From mboxrd@z Thu Jan 1 00:00:00 1970 From: Diane Trout Subject: Bioinformatics package: Bless Date: Thu, 05 Nov 2015 11:49:54 -0800 Message-ID: <2238503.mBpvBuW9qZ@myrada> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="nextPart1608022.SCFXWvUyxc" Content-Transfer-Encoding: 7Bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48097) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZuQXv-0005Sq-60 for guix-devel@gnu.org; Thu, 05 Nov 2015 14:50:08 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZuQXq-0001v9-DI for guix-devel@gnu.org; Thu, 05 Nov 2015 14:50:07 -0500 Received: from chaos.caltech.edu ([131.215.34.119]:44467) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZuQXq-0001sj-77 for guix-devel@gnu.org; Thu, 05 Nov 2015 14:50:02 -0500 Received: from dhcp-54-193.caltech.edu ([131.215.54.193] helo=myrada.ghic.org) by chaos.caltech.edu with esmtpsa (TLS1.0:ECDHE_RSA_AES_256_CBC_SHA1:256) (Exim 4.84) (envelope-from ) id 1ZuQXi-0005zj-Rj for guix-devel@gnu.org; Thu, 05 Nov 2015 11:49:54 -0800 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org This is a multi-part message in MIME format. --nextPart1608022.SCFXWvUyxc Content-Transfer-Encoding: 7Bit Content-Type: text/plain; charset="us-ascii" Hi, One of our users asked me to install a package "bless" that required a newer version of MPI than Debian provides, so I thought I'd try to build a guix package as Guix actually has openmpi 1.8 packaged. The software's home page is: http://sourceforge.net/p/bless-ec/wiki/Home/ The source tarball has the GPL-3 LICENSE file, however it does also contain convenience copies of other source, and in my packaging I only spliced out one -- the pigz dependency. Diane --nextPart1608022.SCFXWvUyxc Content-Disposition: attachment; filename="bless.scm" Content-Transfer-Encoding: 7Bit Content-Type: text/x-scheme; charset="UTF-8"; name="bless.scm" (define-module (gnu packages bioinformatics) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages mpi) #:use-module (gnu packages perl) #:use-module (srfi srfi-1)) (define-public bless (package (name "bless") (version "v1p02") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bless-ec/bless." version ".tgz")) (file-name (string-append name "." version ".tgz")) (sha256 (base32 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) )) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) ("zlib" ,zlib))) (inputs `(("openmpi" ,openmpi) ("pigz" ,pigz))) (arguments '(#:tests? #f ;no "check" target #:phases (alist-cons-after 'unpack 'unpack-tarballs (lambda* (#:key inputs outputs #:allow-other-keys) (substitute* "Makefile" (("-I ./zlib/install/include") (string-append "-I " (assoc-ref inputs "zlib") "/include")) (("./zlib/install/lib/libz.a") (string-append (assoc-ref inputs "zlib") "/lib/libz.a")) ((".(ZLIB) ") "") (("cd pigz/pigz-2.3.3; make") "") ) ;;(substitute* "define.hpp" ;; (("pigz/pigz-2.3.3") (string-append (assoc-ref inputs "pigz"))) ;; (("kmc/bin") ".") (substitute* "parse_args.cpp" (("kmc_binary = .*") (string-append "kmc_binary = \"" (assoc-ref outputs "out") "/bin/kmc\";")) (("pigz_binary = .*") (string-append "pigz_binary = \"" (assoc-ref inputs "pigz") "/bin/pigz\";")) ) #t) (alist-replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (for-each (lambda (file) (install-file file bin)) '("bless" "kmc/bin/kmc") ))) (alist-delete 'configure %standard-phases))))) (home-page "http://sourceforge.net/projects/bless-ec/wiki/Home/") (synopsis "Bloom-filter-based Error Correction Tool for NGS reads") (description "Developed by ESCAD Group, Computational Comparative Genomics Lab, and IMACT Group in university of Illinois at Urbana-Champaign") (license license:gpl3+)) ) --nextPart1608022.SCFXWvUyxc--