Merge branch 'master' into bump/hybpiper

recipes/aletsch/meta.yaml

@@ -1,16 +1,16 @@
 {% set name = "aletsch" %}
-{% set version = "1.1.2" %}
+{% set version = "1.1.3" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 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") }}
 

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") }}
 

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

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:

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:

recipes/hybpiper/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: 0f341fb26dffd39c13b3bfc5c1d568936bcd0edbe9064399e4aa947d5882d220
 
 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

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

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 }}

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}}

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"

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:

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

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:

recipes/sgdemux/meta.yaml

@@ -1,12 +1,14 @@
+{% set name = "sgdemux" %}
 {% set version = "1.2.0" %}
 
 package:
   name: sgdemux
   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