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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2014-12-11 17:37:16 +0100
committerLudovic Courtès <ludo@gnu.org>2014-12-16 18:17:15 +0100
commit81de56479a30651dac542ed392296205c4ea5508 (patch)
tree3d24c8849f179e1c779a205049ad2ce1b4c22f17 /gnu/packages
parentb336da21e92210a9c561f1a4a2a91542a34b782d (diff)
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.scm49
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")