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authorRicardo Wurmus <rekado@elephly.net>2018-06-05 15:42:23 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-06-05 15:42:44 +0200
commit909301591d21d3879276e4ede3cebdcc867184f2 (patch)
treeb70366221b4d21400be672c835d877e3de0d1477 /gnu/packages/bioinformatics.scm
parent97f6e9133a03f37c79e60678dd5670a805cdf693 (diff)
downloadgnu-guix-909301591d21d3879276e4ede3cebdcc867184f2.tar
gnu-guix-909301591d21d3879276e4ede3cebdcc867184f2.tar.gz
gnu: Add sjcount.
* gnu/packages/bioinformatics.scm (sjcount): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm51
1 files changed, 51 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 122d6a740b..432589391b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13164,3 +13164,54 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
include Markov models of discrete and continuous trait evolution and constant
rate speciation and extinction.")
(license license:gpl2+)))
+
+(define-public sjcount
+ ;; There is no tag for version 3.2, nor is there a release archive.
+ (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
+ (revision "1"))
+ (package
+ (name "sjcount")
+ (version (git-version "3.2" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pervouchine/sjcount-full.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; requires a 1.4G test file
+ #:make-flags
+ (list (string-append "SAMTOOLS_DIR="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/"))
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "makefile"
+ (("-I \\$\\{SAMTOOLS_DIR\\}")
+ (string-append "-I" (assoc-ref inputs "samtools")
+ "/include/samtools"))
+ (("-lz ") "-lz -lpthread "))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each (lambda (tool)
+ (install-file tool
+ (string-append (assoc-ref outputs "out")
+ "/bin")))
+ '("j_count" "b_count" "sjcount"))
+ #t)))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/pervouchine/sjcount-full/")
+ (synopsis "Annotation-agnostic splice junction counting pipeline")
+ (description "Sjcount is a utility for fast quantification of splice
+junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This
+version does count multisplits.")
+ (license license:gpl3+))))