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gnu: Add find-circ.

* gnu/packages/bioinformatics.scm (find-circ): New variable.
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Ricardo Wurmus 4 years ago
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commit
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  1. 52
      gnu/packages/bioinformatics.scm

52
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))))
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