From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add bowtie. Date: Tue, 16 Dec 2014 18:07:41 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47904) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Y0vbH-0004wv-Vd for guix-devel@gnu.org; Tue, 16 Dec 2014 12:08:01 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Y0vbC-0005YF-5C for guix-devel@gnu.org; Tue, 16 Dec 2014 12:07:55 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:50115) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Y0vbB-0005Wi-OJ for guix-devel@gnu.org; Tue, 16 Dec 2014 12:07:50 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id E66083804B2 for ; Tue, 16 Dec 2014 18:07:48 +0100 (CET) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 4r-PoSaLR9rW for ; Tue, 16 Dec 2014 18:07:42 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 16 Dec 2014 18:07:42 +0100 (CET) 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 --=-=-= Content-Type: text/plain Attached is a patch to add bowtie to the bioinformatics module. The test suite depends on a couple of Perl modules for which I have previously submitted patches: - [[http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00326.html][Test::Simple]] - [[http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00321.html][Test::Deep]] - [[http://lists.gnu.org/archive/html/guix-devel/2014-12/msg00323.html][Clone]] -- rekado --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename="0001-gnu-Add-bowtie.patch" >From 713bb1145ff901c4069f2fadb210d8eb842981da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 16 Dec 2014 17:52:44 +0100 Subject: [PATCH] gnu: Add bowtie * gnu/packages/bioinformatics.scm (bowtie): New variable. --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f6178a..755287d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -28,6 +28,66 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python)) +(define-public bowtie + (package + (name "bowtie") + (version "2.2.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn")))) + (build-system gnu-build-system) + (inputs `(("perl" ,perl) + ("perl-clone" ,perl-clone) + ("perl-test-deep" ,perl-test-deep) + ("perl-test-simple" ,perl-test-simple) + ("python" ,python-2))) + (arguments + '(#:make-flags '("allall") + #:phases + (alist-cons-after + 'unpack + 'patch-makefile + (lambda _ + (substitute* "Makefile" + (("^CC = .*$") (string-append "CC = " (which "gcc"))) + (("^CPP = .*$") (string-append "CPP = " (which "g++"))) + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))) + (alist-delete + 'configure + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (for-each (lambda (file) + (copy-file file (string-append bin file))) + (find-files "." "bowtie2.*")))) + (alist-replace + 'check + (lambda* (#:key outputs #:allow-other-keys) + (system* "perl" + "scripts/test/simple_tests.pl" + "--bowtie2=./bowtie2" + "--bowtie2-build=./bowtie2-build")) + %standard-phases)))))) + (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") + (synopsis "Fast and sensitive nucleotide sequence read aligner") + (description + "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing +reads to long reference sequences. It is particularly good at aligning reads +of about 50 up to 100s or 1,000s of characters, and particularly good at +aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the +genome with an FM Index to keep its memory footprint small: for the human +genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports +gapped, local, and paired-end alignment modes.") + (license license:gpl3))) + (define-public samtools (package (name "samtools") -- 1.9.3 --=-=-=--