Add several R and Bioconductor recipes

recipes/bioconductor-biseq/build.sh

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

recipes/bioconductor-biseq/meta.yaml

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+package:
+  name: bioconductor-biseq
+  version: 1.16.0
+source:
+  fn: BiSeq_1.16.0.tar.gz
+  url:
+    - http://bioconductor.org/packages/3.5/bioc/src/contrib/BiSeq_1.16.0.tar.gz
+    - https://bioarchive.galaxyproject.org/BiSeq_1.16.0.tar.gz
+    - https://depot.galaxyproject.org/software/BiSeq/BiSeq_1.16.0_src_all.tar.gz
+  md5: c0579533cd705c74f9e8dc513996c713
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+    - bioconductor-biobase
+    - bioconductor-biocgenerics
+    - bioconductor-genomeinfodb
+    - bioconductor-genomicranges
+    - bioconductor-globaltest
+    - 'bioconductor-iranges >=1.17.24'
+    - bioconductor-rtracklayer
+    - bioconductor-s4vectors
+    - 'bioconductor-summarizedexperiment >=0.2.0'
+    - r-base
+    - r-betareg
+    - r-formula
+    - r-lokern
+  run:
+    - bioconductor-biobase
+    - bioconductor-biocgenerics
+    - bioconductor-genomeinfodb
+    - bioconductor-genomicranges
+    - bioconductor-globaltest
+    - 'bioconductor-iranges >=1.17.24'
+    - bioconductor-rtracklayer
+    - bioconductor-s4vectors
+    - 'bioconductor-summarizedexperiment >=0.2.0'
+    - r-base
+    - r-betareg
+    - r-formula
+    - r-lokern
+test:
+  commands:
+    - '$R -e "library(''BiSeq'')"'
+about:
+  home: http://bioconductor.org/packages/3.5/bioc/html/BiSeq.html
+  license: LGPL-3
+  summary: 'The BiSeq package provides useful classes and functions to handle and
+    analyze targeted bisulfite sequencing (BS) data such as reduced-representation
+    bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to
+    detect differentially methylated regions (DMRs). The package takes already aligned
+    BS data from one or multiple samples.'

recipes/bioconductor-gcrma/build.sh

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

recipes/bioconductor-gcrma/meta.yaml

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+package:
+  name: bioconductor-gcrma
+  version: 2.48.0
+source:
+  fn: gcrma_2.48.0.tar.gz
+  url:
+    - http://bioconductor.org/packages/3.5/bioc/src/contrib/gcrma_2.48.0.tar.gz
+    - https://bioarchive.galaxyproject.org/gcrma_2.48.0.tar.gz
+    - https://depot.galaxyproject.org/software/gcrma/gcrma_2.48.0_src_all.tar.gz
+  md5: c3a2f21c6f93458d1a123594e437a210
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+    - 'bioconductor-affy >=1.23.2'
+    - 'bioconductor-affyio >=1.13.3'
+    - bioconductor-biobase
+    - bioconductor-biocinstaller
+    - 'bioconductor-biostrings >=2.11.32'
+    - bioconductor-xvector
+    - r-base
+  run:
+    - 'bioconductor-affy >=1.23.2'
+    - 'bioconductor-affyio >=1.13.3'
+    - bioconductor-biobase
+    - bioconductor-biocinstaller
+    - 'bioconductor-biostrings >=2.11.32'
+    - bioconductor-xvector
+    - r-base
+test:
+  commands:
+    - '$R -e "library(''gcrma'')"'
+about:
+  home: http://bioconductor.org/packages/3.5/bioc/html/gcrma.html
+  license: LGPL
+  summary: 'Background adjustment using sequence information'

recipes/bioconductor-globaltest/build.sh

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

recipes/bioconductor-globaltest/meta.yaml

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+package:
+  name: bioconductor-globaltest
+  version: 5.30.0
+source:
+  fn: globaltest_5.30.0.tar.gz
+  url:
+    - http://bioconductor.org/packages/3.5/bioc/src/contrib/globaltest_5.30.0.tar.gz
+    - https://bioarchive.galaxyproject.org/globaltest_5.30.0.tar.gz
+    - https://depot.galaxyproject.org/software/globaltest/globaltest_5.30.0_src_all.tar.gz
+  md5: baddf5286a53396d041bd459d54dc4af
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+    - bioconductor-annotate
+    - bioconductor-annotationdbi
+    - bioconductor-biobase
+    - r-base
+    - r-survival
+  run:
+    - bioconductor-annotate
+    - bioconductor-annotationdbi
+    - bioconductor-biobase
+    - r-base
+    - r-survival
+test:
+  commands:
+    - '$R -e "library(''globaltest'')"'
+about:
+  home: http://bioconductor.org/packages/3.5/bioc/html/globaltest.html
+  license: 'GPL (>= 2)'
+  summary: 'The global test tests groups of covariates (or features) for association
+    with a response variable. This package implements the test with diagnostic plots
+    and multiple testing utilities, along with several functions to facilitate the
+    use of this test for gene set testing of GO and KEGG terms.'

recipes/bioconductor-simpleaffy/build.sh

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

recipes/bioconductor-simpleaffy/meta.yaml

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+package:
+  name: bioconductor-simpleaffy
+  version: 2.52.0
+source:
+  fn: simpleaffy_2.52.0.tar.gz
+  url:
+    - http://bioconductor.org/packages/3.5/bioc/src/contrib/simpleaffy_2.52.0.tar.gz
+    - https://bioarchive.galaxyproject.org/simpleaffy_2.52.0.tar.gz
+    - https://depot.galaxyproject.org/software/simpleaffy/simpleaffy_2.52.0_src_all.tar.gz
+  md5: aa305099a57b3d868be53dc8c539b74e
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+requirements:
+  build:
+    - 'bioconductor-affy >=1.33.6'
+    - bioconductor-biobase
+    - 'bioconductor-biocgenerics >=0.1.12'
+    - bioconductor-gcrma
+    - bioconductor-genefilter
+    - r-base
+  run:
+    - 'bioconductor-affy >=1.33.6'
+    - bioconductor-biobase
+    - 'bioconductor-biocgenerics >=0.1.12'
+    - bioconductor-gcrma
+    - bioconductor-genefilter
+    - r-base
+test:
+  commands:
+    - '$R -e "library(''simpleaffy'')"'
+about:
+  home: http://bioconductor.org/packages/3.5/bioc/html/simpleaffy.html
+  license: 'GPL (>= 2)'
+  summary: 'Provides high level functions for reading Affy .CEL files, phenotypic
+    data, and then computing simple things with it, such as t-tests, fold changes
+    and the like. Makes heavy use of the affy library. Also has some basic scatter
+    plot functions and mechanisms for generating high resolution journal figures...'