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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-04-28 11:28:16 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-05-04 10:28:27 +0200
commit0b84a0aacade3adb7bf63a352a979d78751338b6 (patch)
tree1b18f4865b2db107536dcad041880bb5b1984e2e /gnu/packages
parent41dd7126570d9d8699d228aa9e6c6d092be816e0 (diff)
gnu: Add samtools-0.1.19.
* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm28
1 files changed, 28 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6fc2bee469..8bc5b868ec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1107,6 +1107,34 @@ variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
(license license:expat)))
+(define-public samtools-0.1
+ ;; This is the most recent version of the 0.1 line of samtools. The input
+ ;; and output formats differ greatly from that used and produced by samtools
+ ;; 1.x and is still used in many bioinformatics pipelines.
+ (package (inherit samtools)
+ (version "0.1.19")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "mirror://sourceforge/samtools/"
+ version "/samtools-" version ".tar.bz2"))
+ (sha256
+ (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments samtools)
+ ((#:tests? tests) #f) ;no "check" target
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append
+ (assoc-ref outputs "out") "/bin")))
+ (mkdir-p bin)
+ (copy-file "samtools"
+ (string-append bin "/samtools")))))
+ (delete 'patch-tests)))))))
+
(define-public ngs-sdk
(package
(name "ngs-sdk")