diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 48 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
2 files changed, 48 insertions, 48 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eef0811d4e..2b3c232d53 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2590,6 +2590,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.") (license license:expat))) +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + ((" zlibbioc,") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ba284759a0..f9d2d125bf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,54 +7952,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rtracklayer - (package - (name "r-rtracklayer") - (version "1.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rtracklayer" version)) - (sha256 - (base32 - "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - ((" zlibbioc,") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/rtracklayer") - (synopsis "R interface to genome browsers and their annotation tracks") - (description - "rtracklayer is an extensible framework for interacting with multiple -genome browsers (currently UCSC built-in) and manipulating annotation tracks -in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit -built-in). The user may export/import tracks to/from the supported browsers, -as well as query and modify the browser state, such as the current viewport.") - (license license:artistic2.0))) - (define-public r-genomicfeatures (package (name "r-genomicfeatures") |