diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b7d65023d..c659bdd09e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + (properties + `((upstream-name . "Rsamtools"))) + (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))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the @code{samtools}, +@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence +Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed +tab-delimited (tabix) files.") + (license license:expat))) + (define-public r-shortread (package (name "r-shortread") |