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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fbff587302..2844c46075 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9328,3 +9328,64 @@ with narrow binding events such as transcription factor ChIP-seq.") adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.") (license license:gpl3+))) + +(define-public gess + (package + (name "gess") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append "http://compbio.uthscsa.edu/" + "GESS_Web/files/" + "gess-" version ".src.tar.gz")) + (sha256 + (base32 + "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((python (assoc-ref inputs "python")) + (out (assoc-ref outputs "out")) + (bin (string-append out "/bin/")) + (target (string-append + out "/lib/python2.7/site-packages/gess/"))) + (mkdir-p target) + (copy-recursively "." target) + ;; Make GESS.py executable + (chmod (string-append target "GESS.py") #o555) + ;; Add Python shebang to the top and make Matplotlib + ;; usable. + (substitute* (string-append target "GESS.py") + (("\"\"\"Description:" line) + (string-append "#!" (which "python") " +import matplotlib +matplotlib.use('Agg') +" line))) + ;; Make sure GESS has all modules in its path + (wrap-program (string-append target "GESS.py") + `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH")))) + (mkdir-p bin) + (symlink (string-append target "GESS.py") + (string-append bin "GESS.py")) + #t)))))) + (inputs + `(("python" ,python-2) + ("python2-pysam" ,python2-pysam) + ("python2-scipy" ,python2-scipy) + ("python2-numpy" ,python2-numpy) + ("python2-networkx" ,python2-networkx) + ("python2-biopython" ,python2-biopython))) + (home-page "http://compbio.uthscsa.edu/GESS_Web/") + (synopsis "Detect exon-skipping events from raw RNA-seq data") + (description + "GESS is an implementation of a novel computational method to detect de +novo exon-skipping events directly from raw RNA-seq data without the prior +knowledge of gene annotation information. GESS stands for the graph-based +exon-skipping scanner detection scheme.") + (license license:bsd-3))) |