From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:57546) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dGAzJ-0005sW-QB for guix-patches@gnu.org; Wed, 31 May 2017 17:17:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dGAzH-0003kk-9y for guix-patches@gnu.org; Wed, 31 May 2017 17:17:05 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:45327) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dGAzH-0003kc-66 for guix-patches@gnu.org; Wed, 31 May 2017 17:17:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1dGAzG-0000mx-UF for guix-patches@gnu.org; Wed, 31 May 2017 17:17:02 -0400 Subject: bug#27175: [PATCH 3/6] gnu: Add gess. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 31 May 2017 23:16:08 +0200 Message-Id: <20170531211611.14094-3-rekado@elephly.net> In-Reply-To: <20170531211611.14094-1-rekado@elephly.net> References: <20170531211611.14094-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 27175@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (gess): New variable. --- gnu/packages/bioinformatics.scm | 61 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d341030b9..3bab10f8c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9290,3 +9290,64 @@ 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))) -- 2.12.2