Merge branch 'master' into revbayes

bioconda · Nov 12, 2024 · 6203c9b · 6203c9b
2 parents 8654bf5 + 13fb86e
commit 6203c9b
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diff --git a/recipes/atlas/build.sh b/recipes/atlas/build.sh
@@ -1,14 +1,27 @@
 #!/bin/bash
 
-export CFLAGS="$CFLAGS -I$PREFIX/include"
-export LDFLAGS="$LDFLAGS -L$PREFIX/lib"
-export LD_LIBRARY_PATH="${PREFIX}/lib"
-export LIBRARY_PATH="${PREFIX}/lib"
-export CPATH="${PREFIX}/include"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
-sed -i.bak 's/^GIT_HEADER/#GIT_HEADER/' makefile
+if [[ `uname` == "Darwin" ]]; then
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+    export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+else
+    export CONFIG_ARGS=""
+fi
 
-make CXX=$CXX ARM=false
+cmake . -GNinja \
+    -DCONDA=ON \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_CXX_COMPILER="${CXX}" \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+    "${CONFIG_ARGS}"
 
-mkdir -p $PREFIX/bin
-cp atlas $PREFIX/bin 
+ninja || exit 1
+
+mkdir -p ${PREFIX}/bin
+cp atlas ${PREFIX}/bin || exit 1
+chmod +x ${PREFIX}/bin/atlas
diff --git a/recipes/atlas/meta.yaml b/recipes/atlas/meta.yaml
@@ -1,39 +1,65 @@
-{% set version = "0.9.9" %}
+{% set version = "2.0.0" %}
 
-package: 
+package:
   name: atlas
   version: {{ version }}
 
 source:
-  url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz
-  sha256: 7b65eae5ab7ff439accd53febf8caa15ad9d8230278eee31fd5c2e95bf021990
+  url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.6.tar.gz
+  sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3
 
 build:
-  number: 3
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("atlas", max_pin="x") }}
 
 requirements:
-    build:
-      - make
-      - {{ compiler('cxx') }}
-      - zlib
-      - armadillo
-      - libblas
-      - openblas
-    host:
-      - zlib
-      - armadillo
-      - libblas
-      - openblas
-    run:
-      - libblas
-      - zlib
-      - armadillo
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - git
+    - ninja
+    - sysroot_linux-64 =2.17  # [linux]
+  host:
+    - armadillo
+    - fmt
+    - htslib
+    - lapack
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - nlohmann_json
+    - openblas
+    - sysroot_linux-64 =2.17  # [linux]
+    - jsoncpp
+    - zlib
+  run:
+    - armadillo
+    - fmt
+    - htslib
+    - lapack
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - nlohmann_json
+    - openblas
+    - sysroot_linux-64 =2.17  # [linux]
+    - jsoncpp
 
 test:
-    commands:
-      - atlas task=recal | grep Wegmann
-
+  commands:
+    - atlas | grep "successfully"
+    - atlas simulate
+    - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta
+    - atlas GLF --bam ATLAS_simulations.bam
+    - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta
+    - atlas majorMinor --glf ATLAS_simulations.glf.gz
+    - rm ATLAS_* *.parameters saf.saf.* || exit 1
+
 about:
-  home: https://bitbucket.org/wegmannlab/atlas/wiki/Home
-  license: GPLv3
-  summary: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
+  home: https://atlaswiki.netlify.app
+  license: MPL-2.0
+  summary: "ATLAS: Analysis Tools for Ancient and Low-depth Samples"
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/biobb_amber/meta.yaml b/recipes/biobb_amber/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_amber" %}
-{% set version = "5.0.2" %}
+{% set version = "5.0.3" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 33cd128cd6b8efb66b83876f978f85447c49e35a98b95bd11e0c74960c76af50
+  sha256: 78dfd40a00c729549fee6f31f96a70dc93e532bd44f267e976cd85e7191e0835
 
 build:
   number: 0

diff --git a/recipes/biobb_analysis/meta.yaml b/recipes/biobb_analysis/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_analysis" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.1" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 8bf930ecd4cff6b3ad3a97a92599913225295725056c5369bd0e7f536bb4008d
+  sha256: 2ecb3df99f6ae37ed68c9849b1224245e526fe66074db0b21957a49128b20ab3
 
 build:
   number: 0

diff --git a/recipes/biobb_mem/meta.yaml b/recipes/biobb_mem/meta.yaml
@@ -0,0 +1,60 @@
+{% set name = "biobb_mem" %}
+{% set version = "5.0.1" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: bb82d828a3be20ca577162aca4ae9a7073598a08f181e079277c7f13f1e1950c
+
+build:
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.9
+    - setuptools
+    - biobb_common ==5.0.0
+    - lipyphilic ==0.10.0
+    - ambertools >=22.5
+    - gromacs
+    - hole2
+  run:
+    - python >=3.9
+    - biobb_common ==5.0.0
+    - lipyphilic ==0.10.0
+    - ambertools >=22.5
+    - gromacs
+    - hole2
+test:
+  imports:
+    - biobb_mem
+    - biobb_mem.mdanalysis_biobb
+    - biobb_mem.lipyphilic_biobb
+    - biobb_mem.ambertools
+
+about:
+  home: https://github.com/bioexcel/biobb_mem
+  license: Apache Software License
+  license_family: APACHE
+  license_file: ''
+  summary: Biobb_mem is the Biobb module for membrane structure analysis.
+  description: "# biobb_mem\n\n### Introduction\nBiobb_mem is the Biobb module for membrane structure analysis.\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_analysis.readthedocs.io/en/latest/).\n\
+    \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://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\
+    Licensed under the\n\
+    [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\
+    \n\
+    ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
+  doc_url: ''
+  dev_url: ''
+
+extra:
+  recipe-maintainers: ''