update and add recipes (#12885)

bioconda · Jan 1, 2019 · 2d2f10b · 2d2f10b
1 parent 8fc94fe
commit 2d2f10b
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Showing 6 changed files with 168 additions and 3 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -803,7 +803,7 @@ recipes/r-dbchip
 recipes/r-asics
 recipes/r-biom
 
-# Deprecated in Bioconductor
+# Deprecated/build fail in Bioconductor
 recipes/bioconductor-atlasrdf
 recipes/bioconductor-jmosaics
 recipes/bioconductor-meshsim
@@ -813,6 +813,7 @@ recipes/bioconductor-rcytoscape
 recipes/bioconductor-browservizdemo
 recipes/bioconductor-pannbuilder
 recipes/bioconductor-splicer
+recipes/bioconductor-flowq
 
 # Old bioconductor version that's no longer available
 recipes/bioconductor-edger/3.12.1

diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.0" %}
+{% set version = "1.0.1" %}
 {% set name = "OUTRIDER" %}
 {% set bioc = "3.8" %}
 
@@ -10,7 +10,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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: 589f062de187f5b31a2ab045181d9f34
+  md5: 89fbc10855ad4fb905ad705dc3002f53
 build:
   number: 0
   rpaths:

diff --git a/recipes/r-htscluster/build.sh b/recipes/r-htscluster/build.sh
@@ -0,0 +1,33 @@
+if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
+  export DISABLE_AUTOBREW=1
+  $R CMD INSTALL --build .
+else
+  mkdir -p $PREFIX/lib/R/library/HTSCluster
+  mv * $PREFIX/lib/R/library/HTSCluster
+  if [[ $target_platform == osx-64 ]]; then
+    pushd $PREFIX
+      for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do
+        pushd $libdir || exit 1
+          for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do
+            echo "fixing SHARED_LIB $SHARED_LIB"
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true
+          done
+        popd
+      done
+    popd
+  fi
+fi
diff --git a/recipes/r-htscluster/meta.yaml b/recipes/r-htscluster/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = '2.0.8' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-htscluster
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/HTSCluster_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/HTSCluster/HTSCluster_{{ version }}.tar.gz
+  sha256: 6f82fa50bd95620fe5dea7c66a1876a6fea0bd46bb3e1aa54806f5060d74cb72
+
+build:
+  number: 0
+  noarch: generic
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+
+  host:
+    - r-base
+    - r-capushe
+    - bioconductobioconductor-edger
+    - r-plotrix
+  run:
+    - r-base
+    - r-capushe
+    - bioconductobioconductor-edger
+    - r-plotrix
+
+test:
+  commands:
+    - $R -e "library('HTSCluster')"           # [not win]
+    - "\"%R%\" -e \"library('HTSCluster')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=HTSCluster
+  license: GPL (>= 3)
+  summary: A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome
+    sequencing (RNA-seq) data. Parameter estimation is performed using either the EM
+    or CEM algorithm, and the slope heuristics are used for model selection (i.e., to
+    choose the number of clusters).
+  license_family: GPL3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
diff --git a/recipes/r-nbpseq/build.sh b/recipes/r-nbpseq/build.sh
@@ -0,0 +1,33 @@
+if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then
+  export DISABLE_AUTOBREW=1
+  $R CMD INSTALL --build .
+else
+  mkdir -p $PREFIX/lib/R/library/NBPSeq
+  mv * $PREFIX/lib/R/library/NBPSeq
+  if [[ $target_platform == osx-64 ]]; then
+    pushd $PREFIX
+      for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do
+        pushd $libdir || exit 1
+          for SHARED_LIB in $(find . -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R"); do
+            echo "fixing SHARED_LIB $SHARED_LIB"
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "$PREFIX"/lib/R/lib/libR.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/local/clang4/lib/libomp.dylib "$PREFIX"/lib/libomp.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "$PREFIX"/lib/libquadmath.0.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "$PREFIX"/lib/libgfortran.3.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libgcc_s.1.dylib "$PREFIX"/lib/libgcc_s.1.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libiconv.2.dylib "$PREFIX"/sysroot/usr/lib/libiconv.2.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libncurses.5.4.dylib "$PREFIX"/sysroot/usr/lib/libncurses.5.4.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libicucore.A.dylib "$PREFIX"/sysroot/usr/lib/libicucore.A.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libexpat.1.dylib "$PREFIX"/lib/libexpat.1.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libcurl.4.dylib "$PREFIX"/lib/libcurl.4.dylib $SHARED_LIB || true
+            install_name_tool -change /usr/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true
+            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "$PREFIX"/lib/libc++.1.dylib $SHARED_LIB || true
+          done
+        popd
+      done
+    popd
+  fi
+fi
diff --git a/recipes/r-nbpseq/meta.yaml b/recipes/r-nbpseq/meta.yaml
@@ -0,0 +1,49 @@
+{% set version = '0.3.0' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-nbpseq
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/NBPSeq_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/NBPSeq/NBPSeq_{{ version }}.tar.gz
+  sha256: 7e251fa017d91ffa7b0c5e740859db4aa4f9bc3b46632983e03c4da161a79e50
+
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}        # [not win]
+    - {{native}}toolchain        # [win]
+    - {{posix}}filesystem        # [win]
+    - {{posix}}make
+    - {{posix}}sed               # [win]
+    - {{posix}}coreutils         # [win]
+    - {{posix}}zip               # [win]
+  host:
+    - r-base
+    - bioconductor-qvalue
+  run:
+    - r-base
+    - {{native}}gcc-libs         # [win]
+    - bioconductor-qvalue
+
+test:
+  commands:
+    - $R -e "library('NBPSeq')"           # [not win]
+    - "\"%R%\" -e \"library('NBPSeq')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=NBPSeq
+  license: GPL-2
+  summary: Negative Binomial (NB) models for two-group comparisons and regression inferences
+    from RNA-Sequencing Data.
+  license_family: GPL2
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'