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01/01: gnu: Add sjcount.
From: |
Ricardo Wurmus |
Subject: |
01/01: gnu: Add sjcount. |
Date: |
Tue, 5 Jun 2018 09:43:34 -0400 (EDT) |
rekado pushed a commit to branch rhel6
in repository guix.
commit 19efd5b905619ed6ff34b42c9381c248528c7eab
Author: Ricardo Wurmus <address@hidden>
Date: Tue Jun 5 15:42:23 2018 +0200
gnu: Add sjcount.
* gnu/packages/bioinformatics.scm (sjcount): New variable.
---
gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3e1f0f0..5c7af60 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13028,3 +13028,54 @@ 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+))))