[BULK] Update 261018 (#11611)

* Apparently the r-rgeos bit works properly now.

* Add tissueenrich and try to fix scpipe on Linux

recipes/bioconductor-derfinderplot/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-fourcseq/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-nadfinder/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-rariant/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-recount/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-reportingtools/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-riboprofiling/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-scpipe/build.sh

@@ -1,4 +1,12 @@
 #!/bin/bash
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
-$R CMD INSTALL --build .
+# We need gcc >= 4.9 and the Makevars are just getting ignored
+if [[ $target_platform =~ linux.* ]] ; then
+    foo=`which g++`
+    rm $foo
+    ln -s $GXX $foo
+    ln -s ${PREFIX}/lib/libgfortran.so.3 ${PREFIX}/lib/libgfortran.so
+    export LIBRARY_PATH=${PREFIX}/lib
+fi
+$R CMD INSTALL --build .

recipes/bioconductor-scpipe/conda_build_config.yaml

@@ -1,2 +1,8 @@
 r_base:
   - 3.5.1
+c_compiler:     
+  - gcc      # [linux]  
+  - clang    # [osx]
+cxx_compiler:     
+  - gxx      # [linux]  
+  - clangxx    # [osx]

recipes/bioconductor-scpipe/meta.yaml

@@ -60,6 +60,7 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - {{ compiler('fortran') }}
     - make
 test:
   commands:

recipes/bioconductor-somaticsignatures/conda_build_config.yaml

@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1

recipes/bioconductor-tissueenrich/build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+$R CMD INSTALL --build .

recipes/bioconductor-tissueenrich/meta.yaml

@@ -0,0 +1,42 @@
+{% set version = "1.0.7" %}
+{% set name = "TissueEnrich" %}
+{% set bioc = "3.7" %}
+
+package:
+  name: 'bioconductor-{{ name|lower }}'
+  version: '{{ version }}'
+source:
+  url:
+    - 'http://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'
+  sha256: c910cdf72450093540ea05ed7bdd95733812ca18103f68f21c56f7496669e314
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  host:
+    - 'bioconductor-gseabase >=1.42.0,<1.44.0'
+    - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0'
+    - r-base
+    - 'r-dplyr >=0.7.3'
+    - 'r-ensurer >=1.1.0'
+    - 'r-ggplot2 >=2.2.1'
+    - 'r-tidyr >=0.8.0'
+  run:
+    - 'bioconductor-gseabase >=1.42.0,<1.44.0'
+    - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0'
+    - r-base
+    - 'r-dplyr >=0.7.3'
+    - 'r-ensurer >=1.1.0'
+    - 'r-ggplot2 >=2.2.1'
+    - 'r-tidyr >=0.8.0'
+test:
+  commands:
+    - '$R -e "library(''{{ name }}'')"'
+about:
+  home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
+  license: 'MIT + file LICENSE'
+  summary: 'The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.'

recipes/xtail/meta.yaml

@@ -18,7 +18,7 @@ build:
 requirements:
   host:
     - bioconductor-genefilter
-    - 'bioconductor-deseq2 ==1.18.1'
+    - 'bioconductor-deseq2 >=1.18.1'
     - r-base
     - 'r-rcpp >=0.11.0'
     - r-rcpparmadillo
@@ -32,7 +32,7 @@ requirements:
     - bioconductor-iranges
     - 'bioconductor-s4vectors >=0.9.25'
     - 'bioconductor-summarizedexperiment >=1.8.0'
-    - 'bioconductor-deseq2 ==1.18.1'
+    - 'bioconductor-deseq2 >=1.18.1'
     - r-base
     - r-ggplot2
     - r-hmisc