Merge branch 'master' into patch-8

bioconda · Nov 4, 2024 · 2e649ba · 2e649ba
2 parents 98be845 + a425455
commit 2e649ba
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diff --git a/recipes/aletsch/meta.yaml b/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") }}
 

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

diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 900e0e67c251f12989154113c54d2b32
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -74,3 +74,6 @@ about:
   description: 'bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.'
   license_file: LICENSE
 
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "1.34.0" %}
+{% set version = "1.38.0" %}
 {% set name = "ProtGenerics" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
@@ -11,7 +11,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 5d55c00588169aa089bb457e2d94669a
+  md5: 7e7211a9fa758ca6f1b701c86e892895
 build:
   number: 0
   rpaths:

diff --git 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

diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "cogent3" %}
-{% set version = "2024.7.19a8" %}
+{% set version = "2024.7.19a9" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 7d046813b004c09de379b6d001b48ff93c0193923cc5b809efb5cfa25fb278c7
+  sha256: 5f1ab042294f718a77e0d8fa8adf3b20fefe9ef5a47b1c2092e50e8560883afa
 
 build:
   noarch: python

diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml
@@ -1,24 +1,24 @@
-{% set version = "0.30.0" %}
+{% set version = "0.31.0" %}
 # This package should be migrated to conda-forge due to general utility
 # In that case it needs to be built from source
 package:
   name: csvtk
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('csvtk', max_pin='x.x') }}
 
 source:
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx and x86_64]
-    md5: c415255e265ba0cd547806fdbda05652 # [osx and x86_64]
+    md5: 5a23d000a1fc068360e1aeb439f3ae25 # [osx and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_arm64.tar.gz # [arm64]
-    md5: dd8a84c301d378ab7ff28c85d37fbefa # [arm64]
+    md5: 6aa24ce286910e83d95d28a21905f1d8 # [arm64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux and x86_64]
-    md5: 8f5877d4fbea89609d64bd2679956476 # [linux and x86_64]
+    md5: 09bc8c3288f028239c94d4c935ac7a6f # [linux and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_arm64.tar.gz # [aarch64]
-    md5: 2a6dd840291d23971ff538eaf3de00ec # [aarch64]
+    md5: f7a5b8839459d7d55685056331670eec # [aarch64]
 
 test:
   commands:

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

diff --git a/recipes/derna/build.sh b/recipes/derna/build.sh
@@ -2,12 +2,21 @@
 
 set -xe
 
+mkdir -p $PREFIX/bin
+
 export C_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 
-mkdir build
-cd build
-cmake ..
-make -j ${CPU_COUNT}
-mkdir -p $PREFIX/bin
-cp derna $PREFIX/bin
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+cmake --build build  -j ${CPU_COUNT} -v
+chmod 0755 build/derna
+mv build/derna $PREFIX/bin
diff --git a/recipes/derna/meta.yaml b/recipes/derna/meta.yaml
@@ -1,15 +1,15 @@
-{% set version = "1.0.3" %}
+{% set version = "1.0.4" %}
 
 package:
   name: derna
   version: {{ version }}
 
 source:
   url: https://github.com/elkebir-group/derna/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: d7e2fdbe733d03f9e617ea325a43283c0e4e298780253cf2e7da7ad07d3aafc5
+  sha256: eb5fabf0e01d9507ceca3fc687e8c67a9cec91c77e75d2c4f7d310ac926a79cb
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('derna', max_pin="x") }}
 
@@ -25,12 +25,13 @@ test:
     - derna -h
 
 about:
-  home: https://github.com/elkebir-group/derna
+  home: "https://github.com/elkebir-group/derna"
   license: BSD-3-Clause
   license_family: BSD
   license_file: LICENSE
   summary: "RNA sequence design for a target protein sequence."
-  dev_url: https://github.com/elkebir-group/derna
+  dev_url: "https://github.com/elkebir-group/derna"
+  doc_url: "https://github.com/elkebir-group/derna/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:

diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio-minimal
   version: {{ version }}
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic

diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio
   version: {{ version }}
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic

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

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

diff --git 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: