From 8754263e6c17f7e4afcab9df9f5d54f71ae73320 Mon Sep 17 00:00:00 2001
From: Alex Fraser <79180900+AlexSCFraser@users.noreply.github.com>
Date: Fri, 15 Nov 2024 10:45:30 -0800
Subject: [PATCH 01/57] Update SACCHARIS (#52118)

* Add recipe for saccharis 2.0 dev18 build 1 to bioconda

* updated to use git tag

* updated to use a python package generated from setuptools build, with sha256 hash, and added --single-version-externally-managed --record=record.txt args to setup.py install as per bioconda test suite

* lowercased hash, since it's case-sensitive

* added filename as "fn: saccharis-{{ version }}.tar.gz"

* removed filename since bioconda considers it an error

* update url link

* update sha256

* remove unneeded comments

* remove tests which write files

* remove tests which write files, with comment

* add new release data to bioconda recipe

* change build number to zero to satisfy bioconda linter

* add blast dependency

* add run_exports breaking change behaviour

* change name to lowercase in run_exports

* fix spacing

* nesting issue

* remove nesting

* fix version spacing

* update to dev20

* update to dev20

* update to dev21

* fix >= sign

* increment build to fix small error

* update file hash and increment build

* revert 2.0.1 to working dev21 build

* upload 2.0.1 dev21 version with fixed database download

* upload 2.0.1 dev21 version with another database download fix

* increment build num

* increment build num

* increment build num

* update setuptools build requirements

* update setuptools build requirements

* update to build 3, which replaces wget with requests

* update hash

* increment build with yet another small patch to try and fix these database downloads

* increment build with yet another small patch to try and fix database downloads

* adjust whitespace

* increment to build 6

* update python dependency

* increment to build 7

adds chunk reducing size to database download streaming

* update cazy.org links to https

increment to build 8
---
 recipes/saccharis/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml
index 5dd7db2b51e4d..dc9c7a06898df 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 = "DEFE4B98CFF4F5ED58A102D7FFE0CC219C4EC44C257AC0469255CDC73F124F57" %}
+{% set hash = "C808429EADDAA31E0E611DF0564BA6CA36CE6CBB69A98DFB79CC59972352FD16" %}
 
 
 package:
@@ -9,12 +9,12 @@ 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_7.tar.gz
+  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_8.tar.gz
   sha256: {{ hash|lower }}
 
 build:
   noarch: python
-  number: 7
+  number: 8
 
   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

From 483df4a9f82401554dad5391f70947b7e58c3187 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 13:45:47 -0500
Subject: [PATCH 02/57] Update mvip to 1.1.5 (#52120)

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

diff --git a/recipes/mvip/meta.yaml b/recipes/mvip/meta.yaml
index 613e0bbbd9bb8..4dfddf3a53a2e 100644
--- a/recipes/mvip/meta.yaml
+++ b/recipes/mvip/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mvip" %}
-{% set version = "1.1.4" %}
+{% set version = "1.1.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: ca056513e45714c5988aba02572aa179055b17100a0c4192a274324a02e8cc46
+  sha256: 61f1c5de4bd74b8453eaad5bdd8c95ad46c6b7e10a13977e3734696696785b42
 
 build:
   number: 0

From e717c2f51abef490d3950dad88e84cbf4ec6ed74 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 13:57:31 -0500
Subject: [PATCH 03/57] Update ebi-eva-common-pyutils to 0.6.11 (#52136)

---
 recipes/ebi-eva-common-pyutils/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml
index f06b115b8bb5c..2753d1c68df3b 100644
--- a/recipes/ebi-eva-common-pyutils/meta.yaml
+++ b/recipes/ebi-eva-common-pyutils/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ebi-eva-common-pyutils" %}
-{% set version = "0.6.10" %}
+{% set version = "0.6.11" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz
-  sha256: f143c703e31f40c94ebe366ba5f8a8247b6c825590ac157a7f5495f36aa7accb
+  sha256: 503f15c55b8438295727661486d610e87b7e9c9ca159ff8e373d0533094eb93b
 
 build:
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation

From 4a34a4e0bf462c14bb380cf90f92321d55e59f65 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 13:58:07 -0500
Subject: [PATCH 04/57] Update argo to 0.1.3 (#52133)

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

diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
index 3378a76c20d47..4dd54b605147c 100644
--- a/recipes/argo/meta.yaml
+++ b/recipes/argo/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "argo" %}
-{% set version = "0.1.2" %}
+{% set version = "0.1.3" %}
 
 package:
   name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0
+  sha256: c6be3e1efc744a591524979a53895f9cbd70962a1825d8e2b442f5ffb7a3cc6b
 
 build:
   noarch: python

From 1b7f485abfbaa919b8f696783b930dbadfbd9d0c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 13:58:43 -0500
Subject: [PATCH 05/57] Update virheat to 0.7.3 (#52131)

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

diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml
index f5f2accc2568d..ee07000da75ec 100644
--- a/recipes/virheat/meta.yaml
+++ b/recipes/virheat/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "virheat" %}
-{% set version = "0.7.2" %}
+{% set version = "0.7.3" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz
-  sha256: eb1586cd2d62ea21c398d099c44c73f045bb03dff2a44ac03d787a06ee3490fc
+  sha256: 35ce98dd10af4d2519195c6351321b6f5f26d699ad662c0c5e75f7cec00c3dd1
 
 build:
   entry_points:

From b719247f431579342633431337f5e7bd10146ca5 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:27:52 -0500
Subject: [PATCH 06/57] Update breakfast to 0.4.5 (#52137)

* Update breakfast to 0.4.5

* add run_exports

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/breakfast/meta.yaml | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/recipes/breakfast/meta.yaml b/recipes/breakfast/meta.yaml
index cf7699d277b38..ae6d83de4c28e 100644
--- a/recipes/breakfast/meta.yaml
+++ b/recipes/breakfast/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "breakfast" %}
-{% set version = "0.4.3" %}
+{% set version = "0.4.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,43 +7,44 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/breakfast-{{ version }}.tar.gz
-  sha256: a241e0d4891c62635f1b99559271fb4b7777ffa60ef67e25be579d6750c01b9c
+  sha256: 5dd370d4d6d92d7b161acc5356b3b6c7f454d9c0665a8abac38e5f6c012d3eee
 
 build:
   entry_points:
     - breakfast = breakfast.console:main
+  run_exports:
+    - {{ pin_subpackage('breakfast', max_pin="x.x") }}
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
 
 requirements:
   host:
     - pip
-    - poetry
-    - python >=3.6,<3.11
+    - poetry-core
+    - python >=3.11,<3.13
   run:
-    - click >=8.1.3,<9.0.0
-    - networkx >=2.8,<3.0
-    - numpy >=1.22.3,<2.0.0
-    - pandas >=1.4.2,<2.0.0
+    - click >=8.1.7,<9.0.0
+    - networkx >=3.4.2,<4.0.0
+    - numpy >=2.1.3,<3.0.0
+    - pandas >=2.2.3,<3.0.0
     - python >=3.9,<3.11
-    - scikit-learn >=1.0.2,<2.0.0
-    - scipy >=1.8.0,<2.0.0
+    - scikit-learn >=1.5.2,<2.0.0
+    - scipy >=1.14.1,<2.0.0
 
 test:
   imports:
     - breakfast
   commands:
-    - pip check
     - breakfast --help
-  requires:
-    - pip
 
 about:
   home: https://github.com/rki-mf1/breakfast
-  summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs'
+  summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs.'
   license: MIT
+  license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/rki-mf1/breakfast
 
 extra:
   recipe-maintainers:

From 6b085275fd64fc0c212bb8bcb9c4115b572f838c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:46:41 -0500
Subject: [PATCH 07/57] Update gubbins to 3.4 (#52126)

* Update gubbins to 3.4

* add pip

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/gubbins/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml
index 2166a683609f3..a2454b35b7e55 100644
--- a/recipes/gubbins/meta.yaml
+++ b/recipes/gubbins/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gubbins" %}
-{% set version = "3.3.5" %}
-{% set sha256 = "4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774" %}
+{% set version = "3.4" %}
+{% set sha256 = "ff134b7c1d06eee548e94f417394fb67229caf1b0d35b097a71309017ac7a91d" %}
 
 package:
   name: {{ name|lower }}
@@ -29,6 +29,7 @@ requirements:
     - perl
     - zlib
     - python >=3.8,<3.10
+    - pip
     - scipy
     - setuptools
     - dendropy

From 16501fd51e74bba515119bb1766e0959dccc0a6d Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 15:03:48 -0500
Subject: [PATCH 08/57] Update perl-class-methodmaker to 2.25 (#52134)

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

diff --git a/recipes/perl-class-methodmaker/meta.yaml b/recipes/perl-class-methodmaker/meta.yaml
index c7b7743f1fcf9..008ce2d081dce 100644
--- a/recipes/perl-class-methodmaker/meta.yaml
+++ b/recipes/perl-class-methodmaker/meta.yaml
@@ -1,20 +1,20 @@
 {% set name = "perl-class-methodmaker" %}
-{% set version = "2.24" %}
-{% set sha256 = "5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328" %}
+{% set version = "2.25" %}
+{% set sha256 = "70bd3a6595cc40e54a9521eae3247e7d69166e6783ea5faebd59b84537e1b588" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: http://search.cpan.org/CPAN/authors/id/S/SC/SCHWIGON/class-methodmaker/Class-MethodMaker-2.24.tar.gz
+  url: https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker/Class-MethodMaker-2.25.tar.gz
   sha256: {{ sha256 }}
 
 
 build:
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
-  number: 5
+  number: 0
 
 requirements:
   build:

From 86c0896fb464c18fcc4e92474f16be27bb27fc47 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Fri, 15 Nov 2024 21:08:11 +0100
Subject: [PATCH 09/57] krakentools: alpha_diversity requires scipy (#52125)

* alpha_diversity requires scipy

https://github.com/jenniferlu717/KrakenTools/blob/d4a2fbe2833c2392a724697c0c97a3014e748474/DiversityTools/alpha_diversity.py#L32

* add license, shorten summary, run_exports
---
 recipes/krakentools/meta.yaml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/recipes/krakentools/meta.yaml b/recipes/krakentools/meta.yaml
index 55c5462baa269..0993897f425fe 100644
--- a/recipes/krakentools/meta.yaml
+++ b/recipes/krakentools/meta.yaml
@@ -12,8 +12,9 @@ source:
 
 build:
   noarch: python
-  number: 0
-
+  number: 1
+  run_exports:
+      - {{ pin_subpackage("krakentools", max_pin="x.x") }}
 requirements:
   host:
     - python 
@@ -21,6 +22,7 @@ requirements:
     - python 
     - biopython
     - numpy 
+    - scipy
 
 test:
   commands:
@@ -40,9 +42,8 @@ about:
   home: https://github.com/jenniferlu717/KrakenTools
   license: GPL-3.0
   license_family: GPL
-  summary: {{ name }} is a suite of scripts to be used for post-analysis of
-    Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using
-    {{ name }} with any of the listed programs.
+  license_file: LICENSE
+  summary: {{ name }} scripts for analysis of Kraken/KrakenUniq/Kraken2/Bracken results
 
 extra:
   identifiers:

From d427ce2a8a6c4ca44319b55b3795020da673b38c Mon Sep 17 00:00:00 2001
From: "Filipe G. Vieira" <1151762+fgvieira@users.noreply.github.com>
Date: Fri, 15 Nov 2024 21:08:26 +0100
Subject: [PATCH 10/57] Pinning ggplot2 version (#52124)

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

diff --git a/recipes/merqury/meta.yaml b/recipes/merqury/meta.yaml
index 583ae7429b8e1..d903c7837069f 100644
--- a/recipes/merqury/meta.yaml
+++ b/recipes/merqury/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 3
   noarch: generic
   run_exports:
     - {{ pin_subpackage("merqury", max_pin='x.x') }}  
@@ -22,7 +22,7 @@ requirements:
     - openjdk  >=11.0.1
     - r-base  >=4
     - r-argparse  >=2.0.1
-    - r-ggplot2  >=3.3.2
+    - r-ggplot2  >=3.3.2,<=3.3.6
     - r-scales  >=1.1.1
     - bedtools  >=2.29.2
     - samtools  >=1.10

From 7aa03d7f9f97a5e61f4c5032da8ba107bc9d6763 Mon Sep 17 00:00:00 2001
From: Luan Nguyen <125411678+luan-n-nguyen@users.noreply.github.com>
Date: Sat, 16 Nov 2024 07:08:50 +1100
Subject: [PATCH 11/57] Use openjdk <=21 for hmftools-redux (#52122)

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

diff --git a/recipes/hmftools-redux/meta.yaml b/recipes/hmftools-redux/meta.yaml
index e11d880a8342c..8d940a51d025b 100644
--- a/recipes/hmftools-redux/meta.yaml
+++ b/recipes/hmftools-redux/meta.yaml
@@ -12,13 +12,13 @@ source:
 
 build:
   noarch: generic
-  number: 5
+  number: 6
   run_exports:
     - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}
 
 requirements:
   run:
-    - openjdk >=8
+    - openjdk >=8,<=21
     - sambamba >=1.0.1
 
 test:

From 526220b44db23d0cdf621bfd762848cf0d52526c Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Fri, 15 Nov 2024 20:10:28 +0000
Subject: [PATCH 12/57] Add osx-arm64 to r-facets (#52091)

* Add osx-arm64 to r-facets, r-spp

* Add bioconductor-rsamtools osx-arm64 support - is a dependency for r-spp

* Revert attempt to include r-spp and bioconductor-rsamtools due to excessive dependencies to build for osx-arm64
---
 recipes/r-facets/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/r-facets/meta.yaml b/recipes/r-facets/meta.yaml
index 4bbd9aa678bdd..f0ea43f0f9c9d 100644
--- a/recipes/r-facets/meta.yaml
+++ b/recipes/r-facets/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: aa671d4fc66e10ce2fe4c8b2cbac4946da8a1564627240ea916db6cd8ec2a6c5
 
 build:
-  number: 5
+  number: 6
   run_exports:
     - {{ pin_subpackage("r-facets", max_pin="x") }}
   rpaths:
@@ -39,5 +39,6 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:facets

From 877e2b93d41f3f6d56476d78615671bdfb9f0829 Mon Sep 17 00:00:00 2001
From: Reyhaneh Tavakoli <71424883+reytakop@users.noreply.github.com>
Date: Fri, 15 Nov 2024 21:30:55 +0100
Subject: [PATCH 13/57] fix shebang in sfold (#52138)

* fix shebang in sfold

* edit sed command to accomodate osx

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/sfold/build.sh  | 13 +++++++++----
 recipes/sfold/meta.yaml |  2 +-
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/recipes/sfold/build.sh b/recipes/sfold/build.sh
index d889e43d0bade..b86e125258d17 100755
--- a/recipes/sfold/build.sh
+++ b/recipes/sfold/build.sh
@@ -13,7 +13,12 @@ cp -r STarMir ${SFOLD_DIR}
 
 # modify the sfoldenv file
 cp sfoldenv ${SFOLD_DIR}/sfoldenv
-sed -i "s|SFOLDDIR=.*|SFOLDDIR=${SFOLD_DIR}|g" ${SFOLD_DIR}/sfoldenv
-sed -i "s:/usr/bin/perl:/usr/bin/env perl:" STarMir/*.pl
-sed -i "s:/usr/bin/perl:/usr/bin/env perl:" STarMir/starmir-param/*.pl
-sed -i "s:/usr/bin/perl:/usr/bin/env perl:" bin/*.pl
\ No newline at end of file
+sed -i.bak "s|SFOLDDIR=.*|SFOLDDIR=${SFOLD_DIR}|g" ${SFOLD_DIR}/sfoldenv
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/STarMir/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/STarMir/starmir-param/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/bin/*.pl
+
+rm -rf ${SFOLD_DIR}/*.bak
+rm -rf ${SFOLD_DIR}/STarMir/*.bak
+rm -rf ${SFOLD_DIR}/STarMir/starmir-param/*.bak
+rm -rf ${SFOLD_DIR}/bin/*.bak
diff --git a/recipes/sfold/meta.yaml b/recipes/sfold/meta.yaml
index 37fa4ff38b12a..b6509c09158c3 100644
--- a/recipes/sfold/meta.yaml
+++ b/recipes/sfold/meta.yaml
@@ -7,7 +7,7 @@ source:
   sha256: c25e4d8cf055e13c523ef59f68c8847b66584e36359ce4fb9dc675a97f1a2939
 
 build:
-  number: 2
+  number: 3
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage('sfold', max_pin='x') }}

From 922b7956e96a0d528176198d60e33546ebe044c4 Mon Sep 17 00:00:00 2001
From: farchaab <116543129+farchaab@users.noreply.github.com>
Date: Fri, 15 Nov 2024 21:34:56 +0100
Subject: [PATCH 14/57] constrain snakemake version (#52108)

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

diff --git a/recipes/zamp/meta.yaml b/recipes/zamp/meta.yaml
index 15dc951847f5f..bb8a79067fb0d 100644
--- a/recipes/zamp/meta.yaml
+++ b/recipes/zamp/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 366d1a1bdff60e1a8100298608f20ab2294ef476a1da1bee9c1975641c495f6e
 
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - zamp=zamp.__main__:main
@@ -25,7 +25,7 @@ requirements:
     - setuptools
   run:
     - python >=3.11
-    - snakemake-minimal >=8.0.0
+    - snakemake-minimal >=8.0.0,<=8.24.1
     - Click >=8.1.3
     - attrmap >=0.0.7
     - snaketool-utils >=0.0.5

From 9feedadd3f2b6e5903b5e16c38ce31c301118c0d Mon Sep 17 00:00:00 2001
From: Yasas Wijesekara <34155351+Yasas1994@users.noreply.github.com>
Date: Fri, 15 Nov 2024 21:38:41 +0100
Subject: [PATCH 15/57] version upgrade for jaeger-bio (#52130)

* version upgrade for jaeger-bio

* revisions

* minor review

* Update recipes/jaeger-bio/meta.yaml

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* minor review

* clean up recipe

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/jaeger-bio/meta.yaml | 30 +++++++++++++-----------------
 1 file changed, 13 insertions(+), 17 deletions(-)

diff --git a/recipes/jaeger-bio/meta.yaml b/recipes/jaeger-bio/meta.yaml
index 388ff7957b63e..0e7aa7a4d9a46 100644
--- a/recipes/jaeger-bio/meta.yaml
+++ b/recipes/jaeger-bio/meta.yaml
@@ -1,50 +1,48 @@
 {% set name = "jaeger-bio" %}
-{% set version = "1.1.26" %}
+{% set version = "1.1.30" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 7f7d8794cd04185f7787d92a6ccc89fa59bb58acbe0fe929c6bffbee39a90fe4
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/jaeger_bio-{{ version }}.tar.gz"
+  sha256: ffc54d7257201310ff137dd61dcb1d8afe6c7f95bf2fdf578fec79a16145aeae
 
 build:
   number: 0
-  script: "{{ PYTHON }} -m pip install . --no-cache-dir -vvv"
-  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
-    - {{ pin_subpackage('jaeger-bio', max_pin="x.x.x") }}
+    - {{ pin_subpackage('jaeger-bio', max_pin="x") }}
+  noarch: python
 
 requirements:
   host:
-    - python =3
+    - python >=3.9,<3.12
     - pip
   run:
-    - python =3
-    - pip
     - h5py >=3.8
-    - biopython >=1.78
     - kneed >=0.8.5
     - matplotlib-base >=3.7
     - numpy >=1.24
     - pandas >=1.5
+    - progressbar2 >=4.4.2
     - psutil >=5
+    - pycirclize
+    - pyfastx >=2
+    - python >=3.9,<3.12
     - ruptures >=1.1.9
     - scikit-learn ==1.3.2
-    - seaborn >=0.12.2
-    - tqdm >=4.64.0
-    - tensorflow >=2.15,<2.16
     - parasail-python >=1.3.4
+    - tensorflow >=2.15,<2.16
 
 test:
   imports:
     - jaegeraa
     - jaegeraa.data
     - jaegeraa.nnlib
-
   commands:
-    - Jaeger --help
+    - jaeger --help
 
 about:
   home: "https://github.com/Yasas1994/Jaeger"
@@ -56,7 +54,5 @@ about:
   doc_url: https://readthedocs.org/projects/jaeger-docs/
 
 extra:
-  identifiers:
-    - biotools:jaeger
   recipe-maintainers:
     - Yasas1994

From 1b0d178799e05ab1cc162bb244d6911b52126468 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 15 Nov 2024 16:46:00 -0500
Subject: [PATCH 16/57] Update tttrlib to 0.25.1 (#52127)

* Update tttrlib to 0.25.1

* try building on osx py > 310

* build now works on osx py > 3.10, lets now try building on aarch64 and arm64

* sync cmake build commands with those specified in the documentation

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/tttrlib/build.sh  | 5 ++++-
 recipes/tttrlib/meta.yaml | 8 +++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
index b4013e98b4ad8..b5970e094f4eb 100755
--- a/recipes/tttrlib/build.sh
+++ b/recipes/tttrlib/build.sh
@@ -4,7 +4,7 @@ mkdir b2 && cd b2
 
 if [[ "${target_platform}" == osx-* ]]; then
   # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
-  CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+  export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
   export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
 else
   export CONFIG_ARGS=""
@@ -18,6 +18,9 @@ cmake -S .. -B . \
   -DBUILD_LIBRARY=ON \
   -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
   -DPython_ROOT_DIR="${PREFIX}/bin" \
+  -DBUILD_PYTHON_DOCS=ON \
+  -DBoost_USE_STATIC_LIBS=OFF \
+  -DWITH_AVX=OFF \
   -G Ninja \
   "${CONFIG_ARGS}"
 
diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index d9b4c5bcb9146..daf00affe224d 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "tttrlib" %}
-{% set version = "0.25.0" %}
+{% set version = "0.25.1" %}
 
 package:
   name: {{ name }}
@@ -7,11 +7,10 @@ package:
 
 source:
   url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: e15604ef063257cd87d3bdf266c1d5a448189508f51cdc4156a93cb2b46fe807
+  sha256: a224214e50d7a202ef1d264c64641ab0b26f29bf756a96659489847953b698a6
 
 build:
   number: 0
-  skip: True  # [osx and py > 310]
   run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}'
 
 requirements:
@@ -68,3 +67,6 @@ extra:
   recipe-maintainers:
     - tpeulen
     - khemmen
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

From 37604301f450e29133a5213fa12fba0c791c84b1 Mon Sep 17 00:00:00 2001
From: richard-burhans <burhans@bx.psu.edu>
Date: Sat, 16 Nov 2024 09:43:57 -0500
Subject: [PATCH 17/57] Add rdeval (#52095)

* initial attempt

* adding make as a dependency

* new hash

* adding test

* fixing build.sh

* using version with submodules

* adding zlib

* updates

* update

* foo

* quote

* u

* a

* patch

* zlib

* zlib

* foo

* clean up recipe

* clean up patches

* Update build.sh

* add gfalibs patch

* Update meta.yaml

* Update meta.yaml

* add gfalibs patch

* edit foo.patch

* Update foo.patch

* edit foo.patch

* edit foo.patch

* Update build.sh

* makefile

* makefile

* updating submodule makefile

* bumping build version

* includes

* testing makefile changrs

* make

* patches

* patches

* patches

* patches

* patches

* forgot reads.patch

* upp

* zlib

* zlib

* patch

* patches

* requirememts

* zlib

* zlib

* zlib

* zlib

* reads

* rename patch files

* removed patches

---------

Co-authored-by: Richard C. Burhans <rico@bx.psu.edu>
Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/rdeval/Makefile.patch         | 25 +++++++++++++
 recipes/rdeval/build.sh               | 16 ++++++---
 recipes/rdeval/gfalibs-Makefile.patch | 25 +++++++++++++
 recipes/rdeval/gfalibs.patch          | 30 ----------------
 recipes/rdeval/meta.yaml              |  8 ++---
 recipes/rdeval/zlib.patch             | 52 ---------------------------
 6 files changed, 65 insertions(+), 91 deletions(-)
 create mode 100644 recipes/rdeval/Makefile.patch
 create mode 100644 recipes/rdeval/gfalibs-Makefile.patch
 delete mode 100644 recipes/rdeval/gfalibs.patch
 delete mode 100644 recipes/rdeval/zlib.patch

diff --git a/recipes/rdeval/Makefile.patch b/recipes/rdeval/Makefile.patch
new file mode 100644
index 0000000000000..b9243d5f94b5d
--- /dev/null
+++ b/recipes/rdeval/Makefile.patch
@@ -0,0 +1,25 @@
+--- a/Makefile
++++ b/Makefile
+@@ -12,7 +12,12 @@
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+ 
+-LDFLAGS := -pthread
++ifeq ($(origin LDFLAGS), undefined)
++    LDFLAGS := -pthread
++else
++    LDFLAGS := $(LDFLAGS) -pthread
++endif
++
+ LIBS = -lz
+ 
+ OBJS := main input reads
+@@ -27,7 +32,7 @@
+ all: head validate regenerate
+ 
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
+ 
+ .PHONY: gfalibs
+ gfalibs:
diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh
index 0082bc9545c6a..3f30b2376ac7a 100644
--- a/recipes/rdeval/build.sh
+++ b/recipes/rdeval/build.sh
@@ -2,13 +2,21 @@
 
 set -o errexit
 set -o nounset
-set -o xtrace
+
+if [ -e "$PREFIX/include" ]; then
+    export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include"
+fi
+
+if [ -e "$PREFIX/lib" ]; then
+    export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L$PREFIX/lib"
+fi
+
+echo "CPPFLAGS=\"$CPPFLAGS\""
+echo "LDFLAGS=\"$LDFLAGS\""
 
 cd "$SRC_DIR"
 
-export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include"
-export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
+make
 
-make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -Wno-unused-command-line-argument" LDFLAGS="${LDFLAGS}"
 install -d "$PREFIX/bin"
 install -v -m 0755 build/bin/rdeval "$PREFIX/bin/"
diff --git a/recipes/rdeval/gfalibs-Makefile.patch b/recipes/rdeval/gfalibs-Makefile.patch
new file mode 100644
index 0000000000000..d43d6346dadaa
--- /dev/null
+++ b/recipes/rdeval/gfalibs-Makefile.patch
@@ -0,0 +1,25 @@
+--- a/gfalibs/Makefile
++++ b/gfalibs/Makefile
+@@ -1,4 +1,4 @@
+-CXX = g++
++CXX ?= g++
+ INCLUDE_DIR = -I./include
+ WARNINGS = -Wall -Wextra
+ 
+@@ -8,15 +8,13 @@
+ BUILD = build/bin
+ SOURCE = src
+ INCLUDE = include
+-LDFLAGS :=
+ 
+ SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
+ 
+ all: $(SOURCES)
+-	@
+ 
+ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
+-	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
+     
+ clean:
+ 	$(RM) *.o
diff --git a/recipes/rdeval/gfalibs.patch b/recipes/rdeval/gfalibs.patch
deleted file mode 100644
index e6cc8439bf6c2..0000000000000
--- a/recipes/rdeval/gfalibs.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff --git a/gfalibs/Makefile b/gfalibs/Makefile
-index de9ab9b..90a703c 100644
---- a/gfalibs/Makefile
-+++ b/gfalibs/Makefile
-@@ -1,5 +1,5 @@
--CXX = g++
--INCLUDE_DIR = -I./include
-+CXX = $(CXX)
-+INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap
- WARNINGS = -Wall -Wextra
- 
- CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS)
-@@ -8,7 +8,7 @@ TARGET = gfalibs
- BUILD = build/bin
- SOURCE = src
- INCLUDE = include
--LDFLAGS :=
-+LDFLAGS := -L${PREFIX}/lib -pthread
- 
- SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
- 
-@@ -16,7 +16,7 @@ all: $(SOURCES)
- 	@
- 
- %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
--	$(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
-+	$(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz -lpthread
-     
- clean:
- 	$(RM) *.o
diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml
index ce1571a5436bd..a495d435df647 100644
--- a/recipes/rdeval/meta.yaml
+++ b/recipes/rdeval/meta.yaml
@@ -9,12 +9,11 @@ source:
   url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip
   sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d
   patches:
-    - zlib.patch
-    - foo.patch
-    - gfalibs.patch
+    - Makefile.patch
+    - gfalibs-Makefile.patch
 
 build: 
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}
 
@@ -23,7 +22,6 @@ requirements:
     - {{ compiler('cxx') }}
     - make
   host:
-    - pthread-stubs
     - zlib
 
 test:
diff --git a/recipes/rdeval/zlib.patch b/recipes/rdeval/zlib.patch
deleted file mode 100644
index d1e9639bb43c4..0000000000000
--- a/recipes/rdeval/zlib.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-diff --git a/gfalibs/include/output.h b/gfalibs/include/output.h
-index aabbec0..20f0dc1 100644
---- a/gfalibs/include/output.h
-+++ b/gfalibs/include/output.h
-@@ -12,7 +12,7 @@
- #include "gfa-lines.h"
- #include "gfa.h"
- 
--#include "zlib.h"
-+#include <zlib.h>
- #include "zstream/zstream_common.hpp"
- #include "zstream/ozstream.hpp"
- #include "zstream/ozstream_impl.hpp"
-diff --git a/gfalibs/include/stream-obj.h b/gfalibs/include/stream-obj.h
-index 1faa4df..8e28bf6 100644
---- a/gfalibs/include/stream-obj.h
-+++ b/gfalibs/include/stream-obj.h
-@@ -2,7 +2,7 @@
- #define STREAM_OBJ_H
- 
- #include <fstream>
--#include "zlib.h"
-+#include <zlib.h>
- 
- class membuf : public std::streambuf {
-     
-diff --git a/gfalibs/src/stream-obj.cpp b/gfalibs/src/stream-obj.cpp
-index e9694ee..c6eca26 100644
---- a/gfalibs/src/stream-obj.cpp
-+++ b/gfalibs/src/stream-obj.cpp
-@@ -5,7 +5,7 @@
- 
- #include "bed.h"
- #include "struct.h"
--#include "zlib.h"
-+#include <zlib.h>
- #include "global.h"
- #include "log.h"
- #include "threadpool.h"
-diff --git a/src/reads.cpp b/src/reads.cpp
-index 866f49b..ac714cf 100644
---- a/src/reads.cpp
-+++ b/src/reads.cpp
-@@ -14,7 +14,7 @@
- #include "functions.h" // global functions
- #include "stream-obj.h"
- 
--#include "zlib.h"
-+#include <zlib.h>
- #include "zstream/zstream_common.hpp"
- #include "zstream/ozstream.hpp"
- #include "zstream/ozstream_impl.hpp"

From a8562c2c48a87482d3c70eb020224116531203e4 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 16 Nov 2024 14:44:40 -0500
Subject: [PATCH 18/57] Update zol to 1.5.4 (#52145)

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

diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml
index c0dc3ff0e69d5..9e23356eb84ef 100644
--- a/recipes/zol/meta.yaml
+++ b/recipes/zol/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "zol" %}
-{% set version = "1.5.3" %}
+{% set version = "1.5.4" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 2a7a9bd0ade0306fae95e9066f9d76682c34095519d6f6c46ee6d566d8c77fa3
+  sha256: e313c7c8c896205898727cb566e92a04c58e7671239bd59a9cac0aa3c3610bfd
 
 build:
   number: 0
@@ -26,7 +26,8 @@ requirements:
     - python >=3.10
     - r-base 
     - biopython 
-    - muscle >=5.0
+    - muscle >=5.0,<=5.1 [osx]
+    - muscle >=5.0 [not osx]
     - mcl
     - pal2nal >=14.1
     - hmmer >=3.0.0

From fda03dd75d8b1433bb9d976e7f45c2eb4fc432dc Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 16 Nov 2024 14:50:49 -0500
Subject: [PATCH 19/57] Update bakta to 1.10.1 (#52139)

* Update bakta to 1.10.1

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/bakta/meta.yaml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml
index f99b0be766124..e8647e67bb759 100644
--- a/recipes/bakta/meta.yaml
+++ b/recipes/bakta/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.10.0" %}
+{% set version = "1.10.1" %}
 
 package:
   name: bakta
@@ -6,12 +6,12 @@ package:
 
 source:
   url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
-  sha256: '78f98ead47b45ad5fe66a41be369be72cac36dff6d68073d285c568dc860be98'
+  sha256: '4a13b7362dd46d44edc175956afda2478122b48bfef4fb9581c198b35fd36296'
 
 build:
   noarch: python
   number: 0
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   entry_points:
     - bakta = bakta.main:main
     - bakta_proteins = bakta.proteins:main
@@ -23,10 +23,10 @@ build:
 
 requirements:
   host:
-    - python >=3.9, <3.12
+    - python >=3.9,<3.12
     - pip
   run:
-    - python >=3.9, <3.12
+    - python >=3.9,<3.12
     - biopython >=1.78
     - xopen >=1.5.0
     - requests >=2.25.1
@@ -58,8 +58,8 @@ test:
 
 about:
   home: https://github.com/oschwengers/bakta
-  license: GPLv3
-  license_family: GPL
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
   summary: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
   dev_url: https://github.com/oschwengers/bakta

From 072d656dc2b8bc9381c03d2bf97ea71c3c2d3309 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Sat, 16 Nov 2024 21:09:37 +0100
Subject: [PATCH 20/57] Add new package kestrel in version 1.0.3 (#51810)

* New recipe for kestrel v1.0.3

* fix test

* Apply suggestions from code review

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* Update build.sh

* use SPDX license id

---------

Co-authored-by: Manuel Holtgrewe <Manuel.Holtgrewe@medgen-mainz.de>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
Co-authored-by: richard-burhans <burhans@bx.psu.edu>
---
 recipes/kestrel/build.sh  | 21 +++++++++++++++++++++
 recipes/kestrel/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 recipes/kestrel/build.sh
 create mode 100644 recipes/kestrel/meta.yaml

diff --git a/recipes/kestrel/build.sh b/recipes/kestrel/build.sh
new file mode 100644
index 0000000000000..6069aed727d79
--- /dev/null
+++ b/recipes/kestrel/build.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -euo pipefail
+
+kestrel="${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION}"
+
+mkdir -p "${kestrel}"
+cp -r ./* "${kestrel}"
+chmod +x "${kestrel}/kestrel"
+mkdir -p "${PREFIX}/bin"
+
+if [[ -L "${PREFIX}/bin/kestrel" ]]; then
+    echo "Error: File ${PREFIX}/bin/kestrel already exists"
+    exit 1
+fi
+
+if [[ ! -f "${kestrel}/kestrel" ]]; then
+    echo "Error: Target file ${kestrel}/kestrel does not exist"
+    exit 1
+fi
+ln -s "${kestrel}/kestrel" "${PREFIX}/bin/kestrel" || exit 1
diff --git a/recipes/kestrel/meta.yaml b/recipes/kestrel/meta.yaml
new file mode 100644
index 0000000000000..0bf3d2202ceb8
--- /dev/null
+++ b/recipes/kestrel/meta.yaml
@@ -0,0 +1,38 @@
+{% set name = "kestrel" %}
+{% set version = "1.0.3" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/paudano/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}-linux.tar.gz
+  sha256: 992c579fc52dce7b9d80e6232914da02663a2480d28b672277d80fdfcdda33e3
+
+build:
+  noarch: generic
+  detect_binary_files_with_prefix: true
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('kestrel', max_pin="x") }}
+
+requirements:
+  run:
+    # Enforce a version requirement on openjdk to ensure
+    # it comes from the conda-forge channel and not default.
+    # Many yaks were shaved to bring us this information.
+    # Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906
+    - openjdk >=8.0.144
+
+test:
+  commands:
+    - kestrel
+    - kestrel -h 
+
+about:
+  home: 'https://github.com/paudano/kestrel'
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: COPYING
+  summary: 'Mapping-free variant caller for short-read Illumina data'
+

From b4557b637582ae358a922fa8781e31c313248fd1 Mon Sep 17 00:00:00 2001
From: Giulio Centorame <46871438+GiulioCentorame@users.noreply.github.com>
Date: Sun, 17 Nov 2024 06:29:22 +1000
Subject: [PATCH 21/57] Add recipe for CRAN package locuszoomr (#51580)

* Add recipe for CRAN package locuszoomr

* Make build script executable

* Add error handling for DESCRIPTION

Following the suggestion in [this comment](https://github.com/bioconda/bioconda-recipes/pull/51580#discussion_r1811667065)

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* Add `run_export` statement

* Build as noarch

* Fix recipe name in `run_exports`

Whoops

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* Add additional tests

* Fix recipe names for Bioconductor dependencies

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 recipes/r-locuszoomr/build.sh  |  9 ++++
 recipes/r-locuszoomr/meta.yaml | 83 ++++++++++++++++++++++++++++++++++
 2 files changed, 92 insertions(+)
 create mode 100755 recipes/r-locuszoomr/build.sh
 create mode 100644 recipes/r-locuszoomr/meta.yaml

diff --git a/recipes/r-locuszoomr/build.sh b/recipes/r-locuszoomr/build.sh
new file mode 100755
index 0000000000000..03cb951f643eb
--- /dev/null
+++ b/recipes/r-locuszoomr/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+if [ ! -f DESCRIPTION ]; then
+    echo "Error: DESCRIPTION file not found"
+    exit 1
+fi
+mv DESCRIPTION DESCRIPTION.old || exit 1
+grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION || exit 1
+${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/recipes/r-locuszoomr/meta.yaml b/recipes/r-locuszoomr/meta.yaml
new file mode 100644
index 0000000000000..10a955fc63a37
--- /dev/null
+++ b/recipes/r-locuszoomr/meta.yaml
@@ -0,0 +1,83 @@
+{% set version = '0.3.5' %}
+
+package:
+  name: r-locuszoomr
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/locuszoomr_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/locuszoomr/locuszoomr_{{ version }}.tar.gz
+  sha256: 92c8bb3a84ceed82e3cf142129eb83c21a1eb780cd6c0fb4b084e099917c2c3d
+
+build:
+  run_exports: 
+    - {{ pin_subpackage("r-locuszoomr", max_pin="x.x") }}
+  noarch: generic
+  merge_build_host: True  # [win]
+  number: 0
+
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  host:
+    - r-base
+    - bioconductor-annotationfilter
+    - bioconductor-biocgenerics
+    - bioconductor-genomeinfodb
+    - bioconductor-genomicranges
+    - bioconductor-iranges
+    - r-ldlinkr
+    - r-cowplot
+    - r-dplyr
+    - bioconductor-ensembldb
+    - r-gggrid
+    - r-ggplot2
+    - r-ggrepel
+    - r-memoise
+    - r-plotly
+    - r-rlang
+    - bioconductor-rtracklayer
+    - r-zoo
+
+  run:
+    - r-base
+    - bioconductor-annotationfilter
+    - bioconductor-biocgenerics
+    - bioconductor-genomeinfodb
+    - bioconductor-genomicranges
+    - bioconductor-iranges
+    - r-ldlinkr
+    - r-cowplot
+    - r-dplyr
+    - bioconductor-ensembldb
+    - r-gggrid
+    - r-ggplot2
+    - r-ggrepel
+    - r-memoise
+    - r-plotly
+    - r-rlang
+    - bioconductor-rtracklayer
+    - r-zoo
+
+test:
+  commands:
+    - $R -e "library('locuszoomr')"
+    - $R -e "packageVersion('locuszoomr')"
+    - $R -e "help(package = 'locuszoomr')"
+
+about:
+  home: https://github.com/myles-lewis/locuszoomr
+  license: GPL-3
+  summary: Publication-ready regional gene locus plots similar to those produced by the web interface
+    'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic
+    data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly',
+    allowing flexibility and easy customisation including laying out multiple locus
+    plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess>
+    to query linkage disequilibrium data from the 1000 Genomes Project and can overlay
+    this on plots.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'

From f6eeb47279e22f327336c260c773b771930af423 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 16 Nov 2024 17:28:52 -0500
Subject: [PATCH 22/57] Update zol to 1.5.5 (#52146)

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

diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml
index 9e23356eb84ef..d9994831effb8 100644
--- a/recipes/zol/meta.yaml
+++ b/recipes/zol/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "zol" %}
-{% set version = "1.5.4" %}
+{% set version = "1.5.5" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: e313c7c8c896205898727cb566e92a04c58e7671239bd59a9cac0aa3c3610bfd
+  sha256: fa8f23071c519daf9cfc2c3ca96121d8119dbc55c2359c3901f8ed2081583ddb
 
 build:
   number: 0

From bd51407203ee03ee156f38e41aab30947d68be40 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Sun, 17 Nov 2024 23:57:15 -0600
Subject: [PATCH 23/57] revert aarch64 machine back to medium

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 81ecb0653c316..cf237bd82639b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -9,7 +9,7 @@ executors:
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
-    resource_class: arm.large
+    resource_class: arm.medium
 
 jobs: # a basic unit of work in a run
   build_and_test:

From 885c747e0375a61f0b0f13bb9fead3a1ab54ad3a Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 18 Nov 2024 02:38:17 -0600
Subject: [PATCH 24/57] Update libmaus2 to v2.0.183 (#52154)

* Update libmaus2 to v2.0.183

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* clean up recipe

* try large aarch64 machine
---
 .circleci/config.yml       |  2 +-
 recipes/libmaus2/build.sh  | 14 +++++---
 recipes/libmaus2/meta.yaml | 48 ++++++++++++++++---------
 recipes/libmaus2/patch     | 72 +++++++++++++++++++++-----------------
 4 files changed, 80 insertions(+), 56 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index cf237bd82639b..81ecb0653c316 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -9,7 +9,7 @@ executors:
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
-    resource_class: arm.medium
+    resource_class: arm.large
 
 jobs: # a basic unit of work in a run
   build_and_test:
diff --git a/recipes/libmaus2/build.sh b/recipes/libmaus2/build.sh
index cdd58fb79e892..7d73807646dd1 100644
--- a/recipes/libmaus2/build.sh
+++ b/recipes/libmaus2/build.sh
@@ -1,10 +1,14 @@
 #!/bin/bash
 set -eu
-export LIBS="-lstdc++fs -lcurl"
+export LIBS="-lstdc++fs -lcurl -lz -ldeflate"
 
-./configure --prefix $PREFIX --with-snappy --with-io_lib
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" CC="${CC}" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	--with-snappy --with-io_lib --with-libdeflate \
+	--with-libsecrecy --with-nettle \
+	--with-lzma --with-gmp
 
-cat config.log
-
-make -j${CPU_COUNT}
+make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/libmaus2/meta.yaml b/recipes/libmaus2/meta.yaml
index 3d8c6738d991c..7a7a7f2f344b6 100644
--- a/recipes/libmaus2/meta.yaml
+++ b/recipes/libmaus2/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "libmaus2" %}
-{% set version = "2.0.810" %}
-{% set datestamp = "20220216151520" %}
-{% set sha256hash = "6639289aba6bbece3057ab7d1782a1b94b80a9ae22fc3d136a78ba8f7b9edaee" %}
+{% set version = "2.0.813" %}
+{% set datestamp = "20221210220409" %}
+{% set sha256 = "4125f8daefd6900185675026498369457088e25e81029597659249be49cd5261" %}
 
 package:
   name: {{ name }}
@@ -10,47 +10,61 @@ package:
 build:
   # There's some issue with clang
   skip: True  # [osx]
-  number: 6
+  number: 0
   run_exports:
-    - {{ pin_subpackage('libmaus2', max_pin='x.x') }}
+    - {{ pin_subpackage('libmaus2', max_pin='x') }}
 
 source:
   url: https://gitlab.com/german.tischler/libmaus2/-/archive/{{ version }}-release-{{ datestamp }}/libmaus2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
-  patches:
+  sha256: {{ sha256 }}
+  #patches:
     # Until gcc >=8 is being used
-    - patch
+    #- patch
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
     - boost-cpp
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - libcurl
     # snappy 1.1.9 introduced a binary incompatible build change (https://github.com/mhx/dwarfs/issues/56#issuecomment-896857211)
     # enabling -fno-rtti. libmaus needs typeid, which is only available with activated rtti.
     # Hence, we stick with snappy 1.1.8
-    - snappy =1.1.8 
+    - snappy =1.1.8
     - staden_io_lib >=1.14.14
+    - libdeflate
+    - gmp
+    - nettle
+    - zlib
   run:
     - boost-cpp
-    - libcurl
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - snappy =1.1.8
     - staden_io_lib >=1.14.14
-  ignore_run_exports:
-    - snappy
-
-about:
-  home: https://gitlab.com/german.tischler/libmaus2
-  license: GPL3
-  summary: collection of data structures and algorithms for NGS data
 
 test:
   commands:
     - echo
 
+about:
+  home: https://gitlab.com/german.tischler/libmaus2
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: GPLv3
+  summary: "Collection of data structures and algorithms for NGS data."
+  dev_url: https://gitlab.com/german.tischler/libmaus2
+
 extra:
   additional-platforms:
     - linux-aarch64
+  identifiers:
+    - biotools:libmaus
diff --git a/recipes/libmaus2/patch b/recipes/libmaus2/patch
index f66efbfe6c761..1d8376b29a4a1 100644
--- a/recipes/libmaus2/patch
+++ b/recipes/libmaus2/patch
@@ -127,36 +127,6 @@ index 134ff0f4..b8fcfe88 100644
  
  				setHWTReq  (p_hwt_req.string());
  				setHWT     (p_hwt.string());
-diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-index 1e8e53b9..a91d1916 100644
---- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-+++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-@@ -111,11 +111,11 @@ namespace libmaus2
- 				// base tmp directory name
- 				std::string tmpdirname;
- 				// tmpdirname as path object
--				std::filesystem::path tmppath;
--				std::filesystem::path base_tmp_path;
--				std::filesystem::path ds_tmp_path_base_ds_tmp;
--				std::filesystem::path merge_tmp_path;
--				std::filesystem::path ds_tmp_path_merge_ds_tmp;
-+				std::experimental::filesystem::path tmppath;
-+				std::experimental::filesystem::path base_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
-+				std::experimental::filesystem::path merge_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
- 
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
-@@ -333,7 +333,7 @@ namespace libmaus2
- 					return C;
- 				}
- 
--				static std::filesystem::path ensureDirectory(std::filesystem::path path)
-+				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
- 				{
- 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
- 					return path;
 diff --git a/src/libmaus2/util/ArgInfo.cpp b/src/libmaus2/util/ArgInfo.cpp
 index 3802cbb7..8ecd441c 100644
 --- a/src/libmaus2/util/ArgInfo.cpp
@@ -267,6 +237,42 @@ index 2ff71e4a..0714e612 100644
  				dictpath /= digest;
  
  				std::cerr << "[V] writing " << dictpath << " for " << pat.sid << " in " << ref << std::endl;
--- 
-2.33.0
-
+diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+index 180f466..0b69f74 100644
+--- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
++++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+@@ -111,11 +111,11 @@ namespace libmaus2
+ 				// base tmp directory name
+ 				std::string tmpdirname;
+ 				// tmpdirname as path object
+-				std::filesystem::path tmppath;
+-				std::filesystem::path base_tmp_path;
+-				std::filesystem::path ds_tmp_path_base_ds_tmp;
+-				std::filesystem::path merge_tmp_path;
+-				std::filesystem::path ds_tmp_path_merge_ds_tmp;
++				std::experimental::filesystem::path tmppath;
++				std::experimental::filesystem::path base_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
++				std::experimental::filesystem::path merge_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
+ 
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
+@@ -333,7 +333,7 @@ namespace libmaus2
+ 					return C;
+ 				}
+ 
+-				static std::filesystem::path ensureDirectory(std::filesystem::path path)
++				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
+ 				{
+ 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
+ 					return path;
+@@ -358,7 +358,7 @@ namespace libmaus2
+ 					preisasamplingrate(std::min(options.maxpreisasamplingrate,blocksizeprevtwo)),
+ 					V_boundedlcpblockvalues(new libmaus2::util::AtomicArray<uint64_t>(numblocks,0)),
+ 					// tmp directory name
+-					tmpdirname(ensureDirectory(std::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
++					tmpdirname(ensureDirectory(std::experimental::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
+ 					// path object for tmp directory name
+ 					tmppath(tmpdirname),
+ 					base_tmp_path(ensureDirectory(tmppath / "base_tmp")),

From af160e69bb994da54b3ff30133286385bfaf0005 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 18 Nov 2024 03:15:34 -0600
Subject: [PATCH 25/57] Rebuild muse recipe (#52155)

* Rebuild muse recipe

* clean up recipe

* Update meta.yaml

* clean up recipe

* clean up recipe
---
 recipes/muse/fix-install_muse.sh.patch | 15 +++++++-----
 recipes/muse/meta.yaml                 |  5 ++--
 recipes/muse/version.patch             | 32 ++++++++++++++++++++++++++
 3 files changed, 44 insertions(+), 8 deletions(-)
 create mode 100644 recipes/muse/version.patch

diff --git a/recipes/muse/fix-install_muse.sh.patch b/recipes/muse/fix-install_muse.sh.patch
index cd6bcdbd4a8bb..3a4d1a7f2ce65 100644
--- a/recipes/muse/fix-install_muse.sh.patch
+++ b/recipes/muse/fix-install_muse.sh.patch
@@ -1,5 +1,5 @@
 diff --git a/install_muse.sh b/install_muse.sh
-index 7bc2153..f8ab6e3 100755
+index 7bc2153..1ef4b13 100755
 --- a/install_muse.sh
 +++ b/install_muse.sh
 @@ -4,13 +4,21 @@ make clean
@@ -16,15 +16,15 @@ index 7bc2153..f8ab6e3 100755
 -cd boost_1_70_0/
 -./bootstrap.sh
 +cd boost-1.86.0/
-+./bootstrap.sh --with-toolset="${TOOL}" --prefix="${PREFIX}"
++./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
  ./b2 --clean
 -./b2
 +./b2 toolset="${TOOL}" --layout=system link=static \
-+	threading=multi strip=on include="${PREFIX}/include" \
++	threading=multi strip=on \
 +	variant=release address-model=64 install
  
 -cp stage/lib/libboost_iostreams.a ../lib/
-+cp -f ${PREFIX}/lib/libboost_iostreams.a ../lib/
++cp -f lib/libboost_iostreams.a ../lib/
  cd ..
  
  # compile libtcmalloc
@@ -45,7 +45,7 @@ index 7bc2153..f8ab6e3 100755
  cd ..
  
  # combine htslib
-@@ -42,27 +50,15 @@ cd htslib
+@@ -42,27 +50,19 @@ cd htslib
  git checkout 1.9
  #git submodule update --init --recursive
  autoreconf -i
@@ -77,8 +77,11 @@ index 7bc2153..f8ab6e3 100755
 -
 -
 -
--
 +CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" \
 +    CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
 +    LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
 +    make -j"${CPU_COUNT}"
+ 
++rm -rf htslib
++rm -rf gperftools
++rm -rf boost-1.86.0
diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml
index 533c981c9b17f..6b838e934d836 100644
--- a/recipes/muse/meta.yaml
+++ b/recipes/muse/meta.yaml
@@ -12,12 +12,13 @@ source:
   patches:
     - 0001-Makefile.patch
     - fix-install_muse.sh.patch
+    - version.patch
 - url: https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86.0-b2-nodocs.tar.gz
   sha256: 2128a4c96862b5c0970c1e34d76b1d57e4a1016b80df85ad39667f30b1deba26
   folder: boost-1.86.0
 
 build:
-  number: 0
+  number: 1
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage('muse', max_pin="x") }}
@@ -44,7 +45,7 @@ requirements:
 
 test:
   commands:
-    - "MuSE 2>&1 | grep Version > /dev/null"
+    - 'MuSE 2>&1 | grep "Version"'
 
 about:
   home: "https://github.com/wwylab/MuSE"
diff --git a/recipes/muse/version.patch b/recipes/muse/version.patch
new file mode 100644
index 0000000000000..0b826335c5820
--- /dev/null
+++ b/recipes/muse/version.patch
@@ -0,0 +1,32 @@
+diff --git a/src/main_muse.cpp b/src/main_muse.cpp
+old mode 100755
+new mode 100644
+index c2b7ef6..d8ac21d
+--- a/src/main_muse.cpp
++++ b/src/main_muse.cpp
+@@ -362,15 +362,19 @@ int main(int argc, char* argv[]){
+     if(argc < 2)
+         return usage();
+ 
+-	if(strcmp(argv[1], "call") == 0){
++    if(strcmp(argv[1], "call") == 0){
+         get_MuseCallOpts(argc, argv);
+-	}
+-	else if(strcmp(argv[1], "sump") == 0) {
+-		get_MuseSumpOpts(argc-1, argv+1);
+-	}
++    }
++    else if(strcmp(argv[1], "sump") == 0) {
++        get_MuseSumpOpts(argc-1, argv+1);
++    }
++    else if (strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "--v") == 0) {
++        fprintf(stdout, "MuSE %s\n", Version.c_str());
++        return 0; // Successfully printed version
++    } 
+     else {
+         fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+         return 1;
+     }
+-	return 0;
++    return 0;
+ }

From 4defaf7980af108ce6f534198654b93421310c67 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 18 Nov 2024 04:25:10 -0600
Subject: [PATCH 26/57] Update biobambam to v2.0.185 (#52156)

* Update biobambam to v2.0.185

* add zlib

* Update build.sh
---
 recipes/biobambam/build.sh  |  7 ++++++-
 recipes/biobambam/meta.yaml | 32 +++++++++++++++++++++++---------
 2 files changed, 29 insertions(+), 10 deletions(-)

diff --git a/recipes/biobambam/build.sh b/recipes/biobambam/build.sh
index 272f469dffb76..53b04f87a7e43 100644
--- a/recipes/biobambam/build.sh
+++ b/recipes/biobambam/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
 set -eu
-./configure --prefix=${PREFIX}
+
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" \
+	--with-libmaus2 --with-xerces-c --with-gmp \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 make install
diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml
index 482c9c1b272d1..69ad250229d2e 100644
--- a/recipes/biobambam/meta.yaml
+++ b/recipes/biobambam/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "biobambam" %}
-{% set version = "2.0.183" %}
-{% set datestamp = "20210802180148" %}
-{% set sha256hash = "8712ceac509c389111b01dc3429f673dc0f8b77cb2bc48a1ebcf17f6888b2945" %}
+{% set version = "2.0.185" %}
+{% set datestamp = "20221211202123" %}
+{% set sha256 = "e405421e869ac7220c3a7e5da0d24a3c7b4c7b1807e044a439fe68efc88a1f2a" %}
 
 package:
   name: {{ name }}
@@ -9,10 +9,10 @@ package:
 
 source:
   url: https://gitlab.com/german.tischler/biobambam2/-/archive/{{ version }}-release-{{ datestamp }}/biobambam2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
+  sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
@@ -21,19 +21,33 @@ requirements:
   build:
     - make
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
-    - libmaus2 >=2.0.810
+    - libmaus2 >=2.0.813
+    - gmp
+    - xerces-c
+    - zlib
+  run:
+    - libmaus2 >=2.0.813
 
 test:
   commands:
     - bamsormadup --help
     - bamtofastq --help
+
 about:
   home: https://gitlab.com/german.tischler/biobambam2
-  license: GPLv3
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: GPLv3
-  summary: Tools for early stage alignment file processing
+  summary: "Tools for early stage alignment file processing."
+  dev_url: https://gitlab.com/german.tischler/biobambam2
 
 extra:
   additional-platforms:
-    - linux-aarch64
\ No newline at end of file
+    - linux-aarch64
+  identifiers:
+    - biotools:biobambam

From 7b94664386781d6ea2286611a30cafee3c4e23c7 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 05:37:10 -0500
Subject: [PATCH 27/57] Update snk-cli to 0.7.0 (#52149)

* Update snk-cli to 0.6.0

* Update snk-cli to 0.6.1

* Update snk-cli to 0.7.0

---------

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

diff --git a/recipes/snk-cli/meta.yaml b/recipes/snk-cli/meta.yaml
index 9e1434504395f..073af957c0b49 100644
--- a/recipes/snk-cli/meta.yaml
+++ b/recipes/snk-cli/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "snk-cli" %}
-{% set version = "0.5.5" %}
+{% set version = "0.7.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name | replace("-","_") }}-{{ version }}.tar.gz
-  sha256: 5ba6a88aca3473751152cdcd22b0cdc31b0f4034d9eabf859a3dfc6dcc4a487f
+  sha256: eec5fb4411e54a97927586f2cf0018219513a6ef8de1e38ec0741a642521c299
 
 build:
   run_exports:

From 6d4a1cbf341a885503a90ce30d0250ac94069f5b Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 05:37:23 -0500
Subject: [PATCH 28/57] Update svtopovz to 0.2.1 (#52147)

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

diff --git a/recipes/svtopovz/meta.yaml b/recipes/svtopovz/meta.yaml
index d885d82b8a86a..41baadd6ae65c 100644
--- a/recipes/svtopovz/meta.yaml
+++ b/recipes/svtopovz/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "svtopovz" %}
-{% set version = "0.1.1" %}
-{% set shasum = "275acf6d296a04a981bc396e37836324d47eeedef61b04ab8073ac0c95c3b422" %}
+{% set version = "0.2.1" %}
+{% set shasum = "c6161f978bdbacce9bd279971dde712f481cb3659541f183a4014791d4d0f44f" %}
 
 package:
   name: {{ name }}

From 4672012533e420db140d0b7c1a86b2e7f89e6b53 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 06:21:39 -0500
Subject: [PATCH 29/57] Update cnvkit to 0.9.12 (#52151)

* Update cnvkit to 0.9.12

* clean up recipe

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/cnvkit/meta.yaml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml
index f39326c930829..d4ce6da29663e 100644
--- a/recipes/cnvkit/meta.yaml
+++ b/recipes/cnvkit/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cnvkit" %}
-{% set version = "0.9.11" %}
+{% set version = "0.9.12" %}
 
 package:
   name: {{ name }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz
-  sha256: 1763936427184270108fd51219ebc82f542e28339bdec587579b8745f61179a8
+  sha256: 39d65ba3d9c541dfd80986ace298b2d521067d1b81edef7169196b8dcc5d63d5
 
 build:
   noarch: python
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - bioconductor-dnacopy
@@ -49,13 +50,13 @@ test:
     - cnvkit.py -h
 
 about:
-  home: https://github.com/etal/cnvkit
-  license: Apache-2.0
+  home: "https://github.com/etal/cnvkit"
+  license: "Apache-2.0"
   license_family: APACHE
   license_file: LICENSE
-  summary: Copy number variant detection from high-throughput sequencing
-  dev_url: https://github.com/etal/cnvkit
-  doc_url: https://cnvkit.readthedocs.io/en/stable/
+  summary: "Copy number variant detection from high-throughput sequencing."
+  dev_url: "https://github.com/etal/cnvkit"
+  doc_url: "https://cnvkit.readthedocs.io/en/stable"
 
 extra:
   identifiers:

From beba2e057dc3e7959d9815b36092251de0309838 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 06:21:55 -0500
Subject: [PATCH 30/57] Update isoquant to 3.6.2 (#52153)

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

diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml
index ee3930be3b942..b6b2fd3056ed7 100644
--- a/recipes/isoquant/meta.yaml
+++ b/recipes/isoquant/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "IsoQuant" %}
-{% set version = "3.6.1" %}
-{% set sha256 = "6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d" %}
+{% set version = "3.6.2" %}
+{% set sha256 = "b742fe460b44d0d9feb967938176e707cfe4f281c53bf4fe04af2440c31e7862" %}
 
 package:
   name: {{ name | lower }}

From edf75804e9e69fab7b769cfb374448d2114a662f Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 18 Nov 2024 05:30:42 -0600
Subject: [PATCH 31/57] Rebuild muse recipe (#52157)

* Rebuild muse recipe

* try osx

* update patch

* clean up recipe
---
 recipes/muse/fix-install_muse.sh.patch | 38 +++++++++++++++++---------
 recipes/muse/meta.yaml                 | 15 +++++-----
 2 files changed, 33 insertions(+), 20 deletions(-)

diff --git a/recipes/muse/fix-install_muse.sh.patch b/recipes/muse/fix-install_muse.sh.patch
index 3a4d1a7f2ce65..22d3f5f457f2f 100644
--- a/recipes/muse/fix-install_muse.sh.patch
+++ b/recipes/muse/fix-install_muse.sh.patch
@@ -1,8 +1,8 @@
 diff --git a/install_muse.sh b/install_muse.sh
-index 7bc2153..1ef4b13 100755
+index 7bc2153..8a57cf7 100755
 --- a/install_muse.sh
 +++ b/install_muse.sh
-@@ -4,13 +4,21 @@ make clean
+@@ -4,13 +4,20 @@ make clean
  
  mkdir -p lib
  
@@ -15,10 +15,10 @@ index 7bc2153..1ef4b13 100755
  # compile boost library
 -cd boost_1_70_0/
 -./bootstrap.sh
-+cd boost-1.86.0/
-+./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
- ./b2 --clean
+-./b2 --clean
 -./b2
++cd boost-1.87.0.beta1/
++./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
 +./b2 toolset="${TOOL}" --layout=system link=static \
 +	threading=multi strip=on \
 +	variant=release address-model=64 install
@@ -28,30 +28,42 @@ index 7bc2153..1ef4b13 100755
  cd ..
  
  # compile libtcmalloc
-@@ -22,12 +30,12 @@ fi
+@@ -22,12 +29,21 @@ fi
  
  git clone https://github.com/gperftools/gperftools.git
  cd gperftools
 -git checkout gperftools-2.9.1
-+git checkout gperftools-2.16
++git checkout gperftools-2.10
  ./autogen.sh
 -./configure --libdir="$PWD"
 -make -j4
-+./configure --libdir="${PWD}" --prefix="${PREFIX}"
-+make -j${CPU_COUNT}
- make install
+-make install
 -cp libtcmalloc_minimal.a ../lib/
++if [[ $(uname) == 'Darwin' ]]; then
++	export CFLAGS="$CFLAGS -D_XOPEN_SOURCE"
++	./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++	--disable-debugalloc --disable-libunwind
++	make -j"${CPU_COUNT}"
++	make install
++else
++	./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++	--enable-libunwind --enable-frame-pointers
++	make -j"${CPU_COUNT}"
++	make install
++fi
 +cp -f libtcmalloc_minimal.a ../lib/
  cd ..
  
  # combine htslib
-@@ -42,27 +50,19 @@ cd htslib
+@@ -41,28 +57,20 @@ git clone https://github.com/samtools/htslib.git
+ cd htslib
  git checkout 1.9
  #git submodule update --init --recursive
- autoreconf -i
+-autoreconf -i
 -./configure
 -make -j4
 -cp libhts.a ../lib/
++autoreconf -if
 +./configure --enable-libcurl --enable-plugins \
 +	LDFLAGS="-L${PREFIX}/lib -Wl,-R${PREFIX}/lib" \
 +	CPPFLAGS="-I${PREFIX}/include"
@@ -84,4 +96,4 @@ index 7bc2153..1ef4b13 100755
  
 +rm -rf htslib
 +rm -rf gperftools
-+rm -rf boost-1.86.0
++rm -rf boost-1.87.0.beta1
diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml
index 6b838e934d836..2ebcef1e3f1a7 100644
--- a/recipes/muse/meta.yaml
+++ b/recipes/muse/meta.yaml
@@ -13,12 +13,12 @@ source:
     - 0001-Makefile.patch
     - fix-install_muse.sh.patch
     - version.patch
-- url: https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86.0-b2-nodocs.tar.gz
-  sha256: 2128a4c96862b5c0970c1e34d76b1d57e4a1016b80df85ad39667f30b1deba26
-  folder: boost-1.86.0
+- url: https://github.com/boostorg/boost/releases/download/boost-1.87.0.beta1/boost-1.87.0.beta1-b2-nodocs.tar.gz
+  sha256: f12e906fde4c9d04d88c3aa821f00501817a37503441cbca8ce7852a2194aeb0
+  folder: boost-1.87.0.beta1
 
 build:
-  number: 1
+  number: 2
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage('muse', max_pin="x") }}
@@ -26,7 +26,6 @@ build:
 requirements:
   build:
     - {{ compiler('cxx') }}
-    - {{ compiler('c') }}
     - make
     - autoconf
     - automake
@@ -48,15 +47,17 @@ test:
     - 'MuSE 2>&1 | grep "Version"'
 
 about:
-  home: "https://github.com/wwylab/MuSE"
+  home: "https://bioinformatics.mdanderson.org/public-software/muse"
   license: "GPL-2.0-or-later"
   license_family: GPL
   license_file: "LICENSE"
   summary: "An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples."
-  doc_url: "https://bioinformatics.mdanderson.org/public-software/muse"
+  doc_url: "https://github.com/wwylab/MuSE/blob/v{{ version }}/README.md"
   dev_url: "https://github.com/wwylab/MuSE"
 
 extra:
   identifiers:
     - doi:10.1101/gr.278456.123
     - doi:10.1186/s13059-016-1029-6
+  additional-platforms:
+    - linux-aarch64

From 5c6d47ae17d3f15942488366947425eed748aa40 Mon Sep 17 00:00:00 2001
From: Wytamma Wirth <wytamma.wirth@me.com>
Date: Mon, 18 Nov 2024 22:40:53 +1100
Subject: [PATCH 32/57] :heavy_plus_sign: Add graphviz dep (#52143)

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/snk-cli/meta.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/snk-cli/meta.yaml b/recipes/snk-cli/meta.yaml
index 073af957c0b49..809eeffb36f15 100644
--- a/recipes/snk-cli/meta.yaml
+++ b/recipes/snk-cli/meta.yaml
@@ -14,7 +14,7 @@ build:
     - {{ pin_subpackage('snk-cli', max_pin="x.x") }}
   noarch: python
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 0
+  number: 1
 
 requirements:
   host:
@@ -31,6 +31,7 @@ requirements:
     - ascii-art >=5.9,<6.dev0
     - makefun >=1.15,<2.dev0
     - datrie >=0.8.2
+    - graphviz >=2.38.0
 
 test:
   imports:

From 5fbc948b9e5bc6ab265f5910407c801b04a4b2a5 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 12:21:46 -0500
Subject: [PATCH 33/57] Update pathogen-profiler to 4.5.1 (#52163)

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

diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml
index 886f0db348512..12cf7af7e81d4 100644
--- a/recipes/pathogen-profiler/meta.yaml
+++ b/recipes/pathogen-profiler/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "pathogen-profiler" %}
-{% set version = "4.5.0" %}
-{% set sha256 = "55b23983ebd1a4de0e9fd9805a0a3a839fdfc89e61f5605bb58a5966b737349c" %}
+{% set version = "4.5.1" %}
+{% set sha256 = "e48994cb52005f1c2eb5a963bcf9c60d596352d80bf2bcb1e6475653caaf91fb" %}
 
 package:
   name: {{name}}
@@ -13,7 +13,7 @@ source:
 build:
   script: python -m pip install --no-deps --ignore-installed .
   noarch: python
-  number: 1
+  number: 0
   run_exports:
     - { pin_subpackage('pathogen-profiler', max_pin="x") }
 

From 949c1494b44b896fe87126394931110dfb511230 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 12:56:43 -0500
Subject: [PATCH 34/57] Update gfainject to 0.1.1 (#52099)

* Update gfainject to 0.1.1

* add cmake

* add dependencies

* try patch

* update patch

* update sha256

* remove patch

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com>
Co-authored-by: richard-burhans <burhans@bx.psu.edu>
Co-authored-by: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com>
---
 recipes/gfainject/meta.yaml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/recipes/gfainject/meta.yaml b/recipes/gfainject/meta.yaml
index f3d9aa1891954..22b1d7c8084b7 100644
--- a/recipes/gfainject/meta.yaml
+++ b/recipes/gfainject/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gfainject" %}
-{% set version = "0.1.0" %}
+{% set version = "0.1.1" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/AndreaGuarracino/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: a4388e524d5942f53d2fa94a93b2e82c926506c27cfdf04c04fbe8669a7ecebf 
+  sha256: a11f41ee94614d8c089454fdb3d0fb96e2f305db46895e2f64d974fa1707e739 
 
 build:
   number: 0
@@ -17,6 +17,11 @@ build:
 requirements:
   build:
     - {{ compiler('rust') }}
+    - cmake
+    - make
+    - pkg-config
+    - {{ compiler('c') }}      # For zlib-ng compilation
+    - {{ compiler('cxx') }}    # For C++ dependencies if any
 
 test:
   commands:

From 5c8a3a3c404a8ccdcf0c19088adacc38f6bfd0ce Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 13:27:37 -0500
Subject: [PATCH 35/57] Update nextflow to 24.10.1 (#52162)

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

diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml
index 5a044738b8906..e6c8bb30f6e99 100644
--- a/recipes/nextflow/meta.yaml
+++ b/recipes/nextflow/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.10.0" %}
-{% set sha256 = "e848918fb9b85762822c078435d9ff71979a88cccff81ce5babd75d5eee52fe6" %}
+{% set version = "24.10.1" %}
+{% set sha256 = "fd034b2d854010c7dfb7ae1b54d29209f45a2735504fa9c34becac44201f9e75" %}
 
 package:
   name: nextflow

From b86b77ef6cf2d89d07c2957e01ece68cc4fdbd23 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:15:58 -0500
Subject: [PATCH 36/57] Update polap to 0.3.7.2 (#52141)

* Update polap to 0.3.7.2

* Update polap to 0.3.7.2

---------

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

diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml
index 17890cfb02e16..2ca4d29359c56 100644
--- a/recipes/polap/meta.yaml
+++ b/recipes/polap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "polap" %}
-{% set version = "0.3.7.1" %}
-{% set sha256 = "c2a119c986035519b8252f4d85c91cfa060371ee0decc8c5d400b87428a81cfe" %}
+{% set version = "0.3.7.2" %}
+{% set sha256 = "7ac79618aa16cacd8bb5dd6fa7a1284b75bbbeeb526a418c9297d7324e9359c7" %}
 
 package:
   name: "{{ name }}"

From 04dfa6b15e84d3bd11dd553cf37de067371800c4 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:18:22 -0500
Subject: [PATCH 37/57] Update unikseq to 2.0.0 (#52169)

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

diff --git a/recipes/unikseq/meta.yaml b/recipes/unikseq/meta.yaml
index 6eee8a084f202..097d8f6d62ea2 100644
--- a/recipes/unikseq/meta.yaml
+++ b/recipes/unikseq/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.3.5" %}
+{% set version = "2.0.0" %}
 
 package:
   name: unikseq
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/bcgsc/unikseq/releases/download/v{{ version }}/unikseq-{{ version }}.tar.gz
-  sha256: 9b497384ce023a06fd79353c2488455f1517f10e575c86f1f5df1e21463d09e8
+  sha256: 5682d54e15ca41662f958c402c13328f9f19a6dd6a13043e4198679b10a6acb0
   patches:
     - unikseq-bloom.patch
     - unikseq-write-bloom.patch

From f739a41b1dbe2d0f658c2f694857480e827dc54b Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:19:18 -0500
Subject: [PATCH 38/57] Update tb-profiler to 6.4.1 (#52168)

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

diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml
index a32b773cc9d37..87bc58310c21e 100644
--- a/recipes/tb-profiler/meta.yaml
+++ b/recipes/tb-profiler/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "tb-profiler" %}
-{% set version = "6.4.0" %}
-{% set sha256 = "7868c95b1d2578723622f226f254e6bb7d1f35480a575e235f8e0b9984aca166" %}
+{% set version = "6.4.1" %}
+{% set sha256 = "1f325cfc32f3276b52e3e2b5078cce8492b495361799938e4540e1f0dc5d7938" %}
 
 package:
   name: {{name}}

From 0d649b3ee40eaa1d2d8c51f1f6b8b7292d42e087 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:19:49 -0500
Subject: [PATCH 39/57] Update oakvar to 2.12.3 (#52167)

---
 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 c7fe2167f1b4e..aea97c79af554 100644
--- a/recipes/oakvar/meta.yaml
+++ b/recipes/oakvar/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "OakVar" %}
-{% set version = "2.12.2" %}
-{% set sha256 = "1f5f961a2c8d04857bc3a63ae165254501e806ff84dfff39780ea0415505a4c4" %}
+{% set version = "2.12.3" %}
+{% set sha256 = "223ccb54ff43abc144b82d586b537bb111cdaa8a43e2efd05c182e774a911829" %}
 
 package:
   name: {{ name|lower }}

From ebcf6a3a7a72cb92662a13abb160ec0104987dfb Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:20:02 -0500
Subject: [PATCH 40/57] Update teloscope to 0.0.3 (#52161)

Co-authored-by: richard-burhans <burhans@bx.psu.edu>
---
 recipes/teloscope/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/teloscope/meta.yaml b/recipes/teloscope/meta.yaml
index df6fb7ece9654..b8d7346a1e3a0 100644
--- a/recipes/teloscope/meta.yaml
+++ b/recipes/teloscope/meta.yaml
@@ -1,11 +1,11 @@
 {% set name = "teloscope" %}
-{% set version = "0.0.2" %}
+{% set version = "0.0.3" %}
 package:
   name: {{ name }}
   version: {{ version }}
 source:
   url: https://github.com/vgl-hub/teloscope/releases/download/v{{version}}/teloscope.v{{version}}-with_submodules.zip
-  sha256: 1c186d3531686fb37fd5236a87b024a4e0d9923f992baa6425962acf22174418
+  sha256: 73267c978e8175f53f2fef034f110d3c98dd15ea5b0e0b2814c65b34207bc499
 build:
   number: 0
   run_exports:

From c5eaf90e41fedf9d4e40cd5ab6f78d65ca3f355f Mon Sep 17 00:00:00 2001
From: Jeroen Van Goey <j.vangoey@instadeep.com>
Date: Tue, 19 Nov 2024 11:54:05 +0200
Subject: [PATCH 41/57] Add Instanovo (#51796)

* Add `instanovo` recipe

* Add TODO comments

* dependencies of matchms have been updated

* Remove duplicate python lines, remove uper version bound

* Add upper python bound again

* unpin all packages

* re-add pinned packages, add eigen, add doi

* remove eigen, use pytorch-gpu

* Update recipes/instanovo/meta.yaml

* Update recipes/instanovo/meta.yaml

* Update meta.yaml

* Bump version of matchms to 0.28.0

Add TODO comments

dependencies of matchms have been updated

Remove duplicate python lines, remove uper version bound

Add upper python bound again

unpin all packages

re-add pinned packages, add eigen, add doi

remove eigen, use pytorch-gpu

Bump version of matchms to 0.28.0

* Use pytorch instead of pytorch-gpu

* Update meta.yaml

* make numpy version a lower bound

* Dropping all bounds

* Explicitly add pytorch-gpu
See this announcement:
https://dev-discuss.pytorch.org/t/pytorch-deprecation-of-conda-nightly-builds/2590

* Add packges which `pip check` complained about

* remove `pip check`, `pytorch-gpu`, `rdkit`, `lxml`, and `scipy` from `requirements` in `meta.yaml`

---------

Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
---
 recipes/instanovo/meta.yaml | 65 +++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 recipes/instanovo/meta.yaml

diff --git a/recipes/instanovo/meta.yaml b/recipes/instanovo/meta.yaml
new file mode 100644
index 0000000000000..a81bac3f6af7b
--- /dev/null
+++ b/recipes/instanovo/meta.yaml
@@ -0,0 +1,65 @@
+{% set name = "instanovo" %}
+{% set version = "1.0.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/instanovo-{{ version }}.tar.gz
+  sha256: fd9cfc377d9f8da5272f96b2eb4c14c08b579d7a65466aa402601ec6c4b42672
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name | lower, max_pin="x.x") }}
+
+
+requirements:
+  host:
+    - python >=3.10,<3.12
+    - setuptools >=69.1.1
+    - pip
+  run:
+    - click
+    - datasets
+    - hydra-core
+    - jaxtyping
+    - jiwer
+    - matchms
+    - neptune
+    - numpy
+    - omegaconf
+    - pandas
+    - polars
+    - pyopenms
+    - python-dotenv
+    - pytorch-lightning
+    - s3fs
+    - scikit-learn
+    - spectrum_utils
+    - tensorboard
+    - pytorch
+    - tqdm
+
+test:
+  imports:
+    - instanovo
+  commands:
+    - python -c "import instanovo; print(instanovo.__version__)"
+  requires:
+    - pip
+
+about:
+  home: https://github.com/instadeepai/instanovo
+  summary: De novo peptide sequencing with InstaNovo
+  license: Apache-2.0
+  license_file: LICENSE.md
+
+extra:
+  recipe-maintainers:
+    - BioGeek
+  identifiers:
+    - doi:10.1101/2023.08.30.555055 

From c7b594b060288546abc327099e8c671d537e006e Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Tue, 19 Nov 2024 12:40:48 +0000
Subject: [PATCH 42/57] perl-io-compress linux aarch64 support (#52152)

* Add osx-arm64 to r-facets, r-spp

* Add bioconductor-rsamtools osx-arm64 support - is a dependency for r-spp

* Revert attempt to include r-spp and bioconductor-rsamtools due to excessive dependencies to build for osx-arm64

* Add linux-aarch64 and osx-arm64 to perl-io-compress and blast.

* Oops - cut and pasta error

* add name variable to perl-io-compress meta.yaml

* Remove Blast from this patvh

* Update meta.yaml to remove osx-arm64 and show reason

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/perl-io-compress/meta.yaml | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/recipes/perl-io-compress/meta.yaml b/recipes/perl-io-compress/meta.yaml
index 8622771c8e1e5..ec9551d86e261 100644
--- a/recipes/perl-io-compress/meta.yaml
+++ b/recipes/perl-io-compress/meta.yaml
@@ -1,5 +1,6 @@
+{% set name = "perl-io-compress" %}
 package:
-  name: perl-io-compress
+  name: {{ name }}
   version: 2.201
 
 source:
@@ -7,8 +8,10 @@ source:
   sha256: f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad
 
 build:
-  number: 2
-
+  number: 3
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+    
 requirements:
   build:
     - make
@@ -55,6 +58,11 @@ test:
     - IO::Uncompress::RawInflate
     - IO::Uncompress::Unzip
 
+extra:
+  additional-platforms:
+    - linux-aarch64
+    #  perl-compress-raw-bzip2 and perl-scalar-list-utils missing
+    # - osx-arm64
 about:
   home: http://metacpan.org/pod/IO-Compress
   license: perl_5

From f5b84b6390f0e07e3a5aeea8e50be6d51d0e3b7d Mon Sep 17 00:00:00 2001
From: Agnieszka Danek <agnieszkadanek@users.noreply.github.com>
Date: Tue, 19 Nov 2024 13:45:17 +0100
Subject: [PATCH 43/57] Update meta.yaml (#52180)

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

diff --git a/recipes/agc/meta.yaml b/recipes/agc/meta.yaml
index 12d3d1e796fbf..86669ebdbf0b7 100644
--- a/recipes/agc/meta.yaml
+++ b/recipes/agc/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 1
+  number: 2
   script: "mkdir -p ${PREFIX}/bin; cp agc ${PREFIX}/bin"
   run_exports:
     - {{ pin_subpackage('agc', max_pin="x") }}
@@ -31,6 +31,7 @@ test:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   skip-lints:
     - should_be_noarch_generic
     - should_not_be_noarch_source

From 4a92a27c18136844c3455e6e5c9a70b68217005f Mon Sep 17 00:00:00 2001
From: Pau Andrio <andriopau@gmail.com>
Date: Tue, 19 Nov 2024 16:05:37 +0100
Subject: [PATCH 44/57] [biobb_godmd] update 5.0.0 (#52194)

---
 recipes/biobb_godmd/meta.yaml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/recipes/biobb_godmd/meta.yaml b/recipes/biobb_godmd/meta.yaml
index acf1ed0f9ff70..8666ea33a906b 100644
--- a/recipes/biobb_godmd/meta.yaml
+++ b/recipes/biobb_godmd/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "biobb_godmd" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: f697f96f216ce439e058d46842a2507ada30221d7048628fb83676ebf5806c50
+  sha256: edb62b0ca1dc5b8ee89f33cd44e8d2aa6e53ba6fd378f6c193aa6adf603fc282
 
 build:
   number: 0
@@ -18,15 +18,15 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - godmd ==1.0.0
     - emboss
 
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - godmd ==1.0.0
     - emboss
 
@@ -42,7 +42,7 @@ about:
   license: Apache Software License
   license_family: APACHE
   summary: Biobb_godmd is a BioBB category for GOdMD tool (protein conformational transitions).
-  description: "# biobb_godmd\n\n### Introduction\nBiobb_godmd allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ 
+  description: "# biobb_godmd\n\n### Introduction\nBiobb_godmd allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](https://mmb.irbbarcelona.org) at the [BSC](https://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
     \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\

From fad66f17576e3abb2035288fda75c706ad8da590 Mon Sep 17 00:00:00 2001
From: nickjcroucher <n.croucher@imperial.ac.uk>
Date: Tue, 19 Nov 2024 16:46:18 +0000
Subject: [PATCH 45/57] Update to version v2.7.2 (#52159)

* Update to version v2.7.2

* No more py3.8

* Reset build number
---
 recipes/poppunk/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml
index b75e51baa76af..da399ad941f42 100644
--- a/recipes/poppunk/meta.yaml
+++ b/recipes/poppunk/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.7.1" %}
+{% set version = "2.7.2" %}
 {% set name = "PopPUNK" %}
 
 package:
@@ -7,11 +7,11 @@ package:
 
 source:
   url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz
-  sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788
+  sha256: 1ea36fd3dee28b47c7e629eacd5ae5bf6dda3e464c23cfa5f51e63dc3d06e371
 
 build:
   number: 0
-  skip: True  # [py < 38]
+  skip: True # [py < 39]
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   entry_points:
     - poppunk = PopPUNK.__main__:main

From 9bb0bef49bcedb589e9b0b502c66c1c25ffc415b Mon Sep 17 00:00:00 2001
From: Rauf Salamzade <salamzader@gmail.com>
Date: Tue, 19 Nov 2024 13:32:34 -0600
Subject: [PATCH 46/57] Update meta.yaml (#52197)

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

diff --git a/recipes/lsabgc/meta.yaml b/recipes/lsabgc/meta.yaml
index 2f794a8713fad..566c66d3b4984 100644
--- a/recipes/lsabgc/meta.yaml
+++ b/recipes/lsabgc/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 04eadeadd7887883d48112624dd23496c19e2a038605e29fb0102c79badab5f4 
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv"
   run_exports:
@@ -25,7 +25,7 @@ requirements:
     - python >=3.10
     - r-base
     - axel
-    - zol >=1.4.12
+    - zol =1.4.12
     - orthofinder =2.5.5
     - pyseer >=1.3
     - gecco =0.9.6

From 5e30247384025101d8accacab2a913f75cd77b91 Mon Sep 17 00:00:00 2001
From: Anan Ibrahim <81744003+Darcy220606@users.noreply.github.com>
Date: Tue, 19 Nov 2024 20:35:11 +0100
Subject: [PATCH 47/57] Update ampcombi to v.2.0.1 (#52184)

* update recipe to new v 2.0.1

* update code review

* update pinning - code review

* fix link url
---
 recipes/ampcombi/meta.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml
index 1bb7752d2c957..f26e9a314b882 100644
--- a/recipes/ampcombi/meta.yaml
+++ b/recipes/ampcombi/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "AMPcombi" %}
-{% set version = "0.2.2" %}
+{% set version = "2.0.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: da9a179851a8f2041d05ccd10dd45b58099e84059e2e66a9ee405d1913471b58
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ampcombi-{{ version }}.tar.gz
+  sha256: 4bef05aa8433d991b76b81cb2338396c064f2ace5c73642411b2a2467524a0eb
 
 build:
   noarch: python
@@ -32,9 +32,10 @@ requirements:
     - backports.tempfile
     - contextlib2
     - openpyxl
+    - numpy ==1.26.4
     - jsonschema
     - python ==3.11
-    - diamond ==2.0.15
+    - colorama ==0.4.6
     - mmseqs2 ==15.6f452
 
 test:

From 76b58b74b4d6e7f83fb8018622419444ce5c6ee0 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:15:06 -0500
Subject: [PATCH 48/57] Update harpy to 1.12 (#52200)

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

diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml
index a76e823eac517..82f7f13f9ac2d 100644
--- a/recipes/harpy/meta.yaml
+++ b/recipes/harpy/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.11" %}
-{% set sha256 = "e48308505e8ef9e6be2fdce8cb449f9fffe1aabcf1fb6b6e2aba94a8b00ccc71" %}
+{% set version = "1.12" %}
+{% set sha256 = "e6b0ecdd862d154b8c5de6c1414a131e0b5d2f8449edbe85425f9bc9534525db" %}
 
 package:
   name: harpy

From 2b86fcae200de0d2ede53df25979d0dc95d1f06e Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:15:37 -0500
Subject: [PATCH 49/57] Update trgt to 1.3.0 (#52199)

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

diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml
index bb87d98169589..4c3e0712059bf 100644
--- a/recipes/trgt/meta.yaml
+++ b/recipes/trgt/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "trgt" %}
-{% set version = "1.2.0" %}
-{% set trgt_sha256 = "5dec0943d3400fd1677236fa35737e5a442a486fac55188029c3c9164edb3d23" %}
+{% set version = "1.3.0" %}
+{% set trgt_sha256 = "25d1e7a67c13cde0ab196ef8061a048f58c5c8b70c4ab9acd31613a6dab8ef1d" %}
 
 package:
   name: {{ name }}

From 74df104cc1bdce183618fce402eb2fcdf4f6ac4b Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:15:53 -0500
Subject: [PATCH 50/57] Update panfeed to 1.7.0 (#52191)

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

diff --git a/recipes/panfeed/meta.yaml b/recipes/panfeed/meta.yaml
index 833ba2d123065..7e053b67e7b36 100644
--- a/recipes/panfeed/meta.yaml
+++ b/recipes/panfeed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.6.2" %}
+{% set version = "1.7.0" %}
 {% set name = "panfeed" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 71e6e97b29784396421b59511dbca27103acfe31a3f392324d4d0419179340be
+  sha256: dd75396f5fd6cbb27163559f813ea7c2802e2d4444271a2e30190727785811e2
 
 build:
   entry_points:

From 7ac4b0c7ece8f0a221769980e0b7d8154778611d Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:16:10 -0500
Subject: [PATCH 51/57] Update libcifpp to 7.0.8 (#52179)

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

diff --git a/recipes/libcifpp/meta.yaml b/recipes/libcifpp/meta.yaml
index e81459934f2a9..c1e89d66c0293 100644
--- a/recipes/libcifpp/meta.yaml
+++ b/recipes/libcifpp/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "libcifpp" %}
-{% set version = "7.0.7" %}
-{% set sha256 = "0e88805b4704d4a899aeee6df5aaace1d6b47d8ccb3a3f39b35bc5a3997c09ac" %}
+{% set version = "7.0.8" %}
+{% set sha256 = "2297e6649a4f71caf9da5f1d97f59512e7324bb62083bb5b08eb00c1c0385cb3" %}
 
 package:
   name: {{ name|lower }}

From a53d9e36e5f5c897bf74babc253e434d5062c706 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:16:23 -0500
Subject: [PATCH 52/57] Update notramp to 1.1.7 (#52185)

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

diff --git a/recipes/notramp/meta.yaml b/recipes/notramp/meta.yaml
index f4736f09609de..7525c96c6621b 100644
--- a/recipes/notramp/meta.yaml
+++ b/recipes/notramp/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "notramp" %}
-{% set version = "1.1.6" %}
+{% set version = "1.1.7" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,10 +7,10 @@ package:
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: d17dafed1f9afa119c48aca5486c59049774590ca5b90b6802a011d9eaec85ca
+  sha256: 1f6dd890d43943ef934f206ea9fe873b334eef1706fa8eee0fdb609eb8b5bb71
 
 build:
-  number: 1
+  number: 0
   entry_points:
     - notramp = notramp.notramp_main:run_notramp
   script: "{{ PYTHON }} -m pip install . -vv"

From 656915e8c6e1acf5efc535a0e548ae2b9642a76c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:16:41 -0500
Subject: [PATCH 53/57] Update minute to 0.10.1 (#52186)

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

diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml
index aa0fbee72cd69..ca14a1a16b2ab 100644
--- a/recipes/minute/meta.yaml
+++ b/recipes/minute/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.10.0" %}
+{% set version = "0.10.1" %}
 
 package:
   name: minute
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/elsasserlab/minute/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: f784a571601ac2e673fe0783b13e9b7ef8ba8d1e4bab7f48aff67365e607f0fd
+  sha256: 666204aa5ba17fe1c77a156b0987d036ecf7a8792f860745e0741e3ad33b0976
 
 build:
   number: 0

From c158e050b9861dcc11ba231ad448c0c978053675 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:17:02 -0500
Subject: [PATCH 54/57] Update jbrowse2 to 2.17.0 (#52172)

---
 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 b280429eb499e..99e94882dfff8 100644
--- a/recipes/jbrowse2/meta.yaml
+++ b/recipes/jbrowse2/meta.yaml
@@ -1,12 +1,12 @@
 # When updating, check the @jbrowse/cli version in build.sh too
-{% set version = "2.16.1" %}
+{% set version = "2.17.0" %}
 
 package:
   name: jbrowse2
   version: {{ version }}
 
 source:
-  sha256: b869ab507a765e775dd961d5abfb0b1982dd01b3dd7648d9c3d062c2fab32cfe
+  sha256: cf863b95ad3c21d2ceceb05761ae5824b26191e9421ddc0cd2c5073afce22dbe
   url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip
 
 build:

From 49ad21ea56ada5ebff25b27ce32859b0d9f50e03 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:21:39 -0500
Subject: [PATCH 55/57] Update treeswift to 1.1.45 (#52204)

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

diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml
index 9c1e48fd450d3..3a54f7c34eada 100644
--- a/recipes/treeswift/meta.yaml
+++ b/recipes/treeswift/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.1.44" %}
+{% set version = "1.1.45" %}
 
 package:
   name: "treeswift"
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz
-  sha256: c023c8130e29f124cdd3d98d3b29e168a4f150df29dc6a243524e2875d22b799
+  sha256: 3bd1db3a45dbd443051a4f9ecafc99a8e38b23b47a28333878c1eef6e8f67e7e
 
 build:
   noarch: python

From fba927202378dcb629c77b7fc9afff0c16fa44ad Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 19 Nov 2024 15:21:50 -0500
Subject: [PATCH 56/57] Update biobb_godmd to 5.0.0 (#52196)

---
 recipes/biobb_godmd/meta.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/recipes/biobb_godmd/meta.yaml b/recipes/biobb_godmd/meta.yaml
index 8666ea33a906b..d2e69fa755408 100644
--- a/recipes/biobb_godmd/meta.yaml
+++ b/recipes/biobb_godmd/meta.yaml
@@ -18,15 +18,15 @@ build:
 
 requirements:
   host:
-    - python >=3.9
+    - python >=3.8
     - setuptools
-    - biobb_common ==5.0.0
+    - biobb_common ==4.2.0
     - godmd ==1.0.0
     - emboss
 
   run:
-    - python >=3.9
-    - biobb_common ==5.0.0
+    - python >=3.8
+    - biobb_common ==4.2.0
     - godmd ==1.0.0
     - emboss
 
@@ -42,7 +42,7 @@ about:
   license: Apache Software License
   license_family: APACHE
   summary: Biobb_godmd is a BioBB category for GOdMD tool (protein conformational transitions).
-  description: "# biobb_godmd\n\n### Introduction\nBiobb_godmd allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
+  description: "# biobb_godmd\n\n### Introduction\nBiobb_godmd allows the calculation of protein conformational transitions using the GOdMD package. \nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ 
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](https://mmb.irbbarcelona.org) at the [BSC](https://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
     \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\

From 093e4ccadefd9365ed7462d156360ab2c7a90f86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vin=C3=ADcius=20H=2E=20Franceschini-Santos?=
 <vfranceschinisantos@gmail.com>
Date: Tue, 19 Nov 2024 21:23:07 +0100
Subject: [PATCH 57/57] Parm v0.0.7 (#52182)

* Update meta.yaml

* Update meta.yaml

* update parm

* Update meta.yaml

* replace torch-cuda with cuda-toolkit

* Update meta.yaml

* Update meta.yaml

* Remove channels from recipe

* Update meta.yaml

* Update v0.0.7

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: vhfsantos <vfranceschini@gmail.com>
---
 recipes/parm/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/parm/meta.yaml b/recipes/parm/meta.yaml
index 43aa89fff9051..f5ad767d5bbf3 100644
--- a/recipes/parm/meta.yaml
+++ b/recipes/parm/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.0.6" %}
-{% set sha256 = "58853578e42e76ecb9e609cb9b292fa979ae5a999d28126f3c43ac0e986f44a5" %}
+{% set version = "0.0.7" %}
+{% set sha256 = "5f6a94d86ba026ac816eae8e27fbec00d2b25a7c5f5729101474f758d7dcbcc9" %}
 
 package:
   name: parm
@@ -10,7 +10,7 @@ source:
     sha256: {{ sha256 }}
 build:
   noarch: python
-  number: 2
+  number: 0
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage('parm', max_pin="x.x") }}