diff options
author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2014-12-11 17:37:16 +0100 |
---|---|---|
committer | Ludovic Courtès <ludo@gnu.org> | 2014-12-16 18:17:15 +0100 |
commit | 81de56479a30651dac542ed392296205c4ea5508 (patch) | |
tree | 3d24c8849f179e1c779a205049ad2ce1b4c22f17 /gnu/packages | |
parent | b336da21e92210a9c561f1a4a2a91542a34b782d (diff) | |
download | patches-81de56479a30651dac542ed392296205c4ea5508.tar patches-81de56479a30651dac542ed392296205c4ea5508.tar.gz |
gnu: Add bedtools
* gnu/packages/bioinformatics.scm (bedtools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Diffstat (limited to 'gnu/packages')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7e802278ac..a2846f10eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -28,6 +28,55 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python)) +(define-public bedtools + (package + (name "bedtools") + (version "2.22.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl")))) + (build-system gnu-build-system) + (native-inputs `(("python" ,python-2))) + (inputs `(("samtools" ,samtools) + ("zlib" ,zlib))) + (arguments + '(#:test-target "test" + #:phases + (alist-cons-after + 'unpack 'patch-makefile-SHELL-definition + (lambda _ + ;; patch-makefile-SHELL cannot be used here as it does not + ;; yet patch definitions with `:='. Since changes to + ;; patch-makefile-SHELL result in a full rebuild, features + ;; of patch-makefile-SHELL are reimplemented here. + (substitute* "Makefile" + (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n")))) + (alist-delete + 'configure + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (for-each (lambda (file) + (copy-file file (string-append bin (basename file)))) + (find-files "bin" ".*")))) + %standard-phases))))) + (home-page "https://github.com/arq5x/bedtools2") + (synopsis "Tools for genome analysis and arithmetic") + (description + "Collectively, the bedtools utilities are a swiss-army knife of tools for +a wide-range of genomics analysis tasks. The most widely-used tools enable +genome arithmetic: that is, set theory on the genome. For example, bedtools +allows one to intersect, merge, count, complement, and shuffle genomic +intervals from multiple files in widely-used genomic file formats such as BAM, +BED, GFF/GTF, VCF.") + (license license:gpl2))) + (define-public samtools (package (name "samtools") |