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01/01: gnu: Add find-circ.
From: |
Ricardo Wurmus |
Subject: |
01/01: gnu: Add find-circ. |
Date: |
Fri, 24 Aug 2018 05:21:02 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 079cdd9c15b6b94a5d2ff15c7cf2e8621d2a774f
Author: Ricardo Wurmus <address@hidden>
Date: Fri Aug 24 11:19:30 2018 +0200
gnu: Add find-circ.
* gnu/packages/bioinformatics.scm (find-circ): New variable.
---
gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 52 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dce8ab6..cb3c4bc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13406,3 +13406,55 @@ conversions, region filtering, FASTA sequence
extraction and more.")
;; gffread is under Expat, but gclib is under Artistic 2.0
(license (list license:expat
license:artistic2.0)))))
+
+(define-public find-circ
+ ;; The last release was in 2015. The license was clarified in 2017, so we
+ ;; take the latest commit.
+ (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d")
+ (revision "1"))
+ (package
+ (name "find-circ")
+ (version (git-version "1.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/marvin-jens/find_circ.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:phases
+ ;; There is no actual build system.
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (path (getenv "PYTHONPATH")))
+ (for-each (lambda (script)
+ (install-file script bin)
+ (wrap-program (string-append bin "/" script)
+ `("PYTHONPATH" ":" prefix (,path))))
+ '("cmp_bed.py"
+ "find_circ.py"
+ "maxlength.py"
+ "merge_bed.py"
+ "unmapped2anchors.py")))
+ #t)))))
+ (inputs
+ `(("python2" ,python-2)
+ ("python2-pysam" ,python2-pysam)
+ ("python2-numpy" ,python2-numpy)))
+ (home-page "https://github.com/marvin-jens/find_circ")
+ (synopsis "circRNA detection from RNA-seq reads")
+ (description "This package provides tools to detect head-to-tail
+spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
+in RNA-seq data.")
+ (license license:gpl3))))