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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dce8ab62f1..cb3c4bc1fd 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)))) |