From 8520449fec3e9ec3f59f41eb673f0bc3905f3534 Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Thu, 31 Oct 2024 04:40:48 +0000
Subject: [PATCH 01/16] Enable perl-list-moreutils-xs for linux-aarch64
 (#51816)

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

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

From 724d13dd929e9eefd024acd9457672fdd2542f76 Mon Sep 17 00:00:00 2001
From: dslarm <38504854+dslarm@users.noreply.github.com>
Date: Thu, 31 Oct 2024 04:42:15 +0000
Subject: [PATCH 02/16] Add linux-aarch64 and osx-arm64 as targets for sgdemux
 (#51817)

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

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

From 23a484e0d2cbb8da5ccd7d7a5caa57f2e25e3517 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 00:44:32 -0400
Subject: [PATCH 03/16] Update aletsch to 1.1.3 (#51828)

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

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

From 0942664264535c937f661f70ddfb3f121809aebc Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 31 Oct 2024 10:11:52 +0100
Subject: [PATCH 04/16] update gcnvkernel to v 0.9 (#51834)

* update gcnvkernel

* linting

* fix typo

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

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

From 2d8229527a9a5547ce56dd9e2867f17c7c3294e2 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 05:49:21 -0400
Subject: [PATCH 05/16] Update gatk4 to 4.6.1.0 (#48815)

* Update gatk4 to 4.6.0.0

* Update gatk4 to 4.6.1.0

* bump dependencies

---------

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

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

From 0c5f7a2c6ac547c072893a8aaee693e37c15d1ca Mon Sep 17 00:00:00 2001
From: Jessica Mattick <19544292+jmattick@users.noreply.github.com>
Date: Thu, 31 Oct 2024 05:21:17 -0500
Subject: [PATCH 06/16] Update pbjasmine to 2.4.0 (#51818)

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

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

From 3a52d6744ff42765c17b87a0481423d68cca99e2 Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:04:34 +0100
Subject: [PATCH 07/16] change python version (#51790)

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

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

From 9df90ee0632f35e6296414ce5a224aa471787410 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 09:40:35 -0400
Subject: [PATCH 08/16] Update pathogen-profiler to 4.5.0 (#51840)

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

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

From 5048dcec92a7b3f8c4c750a37fde8d68ade5dc4e Mon Sep 17 00:00:00 2001
From: Amirhossein <66441226+nilchia@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:12:30 +0100
Subject: [PATCH 09/16] Add Liana+ to biocodna (#51736)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* meta.yaml created by grayskul

* add run_exports

* Update recipes/liana/meta.yaml

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

* update meta

* Update meta.yaml

* Update meta.yaml

---------

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

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

From b6bf022c2ec77a869af5188f549b5fe275f326e3 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 10:55:57 -0400
Subject: [PATCH 10/16] Update oakvar to 2.11.25 (#51839)

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

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

From 3deb6c106252302b8d60b2aed1f6f003fe304882 Mon Sep 17 00:00:00 2001
From: Adam Taranto <adam.p.taranto@gmail.com>
Date: Fri, 1 Nov 2024 01:56:18 +1100
Subject: [PATCH 11/16] Update TIRmite recipe (#51835)

* Update TIRmite recipe

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

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

From 8076adcec7d083c2554de57524978a461390e1dd Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:00:09 -0400
Subject: [PATCH 12/16] Update tb-profiler to 6.4.0 (#51841)

* Update tb-profiler to 6.4.0

* update deps

* add setuptools

---------

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

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

From a99ab47f10b572d65867220d55052970d6b66d86 Mon Sep 17 00:00:00 2001
From: Ryan Doughty <57912116+rdoughty10@users.noreply.github.com>
Date: Thu, 31 Oct 2024 14:34:37 -0500
Subject: [PATCH 13/16] Update seqscreen meta.yaml  (#51845)

* Update meta.yaml

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

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

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

From b87c8fa6d05c05e5b3641f0341efd18251ebb622 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:32:29 -0400
Subject: [PATCH 14/16] Update aster to 1.19 (#51843)

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

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

From 5a4bc1f1447c80e1ad4c263bce054512b1073d15 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:32:40 -0400
Subject: [PATCH 15/16] Update tirmite to 1.1.6 (#51842)

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

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

From 17f5b45e76c703018dc36c4a5f7152e9b93d55b4 Mon Sep 17 00:00:00 2001
From: Chris Jackson <55370301+chrisjackson-pellicle@users.noreply.github.com>
Date: Fri, 1 Nov 2024 07:39:30 +1100
Subject: [PATCH 16/16] Update - add setuptools to host requirements as
 hybpiper conda build now failing without it (#51829)

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

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

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