From 8cc87962c264b0f4d92252cb2c4c3b8e597bfd4f Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 10:10:15 -0400
Subject: [PATCH 01/65] Update ncbi-stxtyper to 1.0.27 (#51808)

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

diff --git a/recipes/ncbi-stxtyper/meta.yaml b/recipes/ncbi-stxtyper/meta.yaml
index df64553ebb334..875aafe2edabe 100644
--- a/recipes/ncbi-stxtyper/meta.yaml
+++ b/recipes/ncbi-stxtyper/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.25" %}
-{% set sha256 = "adc734340c6a10f1bfc34ca637197e93e1515d0231bd023b33ce4c07aab9578e" %}
+{% set version = "1.0.27" %}
+{% set sha256 = "07966b8c6aa909bb1201c098d3c72eaf067e7b11de1a2ab0f89fb2cf52820382" %}
 
 package:
   name: ncbi-stxtyper

From 5f76a4493aa7b35de83e346a99bc4008b808caa7 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 12:14:11 -0400
Subject: [PATCH 02/65] Update piscem to 0.10.4 (#51799)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update piscem to 0.10.4

* Update build.sh

* Update build.sh

try to fix too-old SDK on OSX x86

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Rob Patro <rob-p@users.noreply.github.com>
---
 recipes/piscem/build.sh  | 6 ++++++
 recipes/piscem/meta.yaml | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/recipes/piscem/build.sh b/recipes/piscem/build.sh
index 482a75a82dec1..b2d78efc2f3e2 100644
--- a/recipes/piscem/build.sh
+++ b/recipes/piscem/build.sh
@@ -4,7 +4,13 @@ unamestr=`uname`
 
 if [ "$unamestr" == 'Darwin' ];
 then
+  if [[ $(uname -m) == 'x86_64' ]]; then
+    echo "OSX x86-64: attempting to fix broken (old) SDK behavior"
+    export CFLAGS="${CFLAGS} -D_LIBCPP_HAS_NO_C11_ALIGNED_ALLOC"
+    export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_HAS_NO_C11_ALIGNED_ALLOC"
+  fi
   export MACOSX_DEPLOYMENT_TARGET=10.15
+  export MACOSX_SDK_VERSION=10.15
   export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
   export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
 else 
diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml
index 0c261497c9b1d..ce3baa0e0adef 100644
--- a/recipes/piscem/meta.yaml
+++ b/recipes/piscem/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.10.3" %}
+{% set version = "0.10.4" %}
 {% set name = "piscem" %}
-{% set sha256 = "5bb7d856e28f7090456bbc9aa81120169cff76b66c47a642916d8d53e35bec8a" %}
+{% set sha256 = "665d3dc54bf4b9c50c02d190112177e270c1b992e61608f34c3e95b0e4a5b5d6" %}
 
 package:
   name: {{ name }}

From bc6caaeae153d9c111396e737c70613a6916d44e Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 13:11:01 -0400
Subject: [PATCH 03/65] Update r-mfassignr to 1.1.2 (#51813)

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

diff --git a/recipes/r-mfassignr/meta.yaml b/recipes/r-mfassignr/meta.yaml
index 421e7b81ce8ea..6787db1e2ee5f 100644
--- a/recipes/r-mfassignr/meta.yaml
+++ b/recipes/r-mfassignr/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mfassignr" %}
-{% set version = "1.1.1" %}
+{% set version = "1.1.2" %}
 {% set github = "https://github.com/RECETOX" %}
 
 package:
@@ -8,7 +8,7 @@ package:
 
 source:
   url: "{{ github }}/MFAssignR/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 11d0c871871e52010978df0273221f95ccd21e950585e19a63d8b40ea23aebcb
+  sha256: 99c15cbbb13609d8331e85cba5d3900f7d006dda9798aa778ea48a00436dd327
 
 build:
   number: 0

From 6be348a08da7b0db861ffbf37617743e09781ec8 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 13:11:16 -0400
Subject: [PATCH 04/65] Update r-recetox-aplcms to 0.13.4 (#51812)

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

diff --git a/recipes/r-recetox-aplcms/meta.yaml b/recipes/r-recetox-aplcms/meta.yaml
index f47239d4c8f56..81fdcd3fa1705 100644
--- a/recipes/r-recetox-aplcms/meta.yaml
+++ b/recipes/r-recetox-aplcms/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "recetox-aplcms" %}
-{% set version = "0.13.3" %}
+{% set version = "0.13.4" %}
 {% set github = "https://github.com/RECETOX/recetox-aplcms" %}
 
 package:
@@ -8,7 +8,7 @@ package:
 
 source:
   url: "https://github.com/RECETOX/recetox-aplcms/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 3b37e51e959cba7cab6691f66dd2bb8279c4112fc5155576e0efef4ded2ad10b
+  sha256: c6c08d7e0def2b4df9f5ae366e0f69bf982d271bb8a4aec165e66c373d45c791
 
 build:
   number: 0

From 466a31e69c5386ad70a26576c766996d06b835f0 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 13:11:25 -0400
Subject: [PATCH 05/65] Update ms2deepscore to 2.3.0 (#51804)

---
 recipes/ms2deepscore/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml
index 4aebeeddd48cc..055b6280d4790 100644
--- a/recipes/ms2deepscore/meta.yaml
+++ b/recipes/ms2deepscore/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2deepscore" %}
-{% set version = "2.2.0" %}
-{% set sha256 = "c4f6458b88cf8ea95e4ec4b7b7872d0f4dc9c9f7e8c5538c8ff2e59c78b8bb15" %}
+{% set version = "2.3.0" %}
+{% set sha256 = "fd62d373aa53944583bd7b0df324015198ea598a2def9cba9f13afd0acd09b18" %}
 
 package:
   name: {{ name|lower }}

From 0f72596b2d5b7d981eec6bdd1d5b81cd4b020039 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 13:11:38 -0400
Subject: [PATCH 06/65] Update scirpy to 0.19.0 (#51803)

* Update scirpy to 0.19.0

* Update meta.yaml

---------

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
---
 recipes/scirpy/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml
index 8fe28e48762f4..59ce888960c89 100644
--- a/recipes/scirpy/meta.yaml
+++ b/recipes/scirpy/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "scirpy" %}
-{% set version = "0.18.0" %}
+{% set version = "0.19.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 7d8f5deb2f6d83aa6f719b051c2d7c8cd1fb27589b64796be4b1a64ec76a708e
+  sha256: 83bc3663e49d7f5ae26e1a54229085af4fcd103304842b23d0aaddae1796e9ba
   folder: "{{ name }}-{{ version }}"
 
 build:
@@ -26,7 +26,7 @@ requirements:
     - hatch-vcs
   run:
     - python >=3.10
-    - anndata >=0.9,<0.10.9
+    - anndata >=0.9
     - awkward >=2.1.0
     - mudata >=0.2.3
     - scanpy >=1.9.3

From 78b2100802f53e96428e22cdc94c85511fd44d7b Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Wed, 30 Oct 2024 12:38:15 -0500
Subject: [PATCH 07/65] Update Deepchopper (#51814)

* 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

* Update meta.yaml

* Update meta.yaml

---------

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/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/deepchopper/meta.yaml b/recipes/deepchopper/meta.yaml
index e8f25dfc9cf70..6a0403762b1d1 100644
--- a/recipes/deepchopper/meta.yaml
+++ b/recipes/deepchopper/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   skip: True  # [py < 310]
   run_exports:
     - {{ pin_subpackage("deepchopper", max_pin="x") }}
@@ -47,6 +47,7 @@ requirements:
     - hydra-core >=1.3.2
     - omegaconf >=2.3.0
     - python-multipart ==0.0.12
+    - deepchopper-cli >=1.2.5
 
 test:
   imports:

From 6f3c49b3d8d3e084a17b56b342a6092a684a7af2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 30 Oct 2024 15:46:06 -0400
Subject: [PATCH 08/65] Update gencove to 2.23.1 (#51819)

---
 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 113e485ce3f40..37526967d5d5d 100644
--- a/recipes/gencove/meta.yaml
+++ b/recipes/gencove/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.23.0" %}
-{% set sha256 = "edb1a4855f88d87c41902745d6f823142747005a29932700afcabc0c216f16e9" %}
+{% set version = "2.23.1" %}
+{% set sha256 = "11a63ea7c5ec624b896a32f7ca4ae42d1b9909cb87eb9f25ec3678e86a7ea2ad" %}
 
 package:
   name: {{ name }}

From 1a8efcf2ccc3669776fe8e0cd4a15287b9434a6b Mon Sep 17 00:00:00 2001
From: Moray Smith <65286772+SwiftSeal@users.noreply.github.com>
Date: Wed, 30 Oct 2024 19:58:36 +0000
Subject: [PATCH 09/65] Update meta.yaml (#51802)

* Update meta.yaml

* Bump build number
---
 recipes/resistify/meta.yaml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml
index cf013f7dc821b..47f4980eaa8d8 100644
--- a/recipes/resistify/meta.yaml
+++ b/recipes/resistify/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   entry_points:
     - resistify = resistify.main:main
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "
@@ -48,9 +48,11 @@ test:
 
 about:
   home: https://github.com/swiftseal/resistify
-  doc_url: "https://github.com/SwiftSeal/resistify/blob/main/README.md"
-  license: MIT
+  dev_url: https://github.com/SwiftSeal/resistify
+  doc_url: https://github.com/SwiftSeal/resistify/blob/main/README.md
+  license: GPL-3.0
   license_file: LICENSE
+  license_url: https://github.com/SwiftSeal/resistify/blob/main/LICENSE
   summary: A resistance gene annotation tool
   description: |
     Resistify is a nucleotide-binding leucine rich repeat (NLR) annotation

From 3e97b7485f1059a9b140cdbd1e52c99fbf1533b7 Mon Sep 17 00:00:00 2001
From: Friederike Hanssen <friederike.hanssen@seqera.io>
Date: Wed, 30 Oct 2024 22:04:55 +0100
Subject: [PATCH 10/65] Update Spring to support ARM (#51773)

* patch build.sh

* bump build number

* Update recipes/spring/build.sh

Drop newlines

* apply review comments

* add run_exports

* add linux-aarch64 build

---------

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/spring/Makefile.patch | 23 +++++++++++++++++++++++
 recipes/spring/build.sh       |  6 +++++-
 recipes/spring/meta.yaml      | 10 ++++++++--
 3 files changed, 36 insertions(+), 3 deletions(-)
 create mode 100644 recipes/spring/Makefile.patch

diff --git a/recipes/spring/Makefile.patch b/recipes/spring/Makefile.patch
new file mode 100644
index 0000000000000..68c4e799d9dd8
--- /dev/null
+++ b/recipes/spring/Makefile.patch
@@ -0,0 +1,23 @@
+diff --git a/src/libbsc/bsc.h b/src/libbsc/bsc.h
+index 25230dc..caca189 100644
+--- a/src/libbsc/bsc.h
++++ b/src/libbsc/bsc.h
+@@ -48,6 +48,7 @@ preprocessor macro LIBBSC_SORT_TRANSFORM_SUPPORT at compile time.
+ #ifndef SPRING_LIBBSC_BSC_H_
+ #define SPRING_LIBBSC_BSC_H_
+ 
++#include <cstdint>
+ #include "params.h"
+ 
+ namespace spring {
+diff --git a/src/util.h b/src/util.h
+index 30bad68..a72a0b6 100644
+--- a/src/util.h
++++ b/src/util.h
+@@ -17,6 +17,7 @@ limitations under the License.
+ 
+ #include <fstream>
+ #include <string>
++#include <cstdint>
+ 
+ namespace spring {
\ No newline at end of file
diff --git a/recipes/spring/build.sh b/recipes/spring/build.sh
index 08e68971964f4..684be7536d398 100644
--- a/recipes/spring/build.sh
+++ b/recipes/spring/build.sh
@@ -8,6 +8,10 @@ export CXXPATH=${PREFIX}/include
 export CFLAGS="$CFLAGS -I$PREFIX/include"
 export CXXFLAGS="$CFLAGS -I$PREFIX/include"
 export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
-cmake -Dspring_optimize_for_portability=ON ..
+if [ $(arch) == "aarch64" ]; then
+   cmake ..
+  else
+      cmake -Dspring_optimize_for_portability=ON ..
+fi
 make
 cp spring $PREFIX/bin
diff --git a/recipes/spring/meta.yaml b/recipes/spring/meta.yaml
index 3025d74de5bd1..8dac430b3ae51 100644
--- a/recipes/spring/meta.yaml
+++ b/recipes/spring/meta.yaml
@@ -5,8 +5,10 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
+  number: 3
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('spring', max_pin="x") }}
 
 source:
   url: https://github.com/shubhamchandak94/Spring/archive/v{{ version }}.tar.gz
@@ -26,5 +28,9 @@ about:
   home: https://github.com/shubhamchandak94/Spring
   license: Free for non-commercial use
   license_file: license.pdf
-  summary: Spring is a compression tool for Fastq files
+  summary: "Spring is a compression tool for Fastq files."
+  dev_url: https://github.com/shubhamchandak94/Spring
 
+extra:
+  additional-platforms:
+    - linux-aarch64

From 448de7c20215cd660bad38a2bd4313c9e1c148ee 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, 30 Oct 2024 22:05:06 +0100
Subject: [PATCH 11/65] Update FMSI to 0.3.1 (#51820)

* Update FMSI to 0.3.1

* Fixed hash.
---
 recipes/fmsi/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/fmsi/meta.yaml b/recipes/fmsi/meta.yaml
index 5db343b3713d3..a8ed730318cfc 100644
--- a/recipes/fmsi/meta.yaml
+++ b/recipes/fmsi/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.3.0" %}
-{% set sha256 = "441d9f5808c7568ae237b5bb45db9328185fee43628eb0a4407ae7da0bdcf3bc" %}
+{% set version = "0.3.1" %}
+{% set sha256 = "c36a21cf134e3aa6172898ebaa01319e2b00f496b1e5bfd81b624908173ba93f" %}
 
 package:
   name: fmsi

From 8024d7a6df7a19e304f23d6b6649c1d9df681298 Mon Sep 17 00:00:00 2001
From: Mary Maranga <38289520+Marysteph@users.noreply.github.com>
Date: Wed, 30 Oct 2024 21:06:22 +0000
Subject: [PATCH 12/65] Update kleborate v3 (#51807)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* update kleborate to version 3.0.5

* clean up recipe

* update-kleborate-v3

* update-kleborate-v3

* update-kleborate-v3

* update-kleborate-v3

* update-kleborate-v3

* update-kleborate-v3

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/kleborate/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/recipes/kleborate/meta.yaml b/recipes/kleborate/meta.yaml
index b1c2fad6fee70..371b9dae8b3b4 100644
--- a/recipes/kleborate/meta.yaml
+++ b/recipes/kleborate/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "kleborate" %}
-{% set version = "3.1.0" %}
+{% set version = "3.1.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kleborate-{{ version }}.tar.gz"
-  sha256: efb249d5b402502ae325d9b189c425464de930a0e455c5060d8aeea35dbbc920
+  sha256: c0a69dbb95bbf64f099cd98eb8ff853025e20f4718b75a4496426c8d0ac57760
 
 build:
   number: 0
@@ -23,6 +23,7 @@ requirements:
   host:
     - pip
     - python >=3.9
+    - setuptools
   run:
     - python >=3.9
     - biopython >=1.83

From 1023401199c1ed8ff31915a53ca17364d936ec66 Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Wed, 30 Oct 2024 22:01:55 +0000
Subject: [PATCH 13/65] Add Linux aarch64 to bioconductor-bambu (#51821)

---
 recipes/bioconductor-bambu/meta.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml
index 0a5192523653c..9eb6587182a64 100644
--- a/recipes/bioconductor-bambu/meta.yaml
+++ b/recipes/bioconductor-bambu/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 900e0e67c251f12989154113c54d2b32
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -74,3 +74,6 @@ about:
   description: 'bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.'
   license_file: LICENSE
 
+extra:
+  additional-platforms:
+    - linux-aarch64

From 8520449fec3e9ec3f59f41eb673f0bc3905f3534 Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Thu, 31 Oct 2024 04:40:48 +0000
Subject: [PATCH 14/65] Enable perl-list-moreutils-xs for linux-aarch64
 (#51816)

---
 recipes/perl-list-moreutils-xs/meta.yaml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/recipes/perl-list-moreutils-xs/meta.yaml b/recipes/perl-list-moreutils-xs/meta.yaml
index 4d35dd71519b8..4f65724892370 100644
--- a/recipes/perl-list-moreutils-xs/meta.yaml
+++ b/recipes/perl-list-moreutils-xs/meta.yaml
@@ -11,7 +11,8 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 3
+  run_exports: '{{ pin_subpackage(name,  max_pin="x.x") }}'
 
 requirements:
   build:
@@ -33,6 +34,10 @@ test:
   imports:
     - List::MoreUtils::XS
 
+extra:
+  additional-platforms:
+  - linux-aarch64
+    
 about:
   home: https://metacpan.org/release/List-MoreUtils-XS
   license: apache_2_0

From 724d13dd929e9eefd024acd9457672fdd2542f76 Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Thu, 31 Oct 2024 04:42:15 +0000
Subject: [PATCH 15/65] Add linux-aarch64 and osx-arm64 as targets for sgdemux
 (#51817)

---
 recipes/sgdemux/meta.yaml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/recipes/sgdemux/meta.yaml b/recipes/sgdemux/meta.yaml
index 6846b7a29256c..7f412931f8a6c 100644
--- a/recipes/sgdemux/meta.yaml
+++ b/recipes/sgdemux/meta.yaml
@@ -1,3 +1,4 @@
+{% set name = "sgdemux" %}
 {% set version = "1.2.0" %}
 
 package:
@@ -5,8 +6,9 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
-
+  number: 3
+  run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}'
+  
 source:
   url: https://github.com/Singular-Genomics/singular-demux/archive/refs/tags/v{{ version }}.tar.gz
   sha256: aa7b61b04e40bdd0dba91cfa57874203745506521e17139bbcfa4d36a5811dc5
@@ -35,3 +37,6 @@ about:
 extra:
   recipe-maintainers:
     - nh13
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

From 23a484e0d2cbb8da5ccd7d7a5caa57f2e25e3517 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 00:44:32 -0400
Subject: [PATCH 16/65] Update aletsch to 1.1.3 (#51828)

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

diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml
index d877735467abd..036c9fa58682e 100644
--- a/recipes/aletsch/meta.yaml
+++ b/recipes/aletsch/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "aletsch" %}
-{% set version = "1.1.2" %}
+{% set version = "1.1.3" %}
 
 package:
   name: "{{ name }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz"
-  sha256: "b081cfcbd2f232dcddab4f9c6ce11f15f41e4319e1f977dd955cca240748d4b5"
+  sha256: "74e1b7e2ff2cb065d02f1e0d45d7e87ae332ccfcef86b6a32af88b2a7005c9f7"
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('aletsch', max_pin="x") }}
 

From 0942664264535c937f661f70ddfb3f121809aebc Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 31 Oct 2024 10:11:52 +0100
Subject: [PATCH 17/65] update gcnvkernel to v 0.9 (#51834)

* update gcnvkernel

* linting

* fix typo

* apply suggestion from error message
---
 recipes/gcnvkernel/meta.yaml | 67 ++++++++++++++++++------------------
 1 file changed, 33 insertions(+), 34 deletions(-)

diff --git a/recipes/gcnvkernel/meta.yaml b/recipes/gcnvkernel/meta.yaml
index f8c6448ea98bb..d8488006c2f2f 100644
--- a/recipes/gcnvkernel/meta.yaml
+++ b/recipes/gcnvkernel/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "gcnvkernel" %}
-{% set version = "0.8" %}
-{% set gatk_version = "4.5.0.0" %}
-{% set gatk_sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %}
+{% set version = "0.9" %}
+{% set gatk_version = "4.6.1.0" %}
+{% set gatk_sha256 = "ac7015c3f0ef1852745ca0ef647adbf8ddef5db63ab485b00bc1ffe654814155" %}
 
 package:
   name: {{ name|lower }}
@@ -13,47 +13,46 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
+  preserve_egg_dir: true
   run_exports:
      - {{ pin_subpackage('gcnvkernel', max_pin="x") }}
 
 requirements:
   build:
-    - conda-forge::python =3.6.10
+    - conda-forge::python =3.10.13
     - unzip
   run:
     # The following are taken from the GATK python environment:
     #
     # https://github.com/broadinstitute/gatk/blob/master/scripts/gatkcondaenv.yml.template
-    - conda-forge::python =3.6.10
-    - pip =21.3.1
-    - conda-forge::mkl =2019.5
-    - conda-forge::mkl-service =2.3.0
-    - conda-forge::numpy =1.17.5
-    - conda-forge::theano =1.0.4
-    - tensorflow <2
-    - conda-forge::scipy =1.0.0
-    - conda-forge::pymc3 =3.1
-    - conda-forge::h5py =2.10.0 
-    - conda-forge::keras =2.2.4
-    - conda-forge::intel-openmp
-    - conda-forge::scikit-learn =0.23.1
-    - conda-forge::matplotlib =3.2.1
-    - conda-forge::pandas =1.0.3
-    - conda-forge::typing_extensions =4.1.1
-    - conda-forge::dill =0.3.4
-    - r-base =3.6.2
-    - r-data.table =1.12.8
-    - r-dplyr =0.8.5
-    - r-getopt =1.20.3
-    - r-ggplot2 =3.3.0
-    - r-gplots =3.0.3
-    - r-gsalib =2.1
-    - r-optparse =1.6.4
-    - r-backports =1.1.10
-    - biopython =1.76
-    - pyvcf =0.6.8
-    - bioconda::pysam =0.15.3
+    - conda-forge::python =3.10.13
+    - conda-forge::pip =23.3.1
+    - conda-forge:blas =1.0=mkl
+    - conda-forge::numpy =1.26.2
+    - conda-forge::pymc =5.10.1
+    - conda-forge::pytensor =2.18.3
+    - conda-forge::scipy =1.11.4
+    - conda-forge::h5py =3.10.0
+    - conda-forge::pytorch =2.1.0=*mkl*100
+    - conda-forge::pytorch-lightning =2.4.0
+    - conda-forge::scikit-learn =1.3.2
+    - conda-forge::matplotlib =3.8.2
+    - conda-forge::pandas =2.1.3
+    - conda-forge::tqdm =4.66.1
+    - conda-forge::dill =0.3.7
+    - conda-forge::biopython =1.84
+    - r-base =4.3.1
+    - r-data.table =1.14.8
+    - r-dplyr =1.1.3
+    - r-getopt =1.20.4
+    - r-ggplot2 =3.4.4
+    - r-gplots =3.1.3
+    - r-gsalib =2.2.1
+    - r-optparse =1.7.3
+    - r-backports =1.4.1
+    - bioconda::pysam =0.22.0
+    - conda-forge::pyvcf =0.6.8
 
 test:
   imports:

From 2d8229527a9a5547ce56dd9e2867f17c7c3294e2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 05:49:21 -0400
Subject: [PATCH 18/65] Update gatk4 to 4.6.1.0 (#48815)

* Update gatk4 to 4.6.0.0

* Update gatk4 to 4.6.1.0

* bump dependencies

---------

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 recipes/gatk4/meta.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml
index f588a9884779c..18eb0e910083e 100644
--- a/recipes/gatk4/meta.yaml
+++ b/recipes/gatk4/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "GATK4" %}
-{% set version = "4.5.0.0" %}
-{% set sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %}
+{% set version = "4.6.1.0" %}
+{% set sha256 = "ac7015c3f0ef1852745ca0ef647adbf8ddef5db63ab485b00bc1ffe654814155" %}
 
 package:
   name: {{ name|lower }}
@@ -18,21 +18,21 @@ build:
 
 requirements:
   host:
-    - r-base =3.6
+    - r-base =4.3.1
     - r-gplots
     - r-ggplot2
     - r-gsalib
     - r-reshape
-    - gcnvkernel =0.8
+    - gcnvkernel =0.9
   run:
     - openjdk >=17,<18
     - python
-    - r-base =3.6
+    - r-base =4.3.1
     - r-gplots
     - r-ggplot2
     - r-gsalib
     - r-reshape
-    - gcnvkernel =0.8
+    - gcnvkernel =0.9
 
 test:
   commands:

From 0c5f7a2c6ac547c072893a8aaee693e37c15d1ca Mon Sep 17 00:00:00 2001
From: Jessica Mattick <19544292+jmattick@users.noreply.github.com>
Date: Thu, 31 Oct 2024 05:21:17 -0500
Subject: [PATCH 19/65] Update pbjasmine to 2.4.0 (#51818)

---
 recipes/pbjasmine/build.sh  |  6 +++---
 recipes/pbjasmine/meta.yaml | 12 +++++++++---
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/recipes/pbjasmine/build.sh b/recipes/pbjasmine/build.sh
index 6b3a4f5a12308..1a89008b66dab 100644
--- a/recipes/pbjasmine/build.sh
+++ b/recipes/pbjasmine/build.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
 
-mkdir -p "${PREFIX}"/bin
-cp jasmine "${PREFIX}"/bin/
-chmod +x "${PREFIX}"/bin/jasmine
+mkdir -p "${PREFIX}/"{bin,lib}
+cp bin/* "${PREFIX}/bin"
+cp lib/* "${PREFIX}/lib"
diff --git a/recipes/pbjasmine/meta.yaml b/recipes/pbjasmine/meta.yaml
index b78cf8d9ba46b..e73d1f40afbb0 100644
--- a/recipes/pbjasmine/meta.yaml
+++ b/recipes/pbjasmine/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pbjasmine" %}
-{% set version = "2.0.0" %}
-{% set sha256 = "7a93e2b3932ed4701ae437f69a9c82b00b6b0718998ba2b137e0b06df0272e1c" %}
+{% set version = "2.4.0" %}
+{% set sha256 = "c987777320b8ef5ff838a9a893b3baf0de5aaa58fbcf9a25e6ec7b4ad0b88231" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://github.com/PacificBiosciences/jasmine/releases/download/v{{ version }}/jasmine
+  url: https://github.com/PacificBiosciences/jasmine/releases/download/v{{ version }}/jasmine.tar.xz
   sha256: {{ sha256 }}
 
 about:
@@ -26,6 +26,12 @@ extra:
 build:
   number: 0
   skip: True  # [osx]
+  binary_relocation: False
+  run_exports:
+    - {{ pin_subpackage('pbjasmine', max_pin='x.x') }}
+requirements:
+  build:
+    - {{ compiler('cxx') }}
 
 test:
   commands:

From 3a52d6744ff42765c17b87a0481423d68cca99e2 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:04:34 +0100
Subject: [PATCH 20/65] change python version (#51790)

---
 recipes/cell2cell/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/cell2cell/meta.yaml b/recipes/cell2cell/meta.yaml
index 0db26e51ae700..5e01f81b216ed 100644
--- a/recipes/cell2cell/meta.yaml
+++ b/recipes/cell2cell/meta.yaml
@@ -11,7 +11,7 @@ source:
 
 build:
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("cell2cell", max_pin="x.x.x") }}
 
@@ -20,11 +20,11 @@ requirements:
     - {{ compiler("cxx") }}
 
   host:
-    - python <=3.8
+    - python <=3.9
     - cython
     - pip
   run:
-    - python <=3.8
+    - python <=3.9
     - numpy >=1.16,<2.0
     - pandas >=1.0.0
     - xlrd >=1.1

From 9df90ee0632f35e6296414ce5a224aa471787410 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:40:35 -0400
Subject: [PATCH 21/65] Update pathogen-profiler to 4.5.0 (#51840)

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

diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml
index db629d9a89746..0b9f275252bb4 100644
--- a/recipes/pathogen-profiler/meta.yaml
+++ b/recipes/pathogen-profiler/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pathogen-profiler" %}
-{% set version = "4.4.0" %}
-{% set sha256 = "42a82777c01f26f1a5c85185960873e173329f9f84e081a1eef0fe66ac940f2e" %}
+{% set version = "4.5.0" %}
+{% set sha256 = "55b23983ebd1a4de0e9fd9805a0a3a839fdfc89e61f5605bb58a5966b737349c" %}
 
 package:
   name: {{name}}

From 5048dcec92a7b3f8c4c750a37fde8d68ade5dc4e Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:12:30 +0100
Subject: [PATCH 22/65] Add Liana+ to biocodna (#51736)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* meta.yaml created by grayskul

* add run_exports

* Update recipes/liana/meta.yaml

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

* update meta

* Update meta.yaml

* Update meta.yaml

---------

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

diff --git a/recipes/liana/meta.yaml b/recipes/liana/meta.yaml
new file mode 100644
index 0000000000000..0b735c8ee063e
--- /dev/null
+++ b/recipes/liana/meta.yaml
@@ -0,0 +1,62 @@
+{% set name = "liana" %}
+{% set version = "1.4.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/liana-{{ version }}.tar.gz
+  sha256: 1172a9bef67ee22d5eb3f27144c61dddec3122bd515b131c9ed5b0529fcbf2d1
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("liana", max_pin="x.x.x") }}
+    
+requirements:
+  host:
+    - python >=3.8,<3.12
+    - poetry-core >=1.0.0
+    - pip
+  run:
+    - python >=3.8,<3.12
+    - anndata >=0.7.4
+    - mudata
+    - scanpy >=1.8.0
+    - numba >=0.54.0
+    - plotnine >=0.10.0
+    - tqdm >=4.0.0,<5.0.0
+    - docrep >=0.3.1
+    - pre-commit >=3.0.0
+    - omnipath >=1.0.6
+    - decoupler >=1.4.0
+    - pydeseq2 >=0.3.5
+    - cell2cell
+    - muon
+    - mofax
+    - mofapy2 >=0.7.0
+    - corneto
+    - cvxpy >=1.4,<2
+    - cylp >=0.91.5,<0.92.0
+    - requests >=2.25.1,<3.0.0
+
+test:
+  imports:
+    - liana
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://liana-py.readthedocs.io
+  summary: 'LIANA+: a one-stop-shop framework for cell-cell communication'
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - nilchia

From b6bf022c2ec77a869af5188f549b5fe275f326e3 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 10:55:57 -0400
Subject: [PATCH 23/65] Update oakvar to 2.11.25 (#51839)

---
 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 6b9359c0a70f9..1650e634f7841 100644
--- a/recipes/oakvar/meta.yaml
+++ b/recipes/oakvar/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.11.24" %}
-{% set sha256 = "72b3f427b66b2bea8a7b36038f6164e3623b6b6d88c945db659fc06c4d6bed3e" %}
+{% set version = "2.11.25" %}
+{% set sha256 = "f808922c851b81568107d8013344f233dddbbd9d0c69313a46c3c9f97ef42edd" %}
 
 package:
   name: {{ name|lower }}

From 3deb6c106252302b8d60b2aed1f6f003fe304882 Mon Sep 17 00:00:00 2001
From: Adam Taranto <adam.p.taranto@gmail.com>
Date: Fri, 1 Nov 2024 01:56:18 +1100
Subject: [PATCH 24/65] Update TIRmite recipe (#51835)

* Update TIRmite recipe

* bump build number, i guess
---
 recipes/tirmite/meta.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml
index 364f4e5917a39..d9c53a198cdcb 100644
--- a/recipes/tirmite/meta.yaml
+++ b/recipes/tirmite/meta.yaml
@@ -14,10 +14,9 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   entry_points:
     - tirmite=tirmite.cmd_tirmite:main
-    - tsplit-LTR=tirmite.cmd_LTR:main
     - tsplit-TIR=tirmite.cmd_TIR:main
   script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv
   run_exports:
@@ -32,7 +31,7 @@ requirements:
     - hatch-vcs
   run:
     - python >=3.8
-    - pandas >=0.20.3
+    - pandas >=0.23.4
     - biopython >=1.70
     - pymummer >=0.10.3
 
@@ -41,7 +40,6 @@ test:
     - tirmite
   commands:
     - tirmite --help
-    - tsplit-LTR --help
     - tsplit-TIR --help
 
 about:

From 8076adcec7d083c2554de57524978a461390e1dd Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:00:09 -0400
Subject: [PATCH 25/65] Update tb-profiler to 6.4.0 (#51841)

* Update tb-profiler to 6.4.0

* update deps

* add setuptools

---------

Co-authored-by: Jody Phelan <jody.phelan@lshtm.ac.uk>
---
 recipes/tb-profiler/meta.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml
index 0d2dcc79dbf30..a32b773cc9d37 100644
--- a/recipes/tb-profiler/meta.yaml
+++ b/recipes/tb-profiler/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "tb-profiler" %}
-{% set version = "6.3.0" %}
-{% set sha256 = "45f3f104a3dd0f2fe07b315e3dc4ab1f0e35be095180363ecc65d41842972140" %}
+{% set version = "6.4.0" %}
+{% set sha256 = "7868c95b1d2578723622f226f254e6bb7d1f35480a575e235f8e0b9984aca166" %}
 
 package:
   name: {{name}}
@@ -19,6 +19,7 @@ build:
 requirements:
   host:
     - python >=3.8
+    - setuptools
     - pip
     - gatk4
     - samtools >=1.10
@@ -28,11 +29,11 @@ requirements:
     - python >=3.8
     - git
     - jinja2
-    - pathogen-profiler =4.3.0
+    - pathogen-profiler =4.5.0
     - filelock
     - docxtpl
     - iqtree
-    # - usher
+    - usher
     - joblib
     - tqdm
     - pysam

From a99ab47f10b572d65867220d55052970d6b66d86 Mon Sep 17 00:00:00 2001
From: Ryan Doughty <57912116+rdoughty10@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:34:37 -0500
Subject: [PATCH 26/65] Update seqscreen meta.yaml  (#51845)

* Update meta.yaml

Updated versions to not be static, nf restrained to DSL1 versions

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

diff --git a/recipes/seqscreen/meta.yaml b/recipes/seqscreen/meta.yaml
index 9c8cbdf6eb2a8..c1d9692c33137 100644
--- a/recipes/seqscreen/meta.yaml
+++ b/recipes/seqscreen/meta.yaml
@@ -10,7 +10,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("seqscreen", max_pin="x.x") }}
 requirements:
@@ -20,7 +20,7 @@ requirements:
     - scikit-learn
     - jinja2
     - biopython
-    - nextflow 21.10.6
+    - nextflow >=22.0.0,<22.11
     - blast >=2.10
     - diamond >=2.0.15
     - centrifuge-core
@@ -36,10 +36,10 @@ requirements:
     - samtools >=1.15.1
     - ete3 >=3.1.2
     - minimap2 >=2.24
-    - ncbi-datasets-cli 13.20.1
+    - ncbi-datasets-cli >=13.20.1
     - pandas >=1.4.3
-    - bwa 0.7.17
-    - pyfasta 0.5.2
+    - bwa >=0.7.17
+    - pyfasta >=0.5.2
 
 test:
   commands:

From b87c8fa6d05c05e5b3641f0341efd18251ebb622 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:32:29 -0400
Subject: [PATCH 27/65] Update aster to 1.19 (#51843)

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

diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml
index 19c285b795681..6d7dce2306868 100644
--- a/recipes/aster/meta.yaml
+++ b/recipes/aster/meta.yaml
@@ -1,13 +1,13 @@
-{% set version = "1.16" %}
+{% set version = "1.19" %}
 {% set name = "ASTER" %}
-{% set sha256 = "c6e80de483a0a59fc0d3a74465b1f793e773b9d79cbd20756c6766136ffbb1a7" %}
+{% set sha256 = "f6d7fd58297ab854a6c869ba5d6715d056a82df8254c0d6cba6d9a6db355f054" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('aster', max_pin="x") }}
 

From 5a4bc1f1447c80e1ad4c263bce054512b1073d15 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:32:40 -0400
Subject: [PATCH 28/65] Update tirmite to 1.1.6 (#51842)

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

diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml
index d9c53a198cdcb..21ba1c785ed09 100644
--- a/recipes/tirmite/meta.yaml
+++ b/recipes/tirmite/meta.yaml
@@ -1,8 +1,8 @@
 {% set name = "tirmite" %}
-{% set version = "1.1.5" %}
+{% set version = "1.1.6" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "01d2180d073da1786d5236296e51952281c58cb1124aa254345b3d6ab63a1721" %}
+{% set hash_value = "9267c94ec12db1c385a5fd6aca8b85d88005ee69ebf42b5e8dd92418454ae26e" %}
 
 package:
   name: '{{ name|lower }}'
@@ -14,7 +14,7 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   entry_points:
     - tirmite=tirmite.cmd_tirmite:main
     - tsplit-TIR=tirmite.cmd_TIR:main

From 17f5b45e76c703018dc36c4a5f7152e9b93d55b4 Mon Sep 17 00:00:00 2001
From: Chris Jackson <55370301+chrisjackson-pellicle@users.noreply.github.com>
Date: Fri, 1 Nov 2024 07:39:30 +1100
Subject: [PATCH 29/65] Update - add setuptools to host requirements as
 hybpiper conda build now failing without it (#51829)

* Add setuptools to host requirements as conda build now failing without it

* Increment build number
---
 recipes/hybpiper/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml
index 069d3780b89be..a6f186243754e 100644
--- a/recipes/hybpiper/meta.yaml
+++ b/recipes/hybpiper/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 7b9d0af243dbdd24cb299cf8e05e65dafa873afc2c7605e3fae74b455457b491
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   entry_points:
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.7
     - pip
+    - setuptools
   run:
     - bbmap >=38.44
     - biopython >=1.80

From 1e374fd0a3ad81c70913172813641b1afd95423c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:00:25 -0400
Subject: [PATCH 30/65] Update harpy to 1.10 (#51574)

* Update harpy to 1.10

* Update harpy to 1.10

* Update harpy to 1.10

* remove pandas

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/harpy/meta.yaml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml
index 7dd9fe1ffeb0c..6e30e61e6e75f 100644
--- a/recipes/harpy/meta.yaml
+++ b/recipes/harpy/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.9" %}
-{% set sha256 = "9b9b717eea2eff2d35b3096d5867f34813d1d7ca9d8946df10844c0635b98fd8" %}
+{% set version = "1.10" %}
+{% set sha256 = "a2664cf94e89f1a1ab20519445c0649425ddf4c9204bdfe91cfc36a77e835f82" %}
 
 package:
   name: harpy
@@ -10,7 +10,7 @@ source:
   sha256: '{{ sha256 }}'
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx or py < 39]
   script_env:
     - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
@@ -36,7 +36,6 @@ requirements:
     - apptainer
     - bcftools =1.20
     - conda >24.7
-    - pandas
     - pysam
     - python
     - rich-click

From db06953f491352f92fe89d2078f5bca37f761b6e Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:05:41 -0400
Subject: [PATCH 31/65] Update phykit to 2.0.1 (#51844)

* Update phykit to 2.0.1

* add run_exports

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/phykit/meta.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml
index 23e84b018047c..98a200dc4142d 100644
--- a/recipes/phykit/meta.yaml
+++ b/recipes/phykit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "phykit" %}
-{% set version = "2.0.0" %}
+{% set version = "2.0.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 32358dc24e564860ce56fa71772599a00d12dc746b6ca2fb046fbca9f4c1e2c3
+  sha256: 34799da77c621afdd50afd3411449a4460f15a52a56bff38b5c9ab7def864302
 
 build:
   noarch: python
@@ -129,8 +129,9 @@ requirements:
   host:
     - pip
     - python >=3
+    - setuptools
   run:
-    - biopython >=1.81
+    - biopython >=1.82
     - numpy >=1.24.0
     - python >=3
     - scipy >=1.11.3

From 5046efd4b98f3c965fc22b7fc5593622c48b1f16 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:05:50 -0400
Subject: [PATCH 32/65] Update teloclip to 0.0.5 (#51838)

* Update teloclip to 0.0.5

* clean up recipe

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/teloclip/meta.yaml | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml
index 288843e270285..08bbe62e72bd4 100644
--- a/recipes/teloclip/meta.yaml
+++ b/recipes/teloclip/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "teloclip" %}
-{% set version = "0.0.4" %}
+{% set version = "0.0.5" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 7f9919c1aa5d3d9f8e21c3a49bc3edccb7d9ef1c4ad0686761a9a9f623999ade
+  sha256: eb699124a35ad44ef9f5a71e2f20cfcefd3b473ac3ef47fc28cf2394610b1f6f
 
 build:
   run_exports:
@@ -17,16 +17,16 @@ build:
   entry_points:
     - teloclip=teloclip.app:main
     - teloclip-extract=teloclip.app_extract:main
-  script: "{{ PYTHON }} -m pip install . -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
 
 requirements:
   host:
-    - python >=3
+    - python >=3.8
     - pip
-    - setuptools
-    - setuptools-scm
+    - hatchling
+    - hatch-vcs
   run:
-    - python >=3
+    - python >=3.8
 
 test:
   imports:
@@ -36,14 +36,13 @@ test:
     - teloclip-extract --help
 
 about:
-  home: https://github.com/Adamtaranto/teloclip
-  license: MIT License
+  home: "https://github.com/Adamtaranto/teloclip"
+  license: MIT
   license_family: MIT
-  license_file: ''
-  summary: A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
-  description: ''
-  doc_url: ''
-  dev_url: ''
+  license_file: 'LICENSE'
+  summary: "A tool for the recovery of unassembled telomeres from soft-clipped read alignments."
+  doc_url: 'https://github.com/Adamtaranto/teloclip/blob/{{ version }}/README.md'
+  dev_url: 'https://github.com/Adamtaranto/teloclip'
 
 extra:
   recipe-maintainers: 

From 114feeef480ea504d175cb13ee3c82211be7212d Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Thu, 31 Oct 2024 22:20:56 +0100
Subject: [PATCH 33/65] hictkpy: add v1.0.0 (#51561)

* Update Conan profiles

* Update build config to be in line with hictk's recipe

* Update patch files

* Update build script

* Bump version

* Update about section

* Update requirements

* Update test requirements

* Update package version pinning

* Make tests verbose

* Enable parallel builds

* Ensure the correct sysroot is used when building on macOS

* Ensure the correct sysroot is used when building on Linux

* Help CMake find NumPy headers

* Export env variables in build script

* Update checksum
---
 recipes/hictkpy/CMakeLists.txt.patch          | 13 ---
 recipes/hictkpy/build.sh                      | 42 ++++++---
 recipes/hictkpy/conan_profiles/{gcc => clang} |  4 +-
 recipes/hictkpy/conanfile.py.patch            | 90 +++++++++++++++++++
 recipes/hictkpy/conanfile.txt.patch           | 35 --------
 recipes/hictkpy/conda_build_config.yaml       |  8 ++
 recipes/hictkpy/meta.yaml                     | 49 +++++-----
 recipes/hictkpy/pyproject.toml.patch          | 16 ++--
 recipes/hictkpy/run_test.sh                   |  2 +-
 9 files changed, 165 insertions(+), 94 deletions(-)
 delete mode 100644 recipes/hictkpy/CMakeLists.txt.patch
 rename recipes/hictkpy/conan_profiles/{gcc => clang} (73%)
 create mode 100644 recipes/hictkpy/conanfile.py.patch
 delete mode 100644 recipes/hictkpy/conanfile.txt.patch
 create mode 100644 recipes/hictkpy/conda_build_config.yaml

diff --git a/recipes/hictkpy/CMakeLists.txt.patch b/recipes/hictkpy/CMakeLists.txt.patch
deleted file mode 100644
index a5c3cb5839689..0000000000000
--- a/recipes/hictkpy/CMakeLists.txt.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 01a1413..b0dcdb4 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -17,6 +17,8 @@ set(CMAKE_C_STANDARD 11)
- # -std=gnu++20 for example when compiling with PCH enabled
- set(CMAKE_CXX_EXTENSIONS OFF)
- 
-+set(CMAKE_OSX_DEPLOYMENT_TARGET 10.15)
-+
- project(
-   hictkpy
-   LANGUAGES C CXX
diff --git a/recipes/hictkpy/build.sh b/recipes/hictkpy/build.sh
index a6d756aa71a09..d3d9558f2169c 100755
--- a/recipes/hictkpy/build.sh
+++ b/recipes/hictkpy/build.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
+CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
 
 scratch=$(mktemp -d)
 export CONAN_HOME="$scratch/conan"
@@ -8,33 +8,47 @@ export CONAN_HOME="$scratch/conan"
 # shellcheck disable=SC2064
 trap "rm -rf '$scratch'" EXIT
 
-declare -a CMAKE_PLATFORM_FLAGS
 if [[ ${HOST} =~ .*darwin.* ]]; then
-  export MACOSX_DEPLOYMENT_TARGET=10.15  # Required to use std::filesystem
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
+  if [[ "$OSX_ARCH" == 'x86_64' ]]; then
+    # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
+    CFLAGS+=' -D_LIBCPP_DISABLE_AVAILABILITY'
+    CXXFLAGS+=' -D_LIBCPP_DISABLE_AVAILABILITY'
+  fi
+  CMAKE_ARGS+=" -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT}"
   conan_profile='apple-clang'
 else
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
-  conan_profile='gcc'
+  # Workaround missing LLVMgold.so on Linux
+  CMAKE_ARGS+=' -DCMAKE_LINKER_TYPE=LLD'
+  CMAKE_ARGS+=" -DCMAKE_TOOLCHAIN_FILE=${RECIPE_DIR}/cross-linux.cmake"
+  conan_profile='clang'
 fi
 
 # Remember to update these profiles when bioconda's compiler toolchains are updated
 mkdir -p "$CONAN_HOME/profiles/"
 ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/default"
 
-# explicitly set CMAKE_OSX_DEPLOYMENT_TARGET
-patch CMakeLists.txt < "${RECIPE_DIR}/CMakeLists.txt.patch"
-
-# Remove unnecessary dependencies from conanfile.txt
-patch conanfile.txt < "${RECIPE_DIR}/conanfile.txt.patch"
+# Remove unnecessary dependencies from conanfile.py
+patch conanfile.py < "${RECIPE_DIR}/conanfile.py.patch"
 
 # Build hictkpy as a shared library
 patch pyproject.toml < "${RECIPE_DIR}/pyproject.toml.patch"
 
-CMAKE_ARGS+=" -DPython_EXECUTABLE=$PYTHON"
+# See https://github.com/conda-forge/conda-forge.github.io/pull/2321
+Python_INCLUDE_DIR="$("$PYTHON" -c 'import sysconfig; print(sysconfig.get_path("include"))')"
+Python_NumPy_INCLUDE_DIR="$("$PYTHON" -c 'import numpy; print(numpy.get_include())')"
+
+CMAKE_ARGS+=" -DPython_EXECUTABLE:PATH=${PYTHON}"
+CMAKE_ARGS+=" -DPython_INCLUDE_DIR:PATH=${Python_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython_NumPy_INCLUDE_DIR=${Python_NumPy_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython3_EXECUTABLE:PATH=${PYTHON}"
+CMAKE_ARGS+=" -DPython3_INCLUDE_DIR:PATH=${Python_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython3_NumPy_INCLUDE_DIR=${Python_NumPy_INCLUDE_DIR}"
+
+echo "CFLAGS='$CFLAGS'"
+echo "CXXFLAGS='$CXXFLAGS'"
+echo "CMAKE_ARGS='$CMAKE_ARGS'"
 
-echo "$CMAKE_ARGS"
-export CMAKE_ARGS
+export CMAKE_ARGS CMAKE_BUILD_PARALLEL_LEVEL CFLAGS CXXFLAGS
 
 SETUPTOOLS_SCM_PRETEND_VERSION="$PKG_VERSION" \
 "$PYTHON" -m pip install "$SRC_DIR" -vv
diff --git a/recipes/hictkpy/conan_profiles/gcc b/recipes/hictkpy/conan_profiles/clang
similarity index 73%
rename from recipes/hictkpy/conan_profiles/gcc
rename to recipes/hictkpy/conan_profiles/clang
index ef7e2f6219ff1..9ee58cee260e2 100644
--- a/recipes/hictkpy/conan_profiles/gcc
+++ b/recipes/hictkpy/conan_profiles/clang
@@ -1,8 +1,8 @@
 [settings]
 arch=x86_64
 build_type=Release
-compiler=gcc
+compiler=clang
 compiler.cppstd=17
 compiler.libcxx=libstdc++11
-compiler.version=13
+compiler.version=18
 os=Linux
diff --git a/recipes/hictkpy/conanfile.py.patch b/recipes/hictkpy/conanfile.py.patch
new file mode 100644
index 0000000000000..5aed5d1d3f6e0
--- /dev/null
+++ b/recipes/hictkpy/conanfile.py.patch
@@ -0,0 +1,90 @@
+diff --git a/conanfile.py b/conanfile.py
+index a7d5c74..c08b356 100644
+--- a/conanfile.py
++++ b/conanfile.py
+@@ -35,21 +35,11 @@ class HictkpyConan(ConanFile):
+         return 17
+ 
+     def requirements(self):
+-        self.requires("arrow/17.0.0#81be2aa6c49800df8cc163adf4b99e9f")
+-        self.requires("boost/1.86.0#cd839a2082585255010f9e82eea94c7f", force=True)
+         self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
+         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
+-        self.requires("eigen/3.4.0#2e192482a8acff96fe34766adca2b24c")
+-        self.requires("fast_float/6.1.5#e067b96a6271d1b4c255858ca9805bdd")
+-        self.requires("fmt/11.0.2#5c7438ef4d5d69ab106a41e460ce11f3", force=True)
+-        self.requires("hdf5/1.14.4.3#df1467d7374938c231edbe10e83f2bb4", force=True)
+-        self.requires("highfive/2.10.0#3d1bd25944a57fa1bc30a0a22923d528")
+-        self.requires("libdeflate/1.22#f95aebe763153ccbc4cc76c023e42e5a")
+         self.requires("parallel-hashmap/1.4.0#36ac84df77219748440cdb0f23624d56")
+         self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
+         self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
+-        self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03")
+-        self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b", force=True)
+ 
+     def validate(self):
+         if self.settings.get_safe("compiler.cppstd"):
+@@ -58,63 +48,3 @@ class HictkpyConan(ConanFile):
+     def configure(self):
+         if self.settings.compiler in ["clang", "gcc"]:
+             self.settings.compiler.libcxx = "libstdc++11"
+-
+-        self.options["arrow"].compute = True
+-        self.options["arrow"].parquet = False
+-        self.options["arrow"].with_boost = True
+-        self.options["arrow"].with_re2 = True
+-        self.options["arrow"].with_thrift = False
+-        self.options["boost"].system_no_deprecated = True
+-        self.options["boost"].asio_no_deprecated = True
+-        self.options["boost"].filesystem_no_deprecated = True
+-        self.options["boost"].filesystem_version = 4
+-        self.options["boost"].zlib = False
+-        self.options["boost"].bzip2 = False
+-        self.options["boost"].lzma = False
+-        self.options["boost"].zstd = False
+-        self.options["boost"].without_atomic = False
+-        self.options["boost"].without_charconv = True
+-        self.options["boost"].without_chrono = True
+-        self.options["boost"].without_cobalt = True
+-        self.options["boost"].without_container = True
+-        self.options["boost"].without_context = True
+-        self.options["boost"].without_contract = True
+-        self.options["boost"].without_coroutine = True
+-        self.options["boost"].without_date_time = True
+-        self.options["boost"].without_exception = True
+-        self.options["boost"].without_fiber = True
+-        self.options["boost"].without_filesystem = False
+-        self.options["boost"].without_graph = True
+-        self.options["boost"].without_graph_parallel = True
+-        self.options["boost"].without_iostreams = True
+-        self.options["boost"].without_json = True
+-        self.options["boost"].without_locale = True
+-        self.options["boost"].without_log = True
+-        self.options["boost"].without_math = True
+-        self.options["boost"].without_mpi = True
+-        self.options["boost"].without_nowide = True
+-        self.options["boost"].without_process = False
+-        self.options["boost"].without_program_options = True
+-        self.options["boost"].without_python = True
+-        self.options["boost"].without_random = True
+-        self.options["boost"].without_regex = True
+-        self.options["boost"].without_serialization = True
+-        self.options["boost"].without_stacktrace = True
+-        self.options["boost"].without_system = False
+-        self.options["boost"].without_test = True
+-        self.options["boost"].without_thread = True
+-        self.options["boost"].without_timer = True
+-        self.options["boost"].without_type_erasure = True
+-        self.options["boost"].without_url = True
+-        self.options["boost"].without_wave = True
+-        self.options["fmt"].header_only = True
+-        self.options["hdf5"].enable_cxx = False
+-        self.options["hdf5"].hl = False
+-        self.options["hdf5"].threadsafe = False
+-        self.options["hdf5"].parallel = False
+-        self.options["highfive"].with_boost = False
+-        self.options["highfive"].with_eigen = False
+-        self.options["highfive"].with_opencv = False
+-        self.options["highfive"].with_xtensor = False
+-        self.options["spdlog"].header_only = True
+-        self.options["zstd"].build_programs = False
diff --git a/recipes/hictkpy/conanfile.txt.patch b/recipes/hictkpy/conanfile.txt.patch
deleted file mode 100644
index 038babbd4c0df..0000000000000
--- a/recipes/hictkpy/conanfile.txt.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff --git a/conanfile.txt b/conanfile.txt
-index cffb547..66cf415 100644
---- a/conanfile.txt
-+++ b/conanfile.txt
-@@ -5,30 +5,12 @@
- [requires]
- bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c
- concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502
--fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e
--fmt/10.2.1#9199a7a0611866dea5c8849a77467b25
--hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1
--highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5
--libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602
- parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7
- readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83
- span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422
--spdlog/1.13.0#2775cc949e26b339029a852785b6b276
--zstd/1.5.6#67383dae85d33f43823e7751a6745ea1
- 
- [generators]
- CMakeDeps
- 
- [options]
--fmt*:header_only=True
--hdf5*:enable_cxx=False
--hdf5*:hl=False
--hdf5*:threadsafe=False
--hdf5*:parallel=False
--highfive*:with_boost=False
--highfive*:with_eigen=False
--highfive*:with_opencv=False
--highfive*:with_xtensor=False
--spdlog*:header_only=True
--zstd*:build_programs=False
- 
diff --git a/recipes/hictkpy/conda_build_config.yaml b/recipes/hictkpy/conda_build_config.yaml
new file mode 100644
index 0000000000000..3397464cf13fd
--- /dev/null
+++ b/recipes/hictkpy/conda_build_config.yaml
@@ -0,0 +1,8 @@
+c_compiler:             # [linux]
+  - clang               # [linux]
+c_compiler_version:     # [linux]
+  - 18                  # [linux]
+cxx_compiler:           # [linux]
+  - clangxx             # [linux]
+cxx_compiler_version:   # [linux]
+  - 18                  # [linux]
diff --git a/recipes/hictkpy/meta.yaml b/recipes/hictkpy/meta.yaml
index 084412b76ff50..6f9f527301f06 100644
--- a/recipes/hictkpy/meta.yaml
+++ b/recipes/hictkpy/meta.yaml
@@ -1,61 +1,68 @@
 {% set name = "hictkpy" %}
-{% set version = "0.0.5" %}
-{% set sha256 = "e9576a1a719ce378873da15b76e9f7e699748c0486901607e4d7e87c3f0c6556" %}
+{% set version = "1.0.0" %}
+{% set sha256 = "a12c05cba9395ce39eb742b5d1e1a6e0cc0179a5b6981ae8a828ff9aee2c64ce" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: True  # [py < 39]
   run_exports:
-    - {{ pin_subpackage('hictkpy', max_pin='x.x') }}
+    - {{ pin_subpackage('hictkpy', max_pin='x') }}
 
 source:
-  url: https://github.com/paulsengroup/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  url: https://pypi.python.org/packages/source/h/{{ name }}/{{ name }}-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - cmake >=3.25
+    - cmake >=3.29
     - conan >=2
     - make
-    - fast_float >=5
-    - fmt >=10
-    - highfive >=2.7
-    - spdlog >=1.12
+    - eigen >=3.4
+    - fast_float >=6
+    - fmt >=11
+    - highfive >=2.9
+    - spdlog >=1.14
+
   host:
     - python
     - pip
     - hdf5 >=1.12
-    - libdeflate
-    - scikit-build-core
+    - libarrow >=16
+    - libdeflate >=1
+    - lld  # [linux]
+    - nanobind >=2
+    - numpy
+    - scikit-build-core >=0.10
     - setuptools_scm
     - zstd >=1.5
 
   run:
     - python
-    - hdf5 >=1.12
-    - libdeflate
-    - numpy
-    - pandas
-    - scipy
-    - zstd >=1.5
+    - {{ pin_compatible('hdf5', min_pin='1.12') }}
+    - {{ pin_compatible('libdeflate', min_pin='1') }}
+    - {{ pin_compatible('numpy') }}
+    - {{ pin_compatible('pandas', min_pin='2.1') }}
+    - {{ pin_compatible('pyarrow', min_pin='16') }}
+    - {{ pin_compatible('scipy') }}
+    - {{ pin_compatible('zstd', min_pin='1.5') }}
 
 about:
   home: https://github.com/paulsengroup/{{ name }}
   license: MIT
   license_file: LICENSE
-  summary: Python bindings for hictk
+  summary: "Python bindings for hictk: read and write .cool and .hic files directly from Python"
   dev_url: https://github.com/paulsengroup/{{ name }}
-  doc_url: https://github.com/paulsengroup/{{ name }}#readme
+  doc_url: https://{{ name }}.readthedocs.io/en/stable/
 
 test:
    requires:
-     - pytest>=6
+     - pytest>=8
    source_files:
      - test/*
    imports:
diff --git a/recipes/hictkpy/pyproject.toml.patch b/recipes/hictkpy/pyproject.toml.patch
index 6763068194b11..afa8522558a7f 100644
--- a/recipes/hictkpy/pyproject.toml.patch
+++ b/recipes/hictkpy/pyproject.toml.patch
@@ -1,13 +1,13 @@
 diff --git a/pyproject.toml b/pyproject.toml
-index 1a03623..36102d0 100644
+index 5ded5b9..fe8d305 100644
 --- a/pyproject.toml
 +++ b/pyproject.toml
-@@ -49,7 +49,7 @@ HICTK_BUILD_EXAMPLES = "OFF"
- HICTK_BUILD_BENCHMARKS = "OFF"
- HICTK_BUILD_TOOLS = "OFF"
- HICTK_ENABLE_GIT_VERSION_TRACKING = "OFF"
+@@ -74,7 +74,7 @@ wheel.expand-macos-universal-tags = true
+ cmake.build-type = "Release"
+ 
+ [tool.scikit-build.cmake.define]
 -BUILD_SHARED_LIBS = "OFF"
 +BUILD_SHARED_LIBS = "ON"
- CONAN_INSTALL_ARGS = "--settings=compiler.cppstd=17;--build=missing;--update;--options=*/*:shared=False"
- 
- [tool.setuptools_scm]
+ CMAKE_OSX_DEPLOYMENT_TARGET = "10.15"
+ CMAKE_PROJECT_TOP_LEVEL_INCLUDES = { env="HICTKPY_PROJECT_TOP_LEVEL_INCLUDES", default="cmake/conan_provider.cmake" }
+ CONAN_INSTALL_ARGS = { env="HICTKPY_CONAN_INSTALL_ARGS", default="--settings=compiler.cppstd=17;--settings=build_type=Release;--build=missing;--update;--options=*/*:shared=False" }
diff --git a/recipes/hictkpy/run_test.sh b/recipes/hictkpy/run_test.sh
index a6729f994b26e..57e137c421dc2 100644
--- a/recipes/hictkpy/run_test.sh
+++ b/recipes/hictkpy/run_test.sh
@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 
 "$PYTHON" -c 'import hictkpy; print(hictkpy.__version__)'
-"$PYTHON" -m pytest test
+"$PYTHON" -m pytest test -v

From 1c97e5ebd2912cd8055c4b3008e590b2cbc80094 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:22:35 -0400
Subject: [PATCH 34/65] Update piawka to 0.8.8 (#51848)

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

diff --git a/recipes/piawka/meta.yaml b/recipes/piawka/meta.yaml
index 537b4d0c0d15a..20a7425ba148d 100644
--- a/recipes/piawka/meta.yaml
+++ b/recipes/piawka/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "piawka" %}
-{% set version = "0.8.7" %}
+{% set version = "0.8.8" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/novikovalab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 7fc2e1ae564264342cef6cc54a35d8b6796482476553e3e2bb867931f310b4b6
+  sha256: 9a89ba6f23470f5127d30c3b6b55c64e27612fd7d98028c3d69b077676832e08
 
 build:
   noarch: generic

From 9c722122b5a7e74552ea3e16988ce0cde559956b Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:22:58 -0400
Subject: [PATCH 35/65] Update hybpiper to 2.3.1 (#51827)

* Update hybpiper to 2.3.1

* reset build number

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/hybpiper/meta.yaml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml
index a6f186243754e..df405b33da02d 100644
--- a/recipes/hybpiper/meta.yaml
+++ b/recipes/hybpiper/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "hybpiper" %}
-{% set version = "2.3.0" %}
+{% set version = "2.3.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://github.com/mossmatters/HybPiper/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 7b9d0af243dbdd24cb299cf8e05e65dafa873afc2c7605e3fae74b455457b491
+  sha256: 0f341fb26dffd39c13b3bfc5c1d568936bcd0edbe9064399e4aa947d5882d220
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   entry_points:
@@ -39,8 +39,7 @@ requirements:
     - psutil >=5.9.0
     - samtools >=1.14
     - seaborn-base >=0.11.1
-    - spades >=3.15.2  # [osx]
-    - spades >=3.15.4  # [linux]
+    - spades >=4.0.0
     - trimmomatic
 
 test:

From e4a321f7677f0dd093203c70872a9af077b70a21 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:23:07 -0400
Subject: [PATCH 36/65] Update derna to 1.0.4 (#51825)

* Update derna to 1.0.4

* clean up recipe

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/derna/build.sh  | 21 +++++++++++++++------
 recipes/derna/meta.yaml | 11 ++++++-----
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/recipes/derna/build.sh b/recipes/derna/build.sh
index 7898ddc35f18f..0b6e4d0faf8a5 100644
--- a/recipes/derna/build.sh
+++ b/recipes/derna/build.sh
@@ -2,12 +2,21 @@
 
 set -xe
 
+mkdir -p $PREFIX/bin
+
 export C_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 
-mkdir build
-cd build
-cmake ..
-make -j ${CPU_COUNT}
-mkdir -p $PREFIX/bin
-cp derna $PREFIX/bin
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+cmake --build build  -j ${CPU_COUNT} -v
+chmod 0755 build/derna
+mv build/derna $PREFIX/bin
diff --git a/recipes/derna/meta.yaml b/recipes/derna/meta.yaml
index ffafda5a12a70..193695a14d649 100644
--- a/recipes/derna/meta.yaml
+++ b/recipes/derna/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.3" %}
+{% set version = "1.0.4" %}
 
 package:
   name: derna
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://github.com/elkebir-group/derna/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: d7e2fdbe733d03f9e617ea325a43283c0e4e298780253cf2e7da7ad07d3aafc5
+  sha256: eb5fabf0e01d9507ceca3fc687e8c67a9cec91c77e75d2c4f7d310ac926a79cb
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('derna', max_pin="x") }}
 
@@ -25,12 +25,13 @@ test:
     - derna -h
 
 about:
-  home: https://github.com/elkebir-group/derna
+  home: "https://github.com/elkebir-group/derna"
   license: BSD-3-Clause
   license_family: BSD
   license_file: LICENSE
   summary: "RNA sequence design for a target protein sequence."
-  dev_url: https://github.com/elkebir-group/derna
+  dev_url: "https://github.com/elkebir-group/derna"
+  doc_url: "https://github.com/elkebir-group/derna/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:

From d050b74a2e818e20686e3fb80c56fd57dc5daf06 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:25:06 -0400
Subject: [PATCH 37/65] Update gencove to 2.24.0 (#51849)

---
 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 37526967d5d5d..8ed7d83d740ef 100644
--- a/recipes/gencove/meta.yaml
+++ b/recipes/gencove/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.23.1" %}
-{% set sha256 = "11a63ea7c5ec624b896a32f7ca4ae42d1b9909cb87eb9f25ec3678e86a7ea2ad" %}
+{% set version = "2.24.0" %}
+{% set sha256 = "1ec41ae1e663d7ab27b3c1e6af3eccb49e95120d084bae4c25305aab1126e7fb" %}
 
 package:
   name: {{ name }}

From c58c86539fec7864d6de7f5aa5eeac5c148a50ba Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:29:49 -0400
Subject: [PATCH 38/65] Update cogent3 to 2024.7.19a9 (#51850)

---
 recipes/cogent3/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml
index 4d4729025442b..63f3ec5de23da 100644
--- a/recipes/cogent3/meta.yaml
+++ b/recipes/cogent3/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cogent3" %}
-{% set version = "2024.7.19a8" %}
+{% set version = "2024.7.19a9" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 7d046813b004c09de379b6d001b48ff93c0193923cc5b809efb5cfa25fb278c7
+  sha256: 5f1ab042294f718a77e0d8fa8adf3b20fefe9ef5a47b1c2092e50e8560883afa
 
 build:
   noarch: python

From a97949f93872075e047ea2139e011ba829447cb0 Mon Sep 17 00:00:00 2001
From: Luan Nguyen <125411678+luan-n-nguyen@users.noreply.github.com>
Date: Fri, 1 Nov 2024 09:12:44 +1100
Subject: [PATCH 39/65] Update hmftools-purple and hmftools-orange (#51800)

* Update hmftools-orange to 3.7.1-beta.1

* Update hmftools-purple to 4.1_beta.5

* Minor update to jar for hmftools-orange

* Bump build number for hmftools-orange

* edit build number

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/hmftools-orange/meta.yaml | 7 ++++---
 recipes/hmftools-purple/meta.yaml | 6 +++---
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml
index 6db3361d5da0b..df7a40c1b0e4d 100644
--- a/recipes/hmftools-orange/meta.yaml
+++ b/recipes/hmftools-orange/meta.yaml
@@ -1,17 +1,18 @@
 {% set version = "3.7.1_beta" %}
-{% set sha256 = "1592dacf6a75c7d82fbb865b85e17cbb5b04d1acda8cdf5fb61c4a5cf9868929" %}
+{% set beta_suffix = ".2" %}
+{% set sha256 = "c1ba13d266e5197b5cdc20f2691578714784d7669b95f0182f69d174c663e70e" %}
 
 package:
   name: hmftools-orange
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/orange-v{{ version }}/orange_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/orange-v{{ version }}/orange_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('hmftools-orange', max_pin="x") }}
 
diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml
index dcf946ec3ff8b..e112c5fe0bdfe 100644
--- a/recipes/hmftools-purple/meta.yaml
+++ b/recipes/hmftools-purple/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "4.1_beta" %}
-{% set beta_suffix = ".4" %}
-{% set sha256 = "fef88d9bc349aa6a43c2b90fb6ea9835d50c3bd4d9c622190024bb890a0ae7e9" %}
+{% set beta_suffix = ".5" %}
+{% set sha256 = "92c97c12db08383187ed467d2574540672e36df7b5594c202777e1b3f05e8868" %}
 
 package:
   name: hmftools-purple
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage('hmftools-purple', max_pin="x") }}
 

From 159f7eeaa0cc63d1602a85d8de8fe3be6d4675c0 Mon Sep 17 00:00:00 2001
From: Max <visze@users.noreply.github.com>
Date: Fri, 1 Nov 2024 08:07:47 +0100
Subject: [PATCH 40/65] Update seqspec to 0.3.0 (#51805)


From 4e7548c4e67ec9fb3b5689c057925c5459023e47 Mon Sep 17 00:00:00 2001
From: Alex Fraser <79180900+AlexSCFraser@users.noreply.github.com>
Date: Fri, 1 Nov 2024 00:09:58 -0700
Subject: [PATCH 41/65] Update SACCHARIS (#51846)

---
 recipes/saccharis/meta.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml
index de48fd85a18ff..9a871bb5fb6af 100644
--- a/recipes/saccharis/meta.yaml
+++ b/recipes/saccharis/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "SACCHARIS" %}
 {% set version = "2.0.1.dev21" %}
-{% set hash = "B83DC6502A3AB136D1E5F43E4E66CD41A7B884C99B190B781691C56A6D71998F" %}
+{% set hash = "90806FDA7473C4687165277FB7765F201B2E3CE5254B43A0FBC8FBCD8C9B8849" %}
 
 
 package:
@@ -9,12 +9,13 @@ package:
 
 source:
   #  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz
-  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_3.tar.gz
+  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_4.tar.gz
+
   sha256: {{ hash|lower }}
 
 build:
   noarch: python
-  number: 3
+  number: 4
   script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt
   preserve_egg_dir: True  # added because the entry points below seem to be causing a build error
   entry_points:

From 09db4a0bb629f18e94e59810cd14b1616d2c01f6 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 11:40:29 -0400
Subject: [PATCH 42/65] Update kalamari to 5.7.2 (#51867)

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

diff --git a/recipes/kalamari/meta.yaml b/recipes/kalamari/meta.yaml
index 86fd246313eeb..8d4a7dbd29474 100644
--- a/recipes/kalamari/meta.yaml
+++ b/recipes/kalamari/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "Kalamari" %}
-{% set version = "5.7.1" %}
+{% set version = "5.7.2" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/lskatz/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 41a70037424da3658e6c92e3faca335d4cf02301fc74a5b5b27cd2611aef5681
+  sha256: 9f206e8bb949961d2b0f4788dae0deb2941632237391ae04891ea77ef8f02d89
 
 build:
   number: 0

From 0d6951b358be62912206c15a0f38ff6050ee7051 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 12:35:51 -0400
Subject: [PATCH 43/65] Update snakemake to 8.25.1 (#51871)

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

diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml
index 92c9e86c94be7..5ef003764825c 100644
--- a/recipes/snakemake/meta.yaml
+++ b/recipes/snakemake/meta.yaml
@@ -1,7 +1,7 @@
 # Attention: when upgrading the version, please compare below dependencies with
 # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg
 {% set name = "snakemake" %}
-{% set version = "8.25.0" %}
+{% set version = "8.25.1" %}
 
 package:
   name: {{ name }}
@@ -9,7 +9,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz
-  sha256: a9cf1ab8e7c33a6e928f191fc83572e8add8d8383465a036910526d01081bddc
+  sha256: c8f4442473f3af130f237fe5759ebfb03997b44e713cd7c479aba27d71338cd9
 
 build:
   number: 0

From 32db8aac46d791a85c264896a0e9aea0181ee80c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 14:57:36 -0400
Subject: [PATCH 44/65] Update fgbio-minimal to 2.4.0 (#51866)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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

diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml
index ec8d76b58f4d5..49f78563a49ec 100644
--- a/recipes/fgbio-minimal/meta.yaml
+++ b/recipes/fgbio-minimal/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio-minimal
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic

From a959d05d9d4883b317d10166ab67eebbb6f0cf4b Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 2 Nov 2024 19:00:24 +0000
Subject: [PATCH 45/65] Fix usearch path in lOTUs.cfg (#51870)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/lotus2/build.sh  | 4 ++--
 recipes/lotus2/meta.yaml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/lotus2/build.sh b/recipes/lotus2/build.sh
index 5b4edbec842fd..79c1bbc3500d4 100644
--- a/recipes/lotus2/build.sh
+++ b/recipes/lotus2/build.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 SHARE_DIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 
-rm -rf bin/installs/ bin/LCA bin/rtk bin/sdm bin/vsearch configs/sdm_src/
+rm -rf bin/installs/ bin/lambda3* bin/LCA bin/rtk bin/sdm bin/vsearch
 # Configure LotuS2
 cp configs/LotuS.cfg.def lOTUs.cfg
-for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm vsearch; do
+for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm usearch vsearch; do
     sed -i.bak -e "s|^$binary[[:space:]].*|$binary $PREFIX/bin/$binary|" lOTUs.cfg
 done
 for binary in cd-hit fasttree hmmsearch iqtree itsx makeBlastDB RDPjar; do
diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml
index bc46dd5be022e..2da7f320f44bf 100644
--- a/recipes/lotus2/meta.yaml
+++ b/recipes/lotus2/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}

From 208191896467f5e932b006190718532b60d465b3 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 15:12:03 -0400
Subject: [PATCH 46/65] Update fgbio to 2.4.0 (#51869)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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

diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml
index 496337cbe9149..04b43d63f15a4 100644
--- a/recipes/fgbio/meta.yaml
+++ b/recipes/fgbio/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic

From da0cf96d7627ef371337570c3771417fe99c9263 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 15:17:16 -0400
Subject: [PATCH 47/65] Update fgsv to 0.2.1 (#51868)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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

diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml
index 4d064dba5f553..5620d4693947c 100644
--- a/recipes/fgsv/meta.yaml
+++ b/recipes/fgsv/meta.yaml
@@ -1,5 +1,5 @@
-{% set version="0.2.0" %}
-{% set sha256="c2f9536a677e7e99f251cada1338f611cea40477deca144f0c6928505755eb37" %}
+{% set version="0.2.1" %}
+{% set sha256="e3f15c7f1a97c009be65663405194faedf473c2636a3c3d742f463030caba860" %}
 
 
 package:

From 230c74417e94c54f46e798c1ab2c261d1c3c499a Mon Sep 17 00:00:00 2001
From: Wei Shen <shenwei356@gmail.com>
Date: Sun, 3 Nov 2024 03:21:17 +0800
Subject: [PATCH 48/65] Update csvtk to v0.31.0 (#51861)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/csvtk/meta.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml
index 86f0aee7a9418..93700fa5b0691 100644
--- a/recipes/csvtk/meta.yaml
+++ b/recipes/csvtk/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.30.0" %}
+{% set version = "0.31.0" %}
 # This package should be migrated to conda-forge due to general utility
 # In that case it needs to be built from source
 package:
@@ -6,19 +6,19 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('csvtk', max_pin='x.x') }}
   
 source:
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx and x86_64]
-    md5: c415255e265ba0cd547806fdbda05652 # [osx and x86_64]
+    md5: 5a23d000a1fc068360e1aeb439f3ae25 # [osx and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_arm64.tar.gz # [arm64]
-    md5: dd8a84c301d378ab7ff28c85d37fbefa # [arm64]
+    md5: 6aa24ce286910e83d95d28a21905f1d8 # [arm64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux and x86_64]
-    md5: 8f5877d4fbea89609d64bd2679956476 # [linux and x86_64]
+    md5: 09bc8c3288f028239c94d4c935ac7a6f # [linux and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_arm64.tar.gz # [aarch64]
-    md5: 2a6dd840291d23971ff538eaf3de00ec # [aarch64]
+    md5: f7a5b8839459d7d55685056331670eec # [aarch64]
 
 test:
   commands:

From 4c3a2bc29d275e5891588c6252e458e9675c0e4a Mon Sep 17 00:00:00 2001
From: Wei Shen <shenwei356@gmail.com>
Date: Sun, 3 Nov 2024 03:21:52 +0800
Subject: [PATCH 49/65] Update TaxonKit to v0.18.0 (#51862)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/taxonkit/meta.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml
index f1f47d02d7e8c..dd38d454a0249 100644
--- a/recipes/taxonkit/meta.yaml
+++ b/recipes/taxonkit/meta.yaml
@@ -1,23 +1,23 @@
-{% set version = "0.17.0" %}
+{% set version = "0.18.0" %}
 
 package:
   name: taxonkit
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('taxonkit', max_pin='x.x') }}
 
 source:
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx]
-    md5: 5c12cfac4939f966824eda8eb774cf9b # [osx]
+    md5: 2417d0b8a08210690498b98279c16ae0 # [osx]
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_arm64.tar.gz # [arm64]
-    md5: 4077cb27d588cd0c3ed174e80d9a54af # [arm64]
+    md5: 045a509947edf27345889db901291059 # [arm64]
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux and x86_64]
-    md5: bfedc8dbfc2db63460ed31843fc5f3c3 # [linux and x86_64]
+    md5: 5df8f74847a4b5968be787d78d6fc9a7 # [linux and x86_64]
   - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_arm64.tar.gz # [linux and aarch64]
-    md5: d0af9a15d225005705d8af63db6a970d # [linux and aarch64]
+    md5: 451aeaede731780d167b6771ca6d1f0e # [linux and aarch64]
 
 test:
   commands:

From 3fbd6936933f5c52aba472987adc57d7486ade2d Mon Sep 17 00:00:00 2001
From: Xiyu <xiyupeng@iastate.edu>
Date: Sat, 2 Nov 2024 14:29:07 -0500
Subject: [PATCH 50/65] Add amplici package in bioconda (#51847)

* add amplici

* minor changes based on the suggestion

* slightly change meta.yaml file

* edit build.sh

* update meta.yaml

* add gfortran requirement

* test v2.2

* update build.sh

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/amplici/build.sh  | 15 +++++++++++++
 recipes/amplici/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 recipes/amplici/build.sh
 create mode 100644 recipes/amplici/meta.yaml

diff --git a/recipes/amplici/build.sh b/recipes/amplici/build.sh
new file mode 100644
index 0000000000000..3b7588794ae9a
--- /dev/null
+++ b/recipes/amplici/build.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ `uname` == "Darwin" ]]; then
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+    export CONFIG_ARGS=""
+fi
+
+cd src || exit 1
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_C_COMPILER="${CC}" \
+    -DCMAKE_C_FLAGS="${CFLAGS}" \
+    "${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/amplici/meta.yaml b/recipes/amplici/meta.yaml
new file mode 100644
index 0000000000000..5949ed9ee80c6
--- /dev/null
+++ b/recipes/amplici/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = "2.2" %}
+
+package:
+  name: amplici
+  version: {{ version }}
+
+source:
+  url: https://github.com/DormanLab/AmpliCI/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 273362b5449ec29ff411d4c1aa5f89b1ec1eb361c8a9b69a4d89f4409fbdb70e
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("amplici", max_pin="x") }}
+
+requirements:
+  build:
+    - cmake
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - {{ compiler('fortran') }}
+  host:
+    - zlib
+
+about:
+  home: https://github.com/DormanLab/AmpliCI
+  license: BSD 3-Clause
+  license_family: BSD
+  license_file: LICENSE  
+  summary: "AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs."
+  dev_url: https://github.com/DormanLab/AmpliCI
+
+test:
+  commands:
+    - run_AmpliCI -h
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - xiyupeng
+  identifiers:
+    - biotools:amplici
+    - doi:10.1093/bioinformatics/btaa648

From 95bee8c1ef655a7440a0eba6e06adff979591f3c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 15:47:48 -0400
Subject: [PATCH 51/65] Update svision-pro to 2.1 (#51855)

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

diff --git a/recipes/svision-pro/meta.yaml b/recipes/svision-pro/meta.yaml
index 453d9406fca15..923e70cc358ee 100644
--- a/recipes/svision-pro/meta.yaml
+++ b/recipes/svision-pro/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "SVision-pro" %}
-{% set version = "2.0" %}
+{% set version = "2.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/songbowang125/{{ name }}/archive/v{{ version }}.tar.gz
-  sha256: 3892760ee421e1613f64cd7e61bd6876645e739fbf3198439e128fc9e50d1dd1
+  sha256: c642bee23cfad1796929b97c93aff50d10ba25ac1b484b2a1bef210fcb75e151
 
 build:
   number: 0

From f5934f60e08cc93cf8440e6b99e6af045178ce8f Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 16:40:56 -0400
Subject: [PATCH 52/65] Update goldrush to 1.2.1 (#51872)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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

diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml
index f9a23e06eccd6..efce055df5c10 100644
--- a/recipes/goldrush/meta.yaml
+++ b/recipes/goldrush/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "goldrush" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/bcgsc/goldrush/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz
-  sha256: 3f70860ed92b9313dbab16efed65ea7bc6080d78b4e18afc8cb910e086a7f0f7
+  sha256: 0b8b91b0477510d341af1736539416f30f70f67af9bd84161ea51c4c4a0fcc39
 
 build:
   skip: true  # [py < 38 or win or py > 39]

From 00d43e07e7f7318b005fa2533cbe477fc3deb8a4 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 16:41:10 -0400
Subject: [PATCH 53/65] Update nextstrain-cli to 8.5.4 (#51873)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update nextstrain-cli to 8.5.4

* Update meta.yaml

---------

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

diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml
index 88f19b53e3497..0dffea387c08a 100644
--- a/recipes/nextstrain-cli/meta.yaml
+++ b/recipes/nextstrain-cli/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "8.5.3" %}
+{% set version = "8.5.4" %}
 
 package:
   name: nextstrain-cli
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain_cli-{{ version }}.tar.gz
-  sha256: 5401fd3f1b60479cb3b8c0519917fa5df43fdaddd6007e158888283a5c872428
+  sha256: 3aa6c66d038d82de0c3bff2eb1b358599a9efc3f5f446eb523d3c9696aa72854
 
 build:
   number: 0
@@ -21,7 +21,7 @@ requirements:
   host:
     - python >=3.8
     - pip
-
+    - setuptools
   run:
     - python >=3.8
     - docutils

From dc2e4c4c0e241b3e0bda17cfecc6427cee0096f3 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 16:41:44 -0400
Subject: [PATCH 54/65] Update gsmap to 1.71.2 (#51854)

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

diff --git a/recipes/gsmap/meta.yaml b/recipes/gsmap/meta.yaml
index f6100dbb4139b..97fc02a0dd18f 100644
--- a/recipes/gsmap/meta.yaml
+++ b/recipes/gsmap/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gsmap" %}
-{% set version = "1.71.1" %}
+{% set version = "1.71.2" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/gsMap/{{ name }}-{{ version }}.tar.gz"
-  sha256: f81debacf46d3e26614411d938a27345fcb42999a8ef2b740d134e910c2d0bcd
+  sha256: d058fb9c1e346b40cf3e6a1cf27fc6458acf3cdb29eb7d4dd74cb119ab0f88a9
 
 build:
   noarch: python

From 2ba9720b057a5c6b7a61cffefc91503b9440ace3 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Sat, 2 Nov 2024 21:42:04 +0100
Subject: [PATCH 55/65] Sentieon add ARM support (#51837)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Sentieon add ARM support

Add ARM support to Sentieon recipe.

* Update meta.yaml

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/sentieon/meta.yaml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml
index be624c6675928..e2fee90b517d4 100644
--- a/recipes/sentieon/meta.yaml
+++ b/recipes/sentieon/meta.yaml
@@ -4,14 +4,14 @@ package:
   name: sentieon
   version: {{ version }}
 source:
-  - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz # [linux64]
-    sha256: d51d1a192aa9fd3108f4baa5e1d0784ea80af6734fcc1a27a57e15779f43fcf1 # [linux64]
-    patches: # [linux64]
+  - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz
+    sha256: d51d1a192aa9fd3108f4baa5e1d0784ea80af6734fcc1a27a57e15779f43fcf1
+    patches:
       # Fix driver scripts so they resolves location including symlinks
-      - sentieon_symlinks.patch # [linux64]
+      - sentieon_symlinks.patch
 
 build:
-  number: 0
+  number: 1
   skip: True # [not linux64]
   binary_relocation: false
   run_exports:
@@ -41,5 +41,6 @@ about:
   summary: Accelerated performance bioinformatics tools for mapping and variant calling
 
 extra:
-  skip-lints:
-      - should_be_noarch_generic # Supports Linux64 only
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

From bc6055397699a5401689b34deaabfa64fb6bfdd8 Mon Sep 17 00:00:00 2001
From: Wei Shen <shenwei356@gmail.com>
Date: Sun, 3 Nov 2024 11:02:03 +0800
Subject: [PATCH 56/65] Update SeqKit to v2.9.0 (#51860)

---
 recipes/seqkit/meta.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml
index 538a6f2093241..9994fb9779923 100644
--- a/recipes/seqkit/meta.yaml
+++ b/recipes/seqkit/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.8.2" %}
+{% set version = "2.9.0" %}
 
 package:
   name: seqkit
@@ -6,19 +6,19 @@ package:
 
 source:
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx]
-  md5: 03b13956b7e3ef1678db591a79eb68ed # [osx]
+  md5: 50fff73601f3094d664031e5c00674f5 # [osx]
 
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_arm64.tar.gz # [arm64]
-  md5: 0b2716f39c3974a5c3e310bcbd4076eb # [arm64]
+  md5: cf1b7c4b74664f04d3cc361e9c5370a1 # [arm64]
 
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux]
-  md5: 67220b508f3f81c2c8697e6534eed440 # [linux]
+  md5: 83e359c186dee6b49cd4df362d0b6d5a # [linux]
 
   url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_arm64.tar.gz # [aarch64]
-  md5: b83b021850c9447cfc8e0d5751b7be99 # [aarch64]
+  md5: 7a81adcd79553e10552456060c2b17ba # [aarch64]
 
 build:
-  number: 1
+  number: 0
   skip: False
   run_exports:
     - {{ pin_subpackage("seqkit", max_pin="x.x") }}

From be644c5eb7fc0c7b3970cc86756144dc5cca11f7 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Sun, 3 Nov 2024 04:18:15 +0100
Subject: [PATCH 57/65] update version to 1.38.0 (#51877)

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

diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml
index 99dbefecd9faf..ffe275e39ca5f 100644
--- a/recipes/bioconductor-protgenerics/meta.yaml
+++ b/recipes/bioconductor-protgenerics/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "1.34.0" %}
+{% set version = "1.38.0" %}
 {% set name = "ProtGenerics" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
@@ -11,7 +11,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 5d55c00588169aa089bb457e2d94669a
+  md5: 7e7211a9fa758ca6f1b701c86e892895
 build:
   number: 0
   rpaths:

From 4abf5661c4e04e38b10d2e3b27d3451ebcf64014 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Sat, 2 Nov 2024 21:34:56 -0700
Subject: [PATCH 58/65] Bump MUSCLE to 5.2 (#51881)

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
---
 recipes/muscle/build.sh                    |  19 +-
 recipes/muscle/meta.yaml                   |  10 +-
 recipes/muscle/support-linux-aarch64.patch |  14 +-
 recipes/muscle/vcxproj_make.py             | 225 +++++++++++++++++++++
 4 files changed, 251 insertions(+), 17 deletions(-)
 create mode 100644 recipes/muscle/vcxproj_make.py

diff --git a/recipes/muscle/build.sh b/recipes/muscle/build.sh
index 6e358f5e2b44b..a6fb04c9c3860 100644
--- a/recipes/muscle/build.sh
+++ b/recipes/muscle/build.sh
@@ -1,9 +1,18 @@
 #!/bin/bash
+set -e
 
-cd src/
-sed -i.bak -e 's/ -static//' Makefile
+mkdir -p ${PREFIX}/bin
+cd src || exit 1
+echo "0" > gitver.txt
 
-make CXX=$CXX
+cp ${RECIPE_DIR}/vcxproj_make.py .
+chmod +x vcxproj_make.py
+./vcxproj_make.py --openmp --cppcompiler ${CXX}
 
-mkdir -p "$PREFIX"/bin
-cp "$(uname)"/muscle "$PREFIX"/bin/muscle
+# Verify binary exists and is executable
+if [ ! -x ../bin/muscle ]; then
+    echo "Error: muscle binary not found"
+    exit 1
+fi
+
+cp ../bin/muscle ${PREFIX}/bin/muscle
diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml
index 9953f38bd5c3e..f52e85ac70a5e 100644
--- a/recipes/muscle/meta.yaml
+++ b/recipes/muscle/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "muscle" %}
-{% set version = "5.1.0" %}
+{% set version = "5.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/rcedgar/muscle/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d
+  url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 7aff1473241a36da94a88f37920a343fae91d2b6faae22e15c06591d1d0339b6
   patches:
     - support-linux-aarch64.patch
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -30,7 +30,7 @@ about:
   home: https://github.com/rcedgar/muscle
   license: GPL-3.0-only
   license_file: LICENSE
-  summary: "MUSCLE: multiple sequence alignment with high accuracy and high throughput"
+  summary: Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences
 
 extra:
   additional-platforms:
diff --git a/recipes/muscle/support-linux-aarch64.patch b/recipes/muscle/support-linux-aarch64.patch
index 9308bf3333e2b..f9c8e2081e8b8 100644
--- a/recipes/muscle/support-linux-aarch64.patch
+++ b/recipes/muscle/support-linux-aarch64.patch
@@ -1,10 +1,10 @@
-diff --git i/src/myutils.h w/src/myutils.h
-index 49d28ef..8e8167e 100644
---- i/src/myutils.h
-+++ w/src/myutils.h
-@@ -11,7 +11,7 @@
- #define TRACK_ALLOC		0
- #define ALLOC_TOTALS	0
+diff --git a/src/myutils.h b/src/myutils.h
+index a5d8a58..fbf6f9f 100644
+--- a/src/myutils.h
++++ b/src/myutils.h
+@@ -10,7 +10,7 @@
+ #include <cstddef>
+ #include "myalloc.h"
  
 -#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__)
 +#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__aarch64__)
diff --git a/recipes/muscle/vcxproj_make.py b/recipes/muscle/vcxproj_make.py
new file mode 100644
index 0000000000000..739663b29c933
--- /dev/null
+++ b/recipes/muscle/vcxproj_make.py
@@ -0,0 +1,225 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+Usage = (
+    "Convert Visual Studio .vcxproj file in current directory to Makefile and run make."
+)
+
+AP = argparse.ArgumentParser(description=Usage)
+
+# Value opts
+AP.add_argument(
+    "--std",
+    required=False,
+    help="C++ standard option for GCC, e.g. c++11 or c++17 (default none)",
+)
+AP.add_argument(
+    "--cppcompiler",
+    required=False,
+    default="g++",
+    help="C++ compiler command name default g++)",
+)
+AP.add_argument(
+    "--ccompiler",
+    required=False,
+    default="gcc",
+    help="C++ compiler command name default gcc)",
+)
+
+# Flag opts
+AP.add_argument("--debug", required=False, action="store_true", help="Debug build")
+AP.add_argument("--openmp", required=False, action="store_true", help="Requires OMP")
+AP.add_argument(
+    "--pthread", required=False, action="store_true", help="Requires pthread"
+)
+AP.add_argument("--lrt", required=False, action="store_true", help="Requires lrt")
+AP.add_argument(
+    "--symbols",
+    required=False,
+    action="store_true",
+    help="Debug symbols (default if --debug)",
+)
+AP.add_argument(
+    "--nostrip",
+    required=False,
+    action="store_true",
+    help="Don't strip symbols (default if --debug or --symbols)",
+)
+
+Args = AP.parse_args()
+debug = Args.debug
+std = Args.std
+cppcompiler = Args.cppcompiler
+ccompiler = Args.ccompiler
+nostrip = debug or Args.symbols
+symbols = debug or Args.symbols
+
+ProjFileName = None
+HdrNames = []
+for FileName in os.listdir("."):
+    if FileName.endswith(".vcxproj"):
+        ProjFileName = FileName
+    elif FileName.endswith(".h"):
+        HdrNames.append(FileName)
+if ProjFileName is None:
+    sys.stderr.write("\nProject file not found in current directory\n")
+    sys.exit(1)
+
+binary = ProjFileName.replace(".vcxproj", "")
+sys.stderr.write("binary=" + binary + "\n")
+
+compiler_opts = " -ffast-math -march=native"
+linker_opts = " -ffast-math -march=native"
+
+if std:
+    compiler_opts += " --std=" + std
+
+if debug:
+    compiler_opts += " -O0 -DDEBUG"
+    linker_opts += " -O0"
+else:
+    compiler_opts += " -O3 -DNDEBUG"
+    linker_opts += " -O3"
+
+if symbols:
+    compiler_opts += " -g3"
+    linker_opts += " -g3"
+
+if Args.openmp:
+    compiler_opts += " -fopenmp"
+    linker_opts += " -fopenmp"
+
+if Args.pthread:
+    compiler_opts += " -pthread"
+    linker_opts += " -lpthread"
+
+rc = os.system(r"rm -rf o/ ../bin/%s*" % binary)
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- failed to clean\n\n")
+    sys.exit(1)
+sys.stderr.write("clean done.\n")
+
+OBJDIR = "o"
+BINDIR = "../bin"
+
+Fields = ProjFileName.split("/")
+n = len(Fields)
+Name = Fields[n - 1]
+Fields = Name.split(".")
+binary = Fields[0]
+
+CXXNames = []
+CNames = []
+with open(ProjFileName) as File:
+    for Line in File:
+        Line = Line.strip()
+        Line = Line.replace('"', "")
+        Line = Line.replace(" ", "")
+        # <ClCompile Include="betadiv.cpp" />
+        if Line.startswith("<ClCompileInclude"):
+            Fields = Line.split("=")
+            if len(Fields) != 2:
+                continue
+            FileName = Fields[1]
+            FileName = FileName.replace("/>", "")
+            if FileName.endswith(".cpp"):
+                FileName = FileName.replace(".cpp", "")
+                CXXNames.append(FileName)
+            elif FileName.endswith(".c"):
+                FileName = FileName.replace(".c", "")
+                CNames.append(FileName)
+
+assert len(CXXNames) > 0 or len(CNames) > 0
+
+with open("Makefile", "w") as f:
+
+    def Out(s):
+        print(s, file=f)
+
+    BINPATH = "$(BINDIR)/%s" % (binary)
+
+    Out("######################################################")
+    Out("# Makefile is generated by " + sys.argv[0])
+    Out("# Don't edit the Makefile -- update the python script")
+    Out("######################################################")
+    Out("")
+    Out("BINDIR := %s" % BINDIR)
+    Out("OBJDIR := %s" % OBJDIR)
+    Out("BINPATH := %s" % BINPATH)
+
+    if CNames:
+        Out("")
+        Out("CC = " + ccompiler)
+        Out("CFLAGS := $(CFLAGS) " + compiler_opts)
+
+    if CXXNames:
+        Out("")
+        Out("CXX = " + cppcompiler)
+        Out("CXXFLAGS := $(CFLAGS) " + compiler_opts)
+
+    Out("")
+    Out("UNAME_S := $(shell uname -s)")
+    Out("LDFLAGS := $(LDFLAGS) " + linker_opts)
+    Out("ifeq ($(UNAME_S),Linux)")
+    Out("    LDFLAGS += -static")
+    Out("endif")
+
+    Out("")
+    Out("HDRS = \\")
+    for Name in sorted(HdrNames):
+        Out("  %s \\" % Name)
+
+    Out("")
+    Out("OBJS = \\")
+    for Name in CXXNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    for Name in CNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    Out("")
+    Out(".PHONY: clean")
+
+    Out("")
+    Out("$(BINPATH) : $(BINDIR)/ $(OBJDIR)/ $(OBJS)")
+
+    if len(CXXNames) > 0:
+        Cmd = "\t$(CXX) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+    else:
+        Cmd = "\t%(CC) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+
+    if Args.lrt:
+        Cmd += " -lrt"
+    Out(Cmd)
+
+    if not nostrip:
+        Out("	strip $(BINPATH)")
+
+    Out("")
+    Out("$(OBJDIR)/ :")
+    Out("	mkdir -p $(OBJDIR)/")
+
+    Out("")
+    Out("$(BINDIR)/ :")
+    Out("	mkdir -p $(BINDIR)/")
+
+    if CNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.c $(HDRS)")
+        Out("	$(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<")
+
+    if CXXNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.cpp $(HDRS)")
+        Out("	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<")
+
+sys.stderr.write("Makefile done.\n")
+
+rc = os.system("make")
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- make failed\n\n")
+    sys.exit(1)
+sys.stderr.write("make done.\n")

From 5bb866979804b7dd566fa446c4b2b109c8478ada Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 3 Nov 2024 02:42:56 -0500
Subject: [PATCH 59/65] Update rabbitqcplus to 2.3.0 (#51888)

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

diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml
index d85b61e5b355c..ba6390ac5ee70 100644
--- a/recipes/rabbitqcplus/meta.yaml
+++ b/recipes/rabbitqcplus/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.2.9" %}
+{% set version = "2.3.0" %}
 
 package:
   name: rabbitqcplus
@@ -6,10 +6,10 @@ package:
 
 source:
   url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 076cb1e11046d5a41464f74d7df363e2ea337e2cf3ad8e8b0712c5c7df746466
+  sha256: 9ce239d998582c50c373eefc8d5f83763439693fe348206107f27105a22d4aaf
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }}

From 92c334d737865661931512d141a70dad1cf835a9 Mon Sep 17 00:00:00 2001
From: Cormac Kinsella <27350062+CormacKinsella@users.noreply.github.com>
Date: Sun, 3 Nov 2024 10:13:11 +0100
Subject: [PATCH 60/65] update vg to 1.60.0 (#51863)

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

diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml
index 9ec0557e1bc67..4500b2e91bddb 100644
--- a/recipes/vg/meta.yaml
+++ b/recipes/vg/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "vg" %}
-{% set version = "1.59.0" %}
+{% set version = "1.60.0" %}
 
 package:
   name: {{ name }}
@@ -7,9 +7,9 @@ package:
 
 source:
   - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg       # [linux and x86_64]
-    sha256: a2270237c8541867ac345ad924c1641881bc9fd60be157a6d3d29fa910aacfc2    # [linux and x86_64]
+    sha256: 8a014a89301fa3168b19adadfa23753dcfd4af3944493199028ec79c141da22e    # [linux and x86_64]
   - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg-arm64 # [linux and aarch64]
-    sha256: e0df4e81e0c7b3ac1c7f3fc7a7bc8421416256bf2bc4a1ca2b87feebaf40d4d0    # [linux and aarch64]
+    sha256: b7700ac536cee961e0fe6bfd5cfd3b3f93844be47b45f21d67e0a0208fc01bc0    # [linux and aarch64]
 
 build:
   number: 0

From 0d6fa8c3466aa0ce5e3084e851e384f4b82c9f99 Mon Sep 17 00:00:00 2001
From: Parham Kazemi <pkazemi3@gmail.com>
Date: Sun, 3 Nov 2024 05:33:31 -0800
Subject: [PATCH 61/65] Add ntStat (#51884)

* Create meta.yaml

* Create build.sh

* Update meta.yaml
---
 ntstat/build.sh  |  4 ++++
 ntstat/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 ntstat/build.sh
 create mode 100644 ntstat/meta.yaml

diff --git a/ntstat/build.sh b/ntstat/build.sh
new file mode 100644
index 0000000000000..5b5b9d640ee41
--- /dev/null
+++ b/ntstat/build.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+meson setup --buildtype release --prefix=$PREFIX build
+meson install -C build
diff --git a/ntstat/meta.yaml b/ntstat/meta.yaml
new file mode 100644
index 0000000000000..301e6426276d3
--- /dev/null
+++ b/ntstat/meta.yaml
@@ -0,0 +1,48 @@
+{% set version = "1.0.0" %}
+
+package:
+  name: ntstat
+  version: {{ version }}
+
+source:
+  url: https://github.com/bcgsc/ntStat/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 262dc58ab6f781a6816a5d4fc129659c7fa2c3364871320eafb45bfa822fab6a
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('ntstat', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - meson
+    - meson-python
+    - cmake
+  host:
+    - python
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
+    - btllib >=1.7.2
+    - cpp-argparse
+    - cpp-tabulate
+    - indicators
+    - pybind11
+  run:
+    - python
+    - ntcard
+    - matplotlib
+    - numpy
+    - scipy
+    - tabulate
+
+test:
+  commands:
+    - ntstat --version
+    - ntstat count --help
+
+about:
+  home: https://github.com/bcgsc/ntStat
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: 'a toolkit for statistical analysis of k-mer frequency and depth'

From f4f49181943e42535875300ad7d2baeccadf26b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= <andreas.sjodin@gmail.com>
Date: Sun, 3 Nov 2024 14:37:31 +0100
Subject: [PATCH 62/65] Adding msa4u (#51864)

* Adding msa4u

* Add run_export

* Update meta.yaml

Clean up dependencies

* Update meta.yaml

* Fix home url
---
 recipes/msa4u/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 recipes/msa4u/meta.yaml

diff --git a/recipes/msa4u/meta.yaml b/recipes/msa4u/meta.yaml
new file mode 100644
index 0000000000000..a932f8d7df7a1
--- /dev/null
+++ b/recipes/msa4u/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "msa4u" %}
+{% set version = "0.4.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/msa4u-{{ version }}.tar.gz
+  sha256: 0471f334bbc1fbb8ea6c0974c39f9aed59030b32d3d790caf814c8f53c393c17
+
+build:
+  run_exports:    
+    - {{ pin_subpackage("msa4u", max_pin="x.x") }}
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  noarch: python
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - biopython
+    - pandas
+    - reportlab
+    - configs
+
+test:
+  imports:
+    - msa4u
+  commands:
+    - msa4u --help
+
+about:
+  home: https://github.com/GCA-VH-lab/msa4u
+  summary: "A simple visualisation tool for Multiple Sequence Alignment."
+  license: WTFPL
+  license_file: LICENSE

From b1a909e874026d70c1f21918e8e3b0a870d193b3 Mon Sep 17 00:00:00 2001
From: Iyad Ba Gari <39617810+bagari@users.noreply.github.com>
Date: Sun, 3 Nov 2024 09:27:26 -0800
Subject: [PATCH 63/65] Update meta-neuro version 1.0.0 (#51826)

* update meta.yaml file for meta package version 1.0.0

https://bioconda.github.io/recipes/meta/README.html#package-meta

* Update meta.yaml

* Fix boost version compatibility with ITK

* update ITK version to 5.3.0 to prevent install libitk and version 5.4rc02

* update ITK run section at meta.yaml

* Update meta.yaml

* Add libgl-devel

* Update meta.yaml

* update build_variant

* Include test data into meta folder

Moving test data into the meta folder to solve the input data error does not exist during the container test.

* adding test data

* change and saved test data into $PREFIX/share/meta/example

* add python support 3.8-3.11

Python 3.12 will be supported after ITK updates its release.

* update meta.yaml with skipping python 3.12

* debug "No space left on device" issue

* Drop support python 3.8 to solve storage issue, hopefully

* Update build to rebuild and check storage issue.

* Update meta.yaml

* Build only for python 3.10

* incrementing the build number

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update meta.yaml

* Delete conda_build_config.yaml

* Update meta.yaml

* support apple arm

* trying support vtk with egl variant

* Update meta.yaml

* keep only support VTK with osmesa for linux

* Update meta.yaml

* last attempt to build all python variants, hope no space error

* force to skip python 3.12

* Update conda_build_config.yaml

* Update package name from meta to meta-neuro

* update folder name as well

* update name to meta-neuro
---
 recipes/{meta => meta-neuro}/build.sh      | 17 ++++--
 recipes/meta-neuro/conda_build_config.yaml | 18 +++++++
 recipes/{meta => meta-neuro}/meta.yaml     | 60 ++++++++++------------
 3 files changed, 57 insertions(+), 38 deletions(-)
 rename recipes/{meta => meta-neuro}/build.sh (71%)
 mode change 100755 => 100644
 create mode 100644 recipes/meta-neuro/conda_build_config.yaml
 rename recipes/{meta => meta-neuro}/meta.yaml (54%)
 mode change 100755 => 100644

diff --git a/recipes/meta/build.sh b/recipes/meta-neuro/build.sh
old mode 100755
new mode 100644
similarity index 71%
rename from recipes/meta/build.sh
rename to recipes/meta-neuro/build.sh
index b7767bfc0161f..b30b786bedb79
--- a/recipes/meta/build.sh
+++ b/recipes/meta-neuro/build.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -ex
 
 unset LD LINK ARCH
 export CMAKE_INSTALL_RPATH='$ORIGIN/../lib'
@@ -8,8 +9,12 @@ mkdir -p "$PREFIX/bin"
 mkdir -p "$PREFIX/lib"
 mkdir -p "$PREFIX/share"
 mkdir -p $SRC_DIR/build
-cd $SRC_DIR/build || exit 1
 
+## copy small test data:
+mkdir -p $PREFIX/share/meta-neuro/example
+cp $SRC_DIR/resources/test.nii.gz $PREFIX/share/meta-neuro/example/
+
+cd $SRC_DIR/build
 cmake -S $SRC_DIR -B $SRC_DIR/build  \
     -DCMAKE_BUILD_TYPE=Release \
     -DCMAKE_INSTALL_PREFIX=$PREFIX \
@@ -19,10 +24,12 @@ cmake -S $SRC_DIR -B $SRC_DIR/build  \
     -DCMAKE_INSTALL_RPATH=$CMAKE_INSTALL_RPATH \
     -DCMAKE_BUILD_WITH_INSTALL_RPATH=$CMAKE_BUILD_WITH_INSTALL_RPATH
 
-cmake --build . --config Release --parallel ${CPU_COUNT} --verbose || exit 1
-cmake --install . || exit 1
+cmake --build . --config Release --parallel ${CPU_COUNT} --verbose
+cmake --install .
+
+# Clean up build directory
 rm -rf $SRC_DIR/build
 
 # Install MeTA package
-cd ${SRC_DIR} || exit 1
-${PYTHON} -m pip install . --no-deps -vv || exit 1
+cd ${SRC_DIR}
+${PYTHON} -m pip install . --no-deps -vv
diff --git a/recipes/meta-neuro/conda_build_config.yaml b/recipes/meta-neuro/conda_build_config.yaml
new file mode 100644
index 0000000000000..09a4e9197bc16
--- /dev/null
+++ b/recipes/meta-neuro/conda_build_config.yaml
@@ -0,0 +1,18 @@
+build_variant:
+  - "osmesa"  # [linux]
+  - "qt"      # [osx]
+
+python:
+  - 3.11.*  *_cpython
+  - 3.10.*  *_cpython
+  - 3.9.*  *_cpython
+
+python_impl:
+  - cpython
+  - cpython
+  - cpython
+
+numpy:
+  - 1.23.*
+  - 1.22.*
+  - 1.22.*
diff --git a/recipes/meta/meta.yaml b/recipes/meta-neuro/meta.yaml
old mode 100755
new mode 100644
similarity index 54%
rename from recipes/meta/meta.yaml
rename to recipes/meta-neuro/meta.yaml
index 331b63318f57e..dfcd922cb0f7c
--- a/recipes/meta/meta.yaml
+++ b/recipes/meta-neuro/meta.yaml
@@ -1,7 +1,6 @@
-{% set name = "meta" %}
+{% set name = "meta-neuro" %}
 {% set version = "1.0.0" %}
-{% set sha256 = "a35dd5bc3ccffaaf83aa488233467ae85dc5374aea3068c34a6dc85ea29e27a9" %}
-{% set build_variant = "osmesa" if linux else "qt" %}
+{% set sha256 = "c67bcad0899fc3f9c890ee26e9c1c2ab1a892430ce00a9ac090e36697efc9434" %}
 
 package:
   name: {{ name|lower }}
@@ -13,9 +12,9 @@ source:
 
 build:
   number: 0
-  skip: true # [not py39]
+  skip: true  # [win ]
   run_exports:
-    - {{ pin_subpackage('meta', max_pin="x") }}
+    - {{ pin_subpackage('meta-neuro', max_pin="x.x.x") }}
 
 requirements:
   build:
@@ -24,45 +23,38 @@ requirements:
     - make  # [not win]
 
   host:
-    - python >=3.9,<3.10
-    - pip
-    - boost =1.82
-    - itk =5.3.0
-    - libitk =5.3.0
-    - libitk-devel =5.3.0
+    - vtk >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libitk-devel ==5.3.0
     - hdf5 >=1.14.2,<1.14.3.0a0
-    - vtk-base >=9.2.6,<9.3.0 build=*{{ build_variant }}*
-    - libexpat >=2.5.0,<2.6.0
-    - vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libboost-python-devel >=1.82.0,<1.83.0
+    - python
+    - pip
+    - setuptools
 
   run:
-    - qhull
-    - boost =1.82
-    - itk =5.3.0
-    - libitk =5.3.0
-    - libitk-devel =5.3.0
+    - vtk >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libitk-devel ==5.3.0
     - hdf5 >=1.14.2,<1.14.3.0a0
-    - vtk-base >=9.2.6,<9.3.0 build=*{{ build_variant }}*
-    - numpy >=1.21
-    - nibabel
-    - pandas
-    - pyvista
-    - scipy
+    - libboost-python-devel >=1.82.0,<1.83.0
+    - qhull
+    - python
+    - pip
+    - setuptools
+    - numpy
     - tqdm
-    - tslearn
     - dipy
-    - libexpat >=2.5.0,<2.6.0
-    - vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - scipy
+    - pandas
+    - nibabel
+    - tslearn
+    - pyvista
 
 test:
-  source_files:
-    - resources/CST_R.nii.gz
   imports:
     - meta
   commands:
-    - meta --help 2>&1 || exit 1
-    - vtklevelset resources/CST_R.nii.gz CST_R.vtk 0.1 && test -f CST_R.vtk
-    - cmrep_vskel -c 3 -p 1.5 -g CST_R.vtk CST_R_skeleton.vtk && test -f CST_R_skeleton.vtk
+    - vtklevelset $PREFIX/share/meta-neuro/example/test.nii.gz test.vtk 0.1
+    - cmrep_vskel -c 3 -p 1.5 -g test.vtk test_skeleton.vtk
 
 about:
   home: https://github.com/bagari/meta
@@ -76,5 +68,7 @@ about:
 
 extra:
   bulk: true
+  additional-platforms:
+    - osx-arm64
   recipe-maintainers:
     - bagari

From 8085db6165affca6f86b3bb79bde2078e535ba5e Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 3 Nov 2024 13:04:47 -0500
Subject: [PATCH 64/65] Update jbrowse2 to 2.16.1 (#51891)

---
 recipes/jbrowse2/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml
index 077e3f555dfcc..b280429eb499e 100644
--- a/recipes/jbrowse2/meta.yaml
+++ b/recipes/jbrowse2/meta.yaml
@@ -1,12 +1,12 @@
 # When updating, check the @jbrowse/cli version in build.sh too
-{% set version = "2.16.0" %}
+{% set version = "2.16.1" %}
 
 package:
   name: jbrowse2
   version: {{ version }}
 
 source:
-  sha256: 5f58748cf7c3dcbaddbf87e123cfa878f0d64d3e965bd2ac9bda1b359db40dfd
+  sha256: b869ab507a765e775dd961d5abfb0b1982dd01b3dd7648d9c3d062c2fab32cfe
   url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip
 
 build:

From a425455e8dd70c6044381c6155cebac010781f2f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 3 Nov 2024 19:41:28 +0100
Subject: [PATCH 65/65] Revert "Add ntStat (#51884)" (#51892)

This reverts commit 0d6fa8c3466aa0ce5e3084e851e384f4b82c9f99.
---
 ntstat/build.sh  |  4 ----
 ntstat/meta.yaml | 48 ------------------------------------------------
 2 files changed, 52 deletions(-)
 delete mode 100644 ntstat/build.sh
 delete mode 100644 ntstat/meta.yaml

diff --git a/ntstat/build.sh b/ntstat/build.sh
deleted file mode 100644
index 5b5b9d640ee41..0000000000000
--- a/ntstat/build.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-
-meson setup --buildtype release --prefix=$PREFIX build
-meson install -C build
diff --git a/ntstat/meta.yaml b/ntstat/meta.yaml
deleted file mode 100644
index 301e6426276d3..0000000000000
--- a/ntstat/meta.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-{% set version = "1.0.0" %}
-
-package:
-  name: ntstat
-  version: {{ version }}
-
-source:
-  url: https://github.com/bcgsc/ntStat/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 262dc58ab6f781a6816a5d4fc129659c7fa2c3364871320eafb45bfa822fab6a
-
-build:
-  number: 0
-  run_exports:
-    - {{ pin_subpackage('ntstat', max_pin="x") }}
-
-requirements:
-  build:
-    - {{ compiler('cxx') }}
-    - meson
-    - meson-python
-    - cmake
-  host:
-    - python
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
-    - btllib >=1.7.2
-    - cpp-argparse
-    - cpp-tabulate
-    - indicators
-    - pybind11
-  run:
-    - python
-    - ntcard
-    - matplotlib
-    - numpy
-    - scipy
-    - tabulate
-
-test:
-  commands:
-    - ntstat --version
-    - ntstat count --help
-
-about:
-  home: https://github.com/bcgsc/ntStat
-  license: GPL-3.0-or-later
-  license_file: LICENSE
-  summary: 'a toolkit for statistical analysis of k-mer frequency and depth'