile
+index 6272ad5..473407a 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,10 +1,10 @@
+ .PHONY: all clean 
+-CXX=									g++
+-CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O2
+-PROG=									../fmsi
+-INCLUDES-PATH?=.
++CXX=									${CXX}
++CXXFLAGS=							-g -Wall -Wno-unused-function -std=c++17 -O3
++PROG=									${PREFIX}/bin/fmsi
++INCLUDES-PATH?=							${PREFIX}
+ INCLUDES=							-I$(INCLUDES-PATH)/include -L$(INCLUDES-PATH)/lib 
+-LIBS=									-lz -lsdsl -ldivsufsort -ldivsufsort64
++LIBS+=									-lz -lsdsl -ldivsufsort -ldivsufsort64 -L${PREFIX}/lib
+ 
+ all:$(PROG)
+ 
+@@ -14,7 +14,7 @@ include/sdsl/suffix_arrays.hpp: sdsl-lite/build/Makefile
+ 	$(MAKE) -C sdsl-lite/build install
+ 
+ sdsl-lite/build/Makefile:
+-	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../.. ..
++	cd sdsl-lite/build && cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+ 
+ 
+ $(PROG): $(wildcard *.cpp *.c *.h) ./include/sdsl/suffix_arrays.hpp version.h
diff --git a/recipes/fmsi/0002-version.patch b/recipes/fmsi/0002-version.patch
new file mode 100644
index 00000000000000..dc566e265d15bf
--- /dev/null
+++ b/recipes/fmsi/0002-version.patch
@@ -0,0 +1,7 @@
+diff --git a/src/version b/src/version
+index ee1372d..abd4105 100644
+--- a/src/version
++++ b/src/version
+@@ -1 +1 @@
+-0.2.2
++${PKG_VERSION}
diff --git a/recipes/fmsi/build.sh b/recipes/fmsi/build.sh
new file mode 100644
index 00000000000000..aa6c47f645057e
--- /dev/null
+++ b/recipes/fmsi/build.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+mkdir -p ${PREFIX}/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+else
+	export CXXFLAGS="${CXXFLAGS}"
+fi
+
+make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \
+	CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \
+	-j"${CPU_COUNT}"
+
+chmod 0755 ${PREFIX}/bin/fmsi
diff --git a/recipes/fmsi/meta.yaml b/recipes/fmsi/meta.yaml
new file mode 100644
index 00000000000000..1229c7ea942d5d
--- /dev/null
+++ b/recipes/fmsi/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = "0.2.4" %}
+{% set sha256 = "67c930b8bad30e786fb7a59cc8592e1a7231024debc95af7e2c203bb7022b0b3" %}
+
+package:
+  name: fmsi
+  version: {{ version }}
+
+source:
+  url: https://github.com/OndrejSladky/fmsi/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    - 0001-Makefile.patch
+    - 0002-version.patch
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('fmsi', max_pin="x.x") }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - zlib
+    - sdsl-lite
+  run:
+    - sdsl-lite
+
+test:
+  commands:
+    - fmsi -h 2>&1 | grep "FMSI"
+
+about:
+  home: "https://github.com/OndrejSladky/fmsi"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform."
+  dev_url: "https://github.com/OndrejSladky/fmsi"
+  doc_url: "https://github.com/OndrejSladky/fmsi/blob/v{{ version }}/README.md"
+
+extra:
+  identifiers:
+    - doi:10.1101/2024.03.06.583483
+    - doi:10.1101/2023.02.01.526717
+  additional-platforms:
+    - linux-aarch64

From 3be7f86895cd263472864a52c076aa1f60eb97ab Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 15 Oct 2024 23:26:49 -0500
Subject: [PATCH 15/16] lofreq: add osx-arm64 build (#51417)

* lofreq: add osx-arm64 build

* add gsl

* add m4 build_prefix

* remove CPP variable

* add setuptools to host
---
 recipes/lofreq/0001-patches              | 260 +++++++++++++++++++++++
 recipes/lofreq/build.sh                  |  20 +-
 recipes/lofreq/build_failure.osx-64.yaml | 105 ---------
 recipes/lofreq/meta.yaml                 |  27 ++-
 4 files changed, 299 insertions(+), 113 deletions(-)
 create mode 100644 recipes/lofreq/0001-patches
 delete mode 100644 recipes/lofreq/build_failure.osx-64.yaml

diff --git a/recipes/lofreq/0001-patches b/recipes/lofreq/0001-patches
new file mode 100644
index 00000000000000..c711d24f51e118
--- /dev/null
+++ b/recipes/lofreq/0001-patches
@@ -0,0 +1,260 @@
+diff --git a/configure.ac b/configure.ac
+index ec939f5..13494a5 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -146,11 +146,12 @@ AX_PTHREAD([
+         AC_MSG_ERROR([No pthread support on this machine]))
+ #AX_PTHREAD()
+ 
+-
+-# explicit libm check
++# if any of these sit in unusual places use
++# export LDFLAGS="-L$path" before calling configure
+ AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm]))
+ AC_CHECK_LIB(z, gzread,, AC_MSG_ERROR([Could not find libz]))
+-
++AC_CHECK_LIB([gslcblas],[cblas_dgemm])
++AC_CHECK_LIB(gsl, gsl_cdf_poisson_P,, AC_MSG_WARN([libgsl not found. Not using fast approximation]))
+ 
+ # http://www.gnu.org/software/automake/manual/html_node/Python.html
+ AM_PATH_PYTHON([2.7])
+diff --git a/src/lofreq/Makefile.am b/src/lofreq/Makefile.am
+index 102076b..b7c71cf 100644
+--- a/src/lofreq/Makefile.am
++++ b/src/lofreq/Makefile.am
+@@ -1,4 +1,4 @@
+-AM_CFLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../cdflib90/ -I../uthash $(HTSLIB_CPPFLAGS) @AM_CFLAGS@
++AM_CFLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -O3 -I../cdflib90/ -I../uthash $(HTSLIB_CPPFLAGS) @AM_CFLAGS@
+ AM_LDFLAGS = $(LDFLAGS_for_htslib) @AM_LDFLAGS@
+ bin_PROGRAMS = lofreq
+ lofreq_SOURCES = bam_md_ext.c bam_md_ext.h \
+@@ -42,3 +42,4 @@ endif
+ 
+ # note: order matters
+ lofreq_LDADD = $(LIBS_for_htslib) ../cdflib90/libcdf.a
++# -l:libgsl.a -lm
+diff --git a/src/lofreq/lofreq_call.c b/src/lofreq/lofreq_call.c
+index 6537a11..81c0c7b 100644
+--- a/src/lofreq/lofreq_call.c
++++ b/src/lofreq/lofreq_call.c
+@@ -315,7 +315,7 @@ call_alt_ins(const plp_col_t *p, double *bi_err_probs, int bi_num_err_probs,
+                bi_num_err_probs, ins_counts[0], ins_counts[1], ins_counts[2]);
+      // compute p-value for insertion
+      if (snpcaller(bi_pvalues, bi_err_probs, bi_num_err_probs, ins_counts,
+-                   conf->bonf_indel, conf->sig)) {
++                   conf->bonf_indel, conf->sig, conf->approx_threshold_n)) {
+           fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                   __FILE__, __FUNCTION__, __LINE__);
+           return 1;
+@@ -380,7 +380,7 @@ int call_alt_del(const plp_col_t *p, double *bd_err_probs, int bd_num_err_probs,
+ 
+      /* snpcaller for deletion */
+      if (snpcaller(bd_pvalues, bd_err_probs, bd_num_err_probs, del_counts,
+-                   conf->bonf_indel, conf->sig)) {
++                   conf->bonf_indel, conf->sig, conf->approx_threshold_n)) {
+           fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                   __FILE__, __FUNCTION__, __LINE__);
+           return 1;
+@@ -803,7 +803,7 @@ call_snvs(const plp_col_t *p, varcall_conf_t *conf)
+                 bc_num_err_probs, alt_counts[0], alt_counts[1], alt_counts[2], num_snv_tests, conf->bonf_subst, conf->sig);
+ 
+       if (snpcaller(pvalues, bc_err_probs, bc_num_err_probs,
+-                   alt_counts, conf->bonf_subst, conf->sig)) {
++                   alt_counts, conf->bonf_subst, conf->sig, conf->approx_threshold_n)) {
+            fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                    __FILE__, __FUNCTION__, __LINE__);
+            free(bc_err_probs);
+@@ -986,6 +986,7 @@ usage(const mplp_conf_t *mplp_conf, const varcall_conf_t *varcall_conf)
+      fprintf(stderr, "       -C | --min-cov INT           Test only positions having at least this coverage [%d]\n", varcall_conf->min_cov);
+      fprintf(stderr, "                                    (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)\n");
+      fprintf(stderr, "       -d | --max-depth INT         Cap coverage at this depth [%d]\n", mplp_conf->max_depth);
++     fprintf(stderr, "       -t | --approx-threshold INT  Use fast approximation at this depth (might decrease number of calls; off if <= 0) [%d]\n", varcall_conf->approx_threshold_n);
+      fprintf(stderr, "            --illumina-1.3          Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded\n");
+      fprintf(stderr, "            --use-orphan            Count anomalous read pairs (i.e. where mate is not aligned properly)\n");
+      fprintf(stderr, "            --plp-summary-only      No variant calling. Just output pileup summary per column\n");
+@@ -1094,6 +1095,7 @@ for cov in coverage_range:
+ 
+               {"min-cov", required_argument, NULL, 'C'},
+               {"max-depth", required_argument, NULL, 'd'},
++              {"approx-threshold", required_argument, NULL, 't'},
+ 
+               {"illumina-1.3", no_argument, &illumina_1_3, 1},
+               {"use-orphan", no_argument, &use_orphan, 1},
+@@ -1272,6 +1274,10 @@ for cov in coverage_range:
+               mplp_conf.max_depth = atoi(optarg);
+               break;
+ 
++         case 't':
++              varcall_conf.approx_threshold_n = atoi(optarg);
++              break;
++
+          case 'h':
+               usage(& mplp_conf, & varcall_conf);
+               return 0; /* WARN: not printing defaults if some args where parsed */
+diff --git a/src/lofreq/lofreq_uniq.c b/src/lofreq/lofreq_uniq.c
+index 53ad137..af03fe4 100644
+--- a/src/lofreq/lofreq_uniq.c
++++ b/src/lofreq/lofreq_uniq.c
+@@ -309,7 +309,7 @@ uniq_snv(const plp_col_t *p, void *confp)
+           alt_counts[1] = alt_counts[2] = 0;
+ 
+           if (snpcaller(pvalues, err_probs, num_err_probs,
+-                        alt_counts, bonf, alpha)) {
++                        alt_counts, bonf, alpha, -1)) {
+                fprintf(stderr, "FATAL: snpcaller() failed at %s:%s():%d\n",
+                        __FILE__, __FUNCTION__, __LINE__);
+                free(err_probs);
+diff --git a/src/lofreq/plp.c b/src/lofreq/plp.c
+index 808d791..2336445 100644
+--- a/src/lofreq/plp.c
++++ b/src/lofreq/plp.c
+@@ -816,7 +816,11 @@ void compile_plp_col(plp_col_t *plp_col,
+       * n_plp[i] - m
+       */
+      ref_base = (ref && pos < ref_len)? ref[pos] : 'N';
+-
++     /* Added by Ryan Morin in an attempt to mitigate issues with non-ACTG characters in the reference
++     An example position (hg38) affected by this is chr17   83129591  (the reference base is W) */
++     if (! (ref_base == 'A' || ref_base == 'C' || ref_base == 'T' || ref_base == 'G' || ref_base == 'N')){
++          ref_base = 'N';
++     }
+      plp_col_init(plp_col);
+      plp_col->target = strdup(target_name);
+      plp_col->pos = pos;
+@@ -1276,8 +1280,8 @@ check_indel:
+ 
+      for (i = 0; i < NUM_NT4; ++i) {
+           assert(plp_col->fw_counts[i] + plp_col->rv_counts[i] == plp_col->base_quals[i].n);
+-          assert(plp_col->base_quals[i].n == plp_col->baq_quals[i].n);
+-          assert(plp_col->base_quals[i].n == plp_col->map_quals[i].n);
++          /* FIXME only makes sense if BAQ is on assert(plp_col->base_quals[i].n == plp_col->baq_quals[i].n); */
++          /* FIXME only makes sense if MQ is on assert(plp_col->base_quals[i].n == plp_col->map_quals[i].n); */
+           /* assert(plp_col->map_quals[i].n == plp_col->source_quals[i].n);*/
+      }
+ }
+diff --git a/src/lofreq/snpcaller.c b/src/lofreq/snpcaller.c
+index 253430c..f3a8e44 100644
+--- a/src/lofreq/snpcaller.c
++++ b/src/lofreq/snpcaller.c
+@@ -43,6 +43,8 @@
+ #include "fet.h"
+ #include "utils.h"
+ #include "log.h"
++#include "gsl/gsl_randist.h"
++#include "gsl/gsl_cdf.h"
+ 
+ #include "snpcaller.h"
+ #if TIMING
+@@ -635,6 +637,7 @@ init_varcall_conf(varcall_conf_t *c)
+      c->flag |= VARCALL_USE_IDAQ;
+      c->only_indels = 0;
+      c->no_indels = 0;
++     c->approx_threshold_n = -1;
+ }
+ 
+ 
+@@ -1062,7 +1065,8 @@ int
+ snpcaller(long double *snp_pvalues,
+           const double *err_probs, const int num_err_probs,
+           const int *noncons_counts,
+-          const long long int bonf_factor, const double sig_level)
++          const long long int bonf_factor, const double sig_level,
++          const int approx_threshold_n)
+ {
+     double *probvec = NULL;
+     int i;
+@@ -1100,6 +1104,33 @@ snpcaller(long double *snp_pvalues,
+         goto free_and_exit;
+     }
+ 
++/* how to combine ifndef? */
++#ifndef HAVE_LIBGSL
++#ifndef HAVE_LIBGSLCBLAS
++     if (approx_threshold_n>0) {
++          LOG_FATAL("%s\n", "Can't use approximation. It was disabled during compile time");
++          exit(1);
++     }
++#endif
++#endif
++
++/* how to combine ifdef? */
++#ifdef HAVE_LIBGSL
++     #ifdef HAVE_LIBGSLCBLAS
++     /* Only approximate if sufficient data available */
++     if (approx_threshold_n > 0 && num_err_probs > approx_threshold_n) {
++          long double mu = 0;
++          for (int i = 0; i < num_err_probs; ++i) {
++               mu += err_probs[i];
++          }
++          const long double poibin_approximation = 1 - gsl_cdf_poisson_P(max_noncons_count - 1, mu);
++          if (poibin_approximation * (double)bonf_factor > sig_level) {
++               goto free_and_exit;
++          }
++     }
++     #endif
++#endif
++
+     probvec = poissbin(&pvalue, err_probs, num_err_probs,
+                        max_noncons_count, bonf_factor, sig_level);
+ 
+@@ -1120,7 +1151,6 @@ snpcaller(long double *snp_pvalues,
+         goto free_and_exit;
+     }
+ 
+-
+     /* report p-value for each non-consensus base
+      */
+     for (i=0; i<NUM_NONCONS_BASES; i++) {
+diff --git a/src/lofreq/snpcaller.h b/src/lofreq/snpcaller.h
+index 117505c..6822044 100644
+--- a/src/lofreq/snpcaller.h
++++ b/src/lofreq/snpcaller.h
+@@ -59,6 +59,7 @@ typedef struct {
+      int only_indels; 
+      int no_indels; 
+ 
++     int approx_threshold_n; /* when to use fast poisson binomial approximation for early exit */
+ } varcall_conf_t;
+ 
+ 
+@@ -97,7 +98,8 @@ extern int
+ snpcaller(long double *snp_pvalues, const double *err_probs,
+           const int num_err_probs, const int *noncons_counts,
+           const long long int bonf_factor,
+-          const double sig_level);
++          const double sig_level,
++          const int approx_treshold_n);
+ 
+ 
+ #endif
+diff --git a/src/scripts/lofreq2_call_pparallel.py b/src/scripts/lofreq2_call_pparallel.py
+index fc3e82c..64dd3c1 100755
+--- a/src/scripts/lofreq2_call_pparallel.py
++++ b/src/scripts/lofreq2_call_pparallel.py
+@@ -166,16 +166,23 @@ def concat_vcf_files(vcf_files, vcf_out, source=None):
+     """
+ 
+     assert not os.path.exists(vcf_out)
+-
+-    cmd = ['lofreq', 'vcfset', '-a', 'concat', '-o', vcf_out, '-1']
++    #I didn't address the FIXME issue noted above but another bug was fixed here.
++    #This now uses bcftools to overcome systematic failures of merging with certain data sets due to multi-allelic variants
++    cmd = ['bcftools', 'concat', '-a', '-O', 'z', '-o', vcf_out]
+     cmd.extend(vcf_files)
++    idx = ['bcftools','index','-t', vcf_out]
+     try:
+         subprocess.check_call(cmd)
+     except subprocess.CalledProcessError as e:
+         LOG.fatal("The following command failed with return code %d: %s" % (
+             e.returncode, ' '.join(cmd)))
+         sys.exit(1)
+-
++    try:
++        subprocess.check_call(idx)
++    except subprocess.CalledProcessError as e:
++        LOG.fatal("The following command failed with return code %d: %s" % (
++            e.returncode, ' '.join(cmd)))
++        sys.exit(1)
+ 
+ def sq_list_from_bam_samtools(bam):
+     """Extract SQs listed in BAM head using samtools
diff --git a/recipes/lofreq/build.sh b/recipes/lofreq/build.sh
index d349a75b80adb6..8c72001e8eb358 100644
--- a/recipes/lofreq/build.sh
+++ b/recipes/lofreq/build.sh
@@ -1,6 +1,22 @@
 #!/bin/bash
 set -eu -o pipefail
 
-./configure --with-htslib=system --prefix=${PREFIX}
-make -j ${CPU_COUNT}
+export M4="${BUILD_PREFIX}/bin/m4"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
+
+if [[ "$(uname)" == Darwin ]]; then
+	export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
+fi
+
+autoreconf -if
+./configure --with-htslib=system --prefix="${PREFIX}" \
+	CC="${CC}" CFLAGS="${CFLAGS}" \
+	LDFLAGS="${LDFLAGS}" \
+	CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" \
+	PYTHON="${PYTHON}"
+
+make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/lofreq/build_failure.osx-64.yaml b/recipes/lofreq/build_failure.osx-64.yaml
deleted file mode 100644
index f9584cf07d81ef..00000000000000
--- a/recipes/lofreq/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: 4cf287f5a7c455a055c0d13140b029f5521f83c577150eb646297dd597f8e2c7  # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: test failure
-log: |-
-  running install_egg_info
-  Writing $PREFIX/lib/python3.9/site-packages/LoFreq_Star-2.1.5-py3.9.egg-info
-  make[3]: Leaving directory '$SRC_DIR/src/tools'
-  make[2]: Nothing to be done for 'install-data-am'.
-  make[2]: Leaving directory '$SRC_DIR/src/tools'
-  make[1]: Leaving directory '$SRC_DIR/src/tools'
-  make[1]: Entering directory '$SRC_DIR'
-  make[2]: Entering directory '$SRC_DIR'
-  make[2]: Nothing to be done for 'install-exec-am'.
-  make[2]: Nothing to be done for 'install-data-am'.
-  make[2]: Leaving directory '$SRC_DIR'
-  make[1]: Leaving directory '$SRC_DIR'
-
-  Resource usage statistics from building lofreq:
-     Process count: 8
-     CPU time: Sys=0:00:00.3, User=0:00:00.6
-     Memory: 99.9M
-     Disk usage: 8.0K
-     Time elapsed: 0:00:14.7
-
-
-  Packaging lofreq
-  Packaging lofreq-2.1.5-py39h8037bd6_12
-
-
-  WARNING: Importing conda-verify failed.  Please be sure to test your packages.  conda install conda-verify to make this message go away.
-  compiling .pyc files...
-  number of files: 10
-     INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']'
-     INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']'
-     INFO: sysroot: '/opt/X11/' files: '[]'
-     INFO (lofreq,bin/lofreq): Needed DSO lib/libhts.3.dylib found in bioconda/osx-64::htslib==1.20=hec81eee_1
-     INFO (lofreq,bin/lofreq): Needed DSO lib/libz.1.dylib found in conda-forge/osx-64::libzlib==1.2.13=h87427d6_6
-     INFO (lofreq,bin/lofreq): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
-     INFO (lofreq): Interpreted package 'lofreq' is interpreted by 'python'
-  Fixing permissions
-  INFO :: Time taken to mark (prefix)
-          0 replacements in 0 files was 0.04 seconds
-  Files containing CONDA_PREFIX
-  -----------------------------
-  bin/lofreq2_indel_ovlp.py (text): Patching
-  bin/lofreq2_vcfplot.py (text): Patching
-  TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/lofreq-2.1.5-py39h8037bd6_12.tar.bz2
-  Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work' to '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work_moved_lofreq-2.1.5-py39h8037bd6_12_osx-64'
-  shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/work_moved_lofreq-2.1.5-py39h8037bd6_12_osx-64)
-  Reloading output folder (local): ...working... done
-  Solving environment (_test_env): ...working... done
-
-  ## Package Plan ##
-
-    environment location: /opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
-
-
-  The following NEW packages will be INSTALLED:
-
-      bzip2:           1.0.8-h10d778d_5          conda-forge
-      c-ares:          1.28.1-h10d778d_0         conda-forge
-      ca-certificates: 2024.6.2-h8857fd0_0       conda-forge
-      curl:            8.8.0-hea67d85_0          conda-forge
-      htslib:          1.20-hec81eee_1           bioconda
-      krb5:            1.21.2-hb884880_0         conda-forge
-      libcurl:         8.8.0-hf9fcc65_0          conda-forge
-      libcxx:          17.0.6-h88467a6_0         conda-forge
-      libdeflate:      1.20-h49d49c5_0           conda-forge
-      libedit:         3.1.20191231-h0678c8f_2   conda-forge
-      libev:           4.33-h10d778d_2           conda-forge
-      libffi:          3.4.2-h0d85af4_5          conda-forge
-      libnghttp2:      1.58.0-h64cf6d3_1         conda-forge
-      libsqlite:       3.46.0-h1b8f9f3_0         conda-forge
-      libssh2:         1.11.0-hd019ec5_0         conda-forge
-      libzlib:         1.3.1-h87427d6_1          conda-forge
-      lofreq:          2.1.5-py39h8037bd6_12     local
-      ncurses:         6.5-h5846eda_0            conda-forge
-      openssl:         3.3.1-h87427d6_0          conda-forge
-      python:          3.9.19-h7a9c478_0_cpython conda-forge
-      python_abi:      3.9-4_cp39                conda-forge
-      readline:        8.2-h9e318b2_1            conda-forge
-      samtools:        1.5-1                     bioconda
-      tk:              8.6.13-h1abcd95_1         conda-forge
-      tzdata:          2024a-h0c530f3_0          conda-forge
-      xz:              5.2.6-h775f41a_0          conda-forge
-      zlib:            1.3.1-h87427d6_1          conda-forge
-      zstd:            1.5.6-h915ae27_0          conda-forge
-
-  Preparing transaction: ...working... done
-  Verifying transaction: ...working... done
-  Executing transaction: ...working... done
-   lofreq version
-   samtools --help
-  dyld[51805]: Library not loaded: @rpath/libcrypto.1.0.0.dylib
-    Referenced from: <8AD915FB-8A79-34FD-9167-D77089463421> /opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/samtools
-    Reason: tried: '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/../lib/libcrypto.1.0.0.dylib' (no such file), '/usr/local/lib/libcrypto.1.0.0.dylib' (no such file), '/usr/lib/libcrypto.1.0.0.dylib' (no such file, not in dyld cache)
-  /opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/test_tmp/run_test.sh: line 8: 51805 Abort trap: 6           samtools --help
-  WARNING: Tests failed for lofreq-2.1.5-py39h8037bd6_12.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
-  TESTS FAILED: lofreq-2.1.5-py39h8037bd6_12.tar.bz2
-  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
-  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/lofreq_1718124617511/test_tmp
-  version: 2.1.5
-  commit: unknown
-  build-date: Jun 11 2024
-# Last 100 lines of the build log.
diff --git a/recipes/lofreq/meta.yaml b/recipes/lofreq/meta.yaml
index 4dc0e346faf575..0d1ccfe2d70067 100644
--- a/recipes/lofreq/meta.yaml
+++ b/recipes/lofreq/meta.yaml
@@ -1,15 +1,17 @@
-{% set version="2.1.5" %}
+{% set version = "2.1.5" %}
 
 package:
   name: lofreq
   version: {{ version }}
 
 source:
-  url: https://raw.githubusercontent.com/CSB5/lofreq/v{{ version }}/dist/lofreq_star-{{ version }}.tar.gz
-  sha256: 43028af07faa23c7ec0e167855492ae7bd31c4e7f8158114e51ec12aba5fd184
+  url: https://github.com/CSB5/lofreq/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: da85ec4baca21e20a55b5f9ee491cdda2986d0dc672177007a2c70ca1d804fe7
+  patches:
+    - 0001-patches
 
 build:
-  number: 12
+  number: 13
   run_exports:
     - {{ pin_subpackage('lofreq', max_pin='x') }}
 
@@ -17,13 +19,20 @@ requirements:
   build:
     - make
     - {{ compiler('c') }}
+    - autoconf
+    - automake
+    - libtool
   host:
     - python
+    - setuptools  # [py >= 3.12]
     - htslib
+    - samtools
+    - gsl
     - zlib
   run:
     - python
     - samtools
+    - gsl
 
 test:
   commands:
@@ -31,12 +40,18 @@ test:
     - samtools --help
 
 about:
-  home: http://csb5.github.io/lofreq/
+  home: "https://csb5.github.io/lofreq"
   license: MIT
-  summary: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
+  license_family: MIT
+  license_file: LICENSE
+  summary: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data."
+  dev_url: "https://github.com/CSB5/lofreq"
+  doc_url: "https://csb5.github.io/lofreq"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - usegalaxy-eu:lofreq_call
+    - biotools:lofreq

From c5610fa729c2a77291f7abc0885a455dcdd7fad5 Mon Sep 17 00:00:00 2001
From: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com>
Date: Wed, 16 Oct 2024 12:27:04 +0800
Subject: [PATCH 16/16] Xiangyang1984 patch 20 (#51418)

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml
---
 recipes/pneumo-typer/meta.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml
index 815d6fcdac78e6..c397df4f393e89 100644
--- a/recipes/pneumo-typer/meta.yaml
+++ b/recipes/pneumo-typer/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "pneumo-typer" %}
-{% set version = "1.0.2" %}
+{% set version = "1.0.3" %}
 
-{% set sha256 = "755584efcb967c3afe260650af905123f81e192707ee8078ed9d1db22bbfad41" %}
+{% set sha256 = "2e9c4d071a5415281b4cafbdc86ad960e8c0805fa4469a350986109c6457d12e" %}
 
 package:
   name: "{{ name|lower }}"
@@ -12,7 +12,7 @@ source:
     sha256: {{ sha256 }}
     
 build:
-  number: 1
+  number: 0
   noarch: generic
   run_exports:
     - {{ pin_subpackage('pneumo-typer', max_pin="x") }}
@@ -22,9 +22,9 @@ requirements:
   
   run:
     - blast
-    - perl-gd
+    - perl-gd >=2.74
     - perl-gd-svg
-    - perl-svg
+    - perl-svg >=2.87
     - perl-bioperl-core
     - prodigal
     - blat