Merge branch 'master' into master

Author: y3tseng

recipes/biscuit/0001-CMakeLists.patch

@@ -1,8 +1,8 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 75f5632..aafc03d 100644
+index e494ea2..84cb5d7 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -47,8 +47,8 @@ ExternalProject_Add(utils
+@@ -50,8 +50,8 @@ ExternalProject_Add(utils
      GIT_TAG 5f4aeabb42229440a99a5286f8052d3e5dc665cb
      DOWNLOAD_DIR ${LIB_DIR}
      SOURCE_DIR ${LIB_DIR}/utils
@@ -13,7 +13,7 @@ index 75f5632..aafc03d 100644
      INSTALL_COMMAND ""
      BUILD_IN_SOURCE 1
      )
-@@ -59,8 +59,8 @@ ExternalProject_Add(sgsl
+@@ -62,8 +62,8 @@ ExternalProject_Add(sgsl
      GIT_TAG 6533277fd490b68b0c664efc168a1f05de54b010
      DOWNLOAD_DIR ${LIB_DIR}
      SOURCE_DIR ${LIB_DIR}/sgsl
@@ -24,32 +24,32 @@ index 75f5632..aafc03d 100644
      INSTALL_COMMAND ""
      BUILD_IN_SOURCE 1
      )
-@@ -81,11 +81,11 @@ if(APPLE)
+@@ -94,11 +94,11 @@ if(APPLE)
              mkdir -p ${htslib_base} &&
              tar -jxf ${htslib_base}.tar.bz2 --strip-components=1 -C ${htslib_base} &&
              rm -rf htslib &&
 -            mv -f ${htslib_base} htslib
 +            mv -f ${htslib_base} htslib && patch -p1 < $(RECIPE_DIR)/arm_hwcap.patch
          SOURCE_DIR ${LIB_DIR}/htslib
          INSTALL_DIR ${LIB_DIR}/install
--        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> --disable-bz2 --disable-lzma --disable-libcurl
+-        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> --disable-bz2 --disable-lzma --disable-libcurl ${LIBDEFLATE_FLAG}
 -        BUILD_COMMAND make lib-static
-+        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> CC=$ENV{CC} --disable-bz2 --disable-lzma --disable-libcurl
++        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> CC=$ENV{CC} --disable-bz2 --disable-lzma --disable-libcurl ${LIBDEFLATE_FLAG}
 +        BUILD_COMMAND make lib-static CFLAGS=$ENV{CFLAGS}
          INSTALL_COMMAND ""
          BUILD_IN_SOURCE 1
          )
-@@ -97,11 +97,11 @@ else()
+@@ -110,11 +110,11 @@ else()
              mkdir -p ${htslib_base} &&
              tar -jxf ${htslib_base}.tar.bz2 --strip-components=1 -C ${htslib_base} &&
              rm -rf htslib &&
 -            mv -f ${htslib_base} htslib
 +            mv -f ${htslib_base} htslib && patch -p1 < $(RECIPE_DIR)/arm_hwcap.patch
          SOURCE_DIR ${LIB_DIR}/htslib
          INSTALL_DIR ${LIB_DIR}/install
--        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> --disable-bz2 --disable-lzma --disable-libcurl
+-        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> --disable-bz2 --disable-lzma --disable-libcurl ${LIBDEFLATE_FLAG}
 -        BUILD_COMMAND make lib-static
-+        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> CC=$ENV{CC} --disable-bz2 --disable-lzma --disable-libcurl
++        CONFIGURE_COMMAND ${LIB_DIR}/htslib/configure --prefix=<INSTALL_DIR> CC=$ENV{CC} --disable-bz2 --disable-lzma --disable-libcurl ${LIBDEFLATE_FLAG}
 +        BUILD_COMMAND make lib-static CFLAGS=$ENV{CFLAGS}
          INSTALL_COMMAND ""
          BUILD_IN_SOURCE 1

recipes/biscuit/meta.yaml

@@ -1,7 +1,8 @@
-{% set version = "1.6.1.20250415" %}
+{% set name = "biscuit" %}
+{% set version = "1.7.0.20250512" %}
 
 package:
-  name: biscuit
+  name: {{ name }}
   version: {{ version }}
 
 build:
@@ -11,7 +12,7 @@ build:
 
 source:
   url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/release-source.zip
-  sha256: 4291d7a0ee550b930dc6f17fad36dce2a51587e1cb60dbf19ff6fb9e631c6ca5
+  sha256: 13ac091da9aee0f4141737fe01c68ff0299da06297cea8a1557338a2f5f7ee2f
   patches:
     - 0001-CMakeLists.patch
     - 0004-aarch64-ksw.patch  # [aarch64 or arm64]
@@ -26,6 +27,7 @@ requirements:
     - ncurses
     - pthread-stubs
     - libcurl
+    - libdeflate
   run:
     - pthread-stubs
     - perl
@@ -37,13 +39,13 @@ test:
     - build_biscuit_QC_assets.pl -h 2>&1 | grep "Usage"
 
 about:
-  home: https://github.com/huishenlab/biscuit
+  home: "https://github.com/huishenlab/biscuit"
   license: MIT
   license_family: MIT
   license_file: LICENSE
   summary: "A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data."
-  dev_url: https://github.com/huishenlab/biscuit
-  doc_url: https://huishenlab.github.io/biscuit
+  dev_url: "https://github.com/huishenlab/biscuit"
+  doc_url: "https://huishenlab.github.io/biscuit"
 
 extra:
   additional-platforms:

recipes/cpat/build.sh

@@ -2,19 +2,30 @@
 {% set version = "3.0.5" %}
 
 package:
-  name: "{{ name|lower }}"
-  version: "{{ version }}"
-
-build:
-  number: 3
-  skip: True  # [py > 39]
-  run_exports:
-    - {{ pin_subpackage('cpat', max_pin="x") }}
+  name: {{ name|lower }}
+  version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
   sha256: ea7c9216208221f68055f962073622939ff90bbe52ebe36c305ead9f91ed24bc
 
+build:
+  number: 4
+  skip: True  # [py < 38]
+  script:
+    - {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
+    # Prefix '.py' has been removed from v3.0.5
+    # symlinking for reverse compatibility, as suggested in release notes
+    - ln -sf ${PREFIX}/bin/cpat ${PREFIX}/bin/cpat.py
+    - ln -sf ${PREFIX}/bin/make_hexamer_tab ${PREFIX}/bin/make_hexamer_tab.py
+    - ln -sf ${PREFIX}/bin/make_logitModel ${PREFIX}/bin/make_logitModel.py
+  entry_points:
+    - cpat = cpmodule:cpat
+    - make_hexamer_tab = cpmodule:make_hexamer_tab
+    - make_logitModel = cpmodule:make_logitModel
+  run_exports:
+    - {{ pin_subpackage('cpat', max_pin="x") }}
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -35,16 +46,24 @@ requirements:
 
 test:
   commands:
-    - cpat.py -h
-    - make_hexamer_tab.py -h
-    - make_logitModel.py -h
+    - cpat --help
+    - make_hexamer_tab --help
+    - make_logitModel --help
 
 about:
-  home: https://cpat.readthedocs.io/en/latest/
-  license: GPL-2.0-or-later
-  license_file: LICENSE.txt
-  summary: Coding Potential Assessment Tool
+  home: "https://github.com/liguowang/cpat"
+  license: "GPL-2.0-or-later"
+  license_family: GPL
+  license_file: "LICENSE.txt"
+  summary: "Coding Potential Assessment Tool."
+  doc_url: "https://cpat.readthedocs.io/en/latest"
+  dev_url: "https://github.com/liguowang/cpat"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
+  identifiers:
+    - doi:10.1093/nar/gkt006
+    - biotools:cpat
+    - usegalaxy-eu:cpat

recipes/cpat/meta.yaml

@@ -1,19 +1,18 @@
 {% set name = "genedom" %}
-{% set version = "0.2.1" %}
+{% set version = "0.2.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/Edinburgh-Genome-Foundry/genedom/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 2b10083590aecfbfa1faaab55074ecf837931cfa3f33758f9124e915f2aaa549
-  patches: patches/0001-restrict-installed-modules.patch
+  sha256: 0ff304250a6be8b71dcd19969dce3a0b14ffba17731487e28b406e32a86de0d6
 
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
   run_exports: 
     - {{ pin_subpackage('genedom', max_pin="x.x") }}
 
@@ -47,10 +46,12 @@ test:
     - if command -v pytest >/dev/null 2>&1; then pytest tests/; else echo "pytest not available, skipping tests."; fi
 
 about:
-  home: https://github.com/Edinburgh-Genome-Foundry/genedom#
-  summary: "Genetic part standardization"
+  home: "https://github.com/Edinburgh-Genome-Foundry/genedom"
+  summary: "Genetic part standardization."
   license: MIT
-  license_file: LICENCE.txt
+  license_family: MIT
+  #license_file: "LICENCE.txt"
+  dev_url: "https://github.com/Edinburgh-Genome-Foundry/genedom"
 
 extra:
   recipe-maintainers:

recipes/genedom/meta.yaml

@@ -0,0 +1,4 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+# shellcheck disable=SC2086
+${R} CMD INSTALL --build . ${R_ARGS}

recipes/genedom/patches/0001-restrict-installed-modules.patch

@@ -0,0 +1,71 @@
+{% set version = "1.0.0" %}
+
+package:
+  name: r-viber
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url: https://github.com/caravagnalab/VIBER/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: c058904821536e1d659cf27362f5550d9c266681061d480429bb8ed5b1abf5cb
+
+build:
+  noarch: generic
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("r-viber", max_pin="x.x") }}
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - git
+  
+  host:
+    - r-base
+    - r-crayon
+    - r-pio
+    - r-easypar
+    - r-dplyr
+    - r-ggplot2
+    - r-reshape2
+    - r-ctree
+    - r-cli
+
+  run:
+    - r-base
+    - r-crayon
+    - r-pio
+    - r-easypar
+    - r-dplyr
+    - r-ggplot2
+    - r-reshape2
+    - r-ctree
+    - r-cli
+
+test:
+  commands:
+    # You can put additional test commands to be run here.
+    - $R -e "library(VIBER)"           # [not win]
+    - "\"%R%\" -e \"library(VIBER)\""  # [win]
+
+about:
+  home: https://github.com/caravagnalab/VIBER
+  license: GPL-3.0-or-later
+  summary: "Variational Binomial Mixtures."
+  description: |
+    VIBER is a package that implements a variational Bayesian model to
+    fit multi-variate Binomial mixtures. The statistical model is
+    semi-parametric and fit by a variational mean-field approximation to
+    the model posterior. The components are Binomial distributions which
+    can model count data; these can be used to model sequencing counts in
+    the context of cancer, for instance. The package implements methods to
+    fit and visualize clustering results.
+  license_family: GPL3
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+  doc_url: https://caravagnalab.github.io/VIBER/
+
+extra:
+  recipe-maintainers:
+    - elena-buscaroli