From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] gnu: Add proteinortho. Date: Sat, 26 Nov 2016 15:14:16 +1000 Message-ID: <20161126051416.12616-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35959) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cAVJp-0004JR-Hn for guix-devel@gnu.org; Sat, 26 Nov 2016 00:14:34 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cAVJm-0002HN-8W for guix-devel@gnu.org; Sat, 26 Nov 2016 00:14:33 -0500 Received: from mail-pg0-x242.google.com ([2607:f8b0:400e:c05::242]:34515) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cAVJm-0002GA-1W for guix-devel@gnu.org; Sat, 26 Nov 2016 00:14:30 -0500 Received: by mail-pg0-x242.google.com with SMTP id e9so7186500pgc.1 for ; Fri, 25 Nov 2016 21:14:29 -0800 (PST) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id z9sm71254491pfd.29.2016.11.25.21.14.25 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Fri, 25 Nov 2016 21:14:26 -0800 (PST) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (proteinortho): 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 773b590..31e9533 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3693,6 +3693,58 @@ for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.") (license license:gpl2+))) +(define-public proteinortho + (package + (name "proteinortho") + (version "5.15") + (source + (origin + (method url-fetch) + (uri + (string-append + "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" + version "_src.tar.gz")) + (sha256 + (base32 + "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (replace 'configure + ;; There is no configure script, so we modify the Makefile directly. + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("INSTALLDIR=.*") + (string-append + "INSTALLDIR=" (assoc-ref outputs "out") "/bin"))) + #t)) + (add-before 'install 'make-install-directory + ;; The install directory is not created during 'make install'. + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) + #t)) + (add-after 'install 'wrap-programs + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((path (getenv "PATH")) + (out (assoc-ref outputs "out")) + (binary (string-append out "/bin/proteinortho5.pl"))) + (wrap-program binary `("PATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("perl" ,perl) + ("python" ,python-2) + ("blast+" ,blast+))) + (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") + (synopsis "Detect orthologous genes across species") + (description + "Proteinortho is a tool to detect orthologous genes across different +species. For doing so, it compares similarities of given gene sequences and +clusters them to find significant groups. The algorithm was designed to handle +large-scale data and can be applied to hundreds of species at once.") + (license license:gpl2+))) + (define-public pyicoteo (package (name "pyicoteo") -- 2.10.2