From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add Jellyfish. Date: Fri, 18 Dec 2015 17:42:31 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58408) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a9y7C-0001ro-9Z for guix-devel@gnu.org; Fri, 18 Dec 2015 11:42:47 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a9y78-0004FU-7g for guix-devel@gnu.org; Fri, 18 Dec 2015 11:42:46 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:60877) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a9y77-0004El-So for guix-devel@gnu.org; Fri, 18 Dec 2015 11:42:42 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 58A052808CD for ; Fri, 18 Dec 2015 17:42:40 +0100 (CET) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id Utn4NbVvQWaA for ; Fri, 18 Dec 2015 17:42:34 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 18 Dec 2015 17:42:33 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-Jellyfish.patch" 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 >From 9fcbc3e10773c7ee73b232c8e16e20a807318bbc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 18 Dec 2015 17:40:02 +0100 Subject: [PATCH] gnu: Add Jellyfish. * gnu/packages/bioinformatics.scm (jellyfish): New variable. --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c350ff..430c568 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -56,6 +56,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages textutils) + #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages vim) #:use-module (gnu packages web) @@ -1756,6 +1757,46 @@ to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.") (license license:gpl3+))) +(define-public jellyfish + (package + (name "jellyfish") + (version "2.2.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/gmarcais/Jellyfish/" + "releases/download/v" version + "/jellyfish-" version ".tar.gz")) + (sha256 + (base32 + "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'set-SHELL-variable + (lambda _ + ;; generator_manager.hpp either uses /bin/sh or $SHELL + ;; to run tests. + (setenv "SHELL" (which "bash")) + #t))))) + (native-inputs + `(("bc" ,bc) + ("time" ,time) + ("gunzip" ,gzip))) + (synopsis "Tool for fast counting of k-mers in DNA") + (description + "Jellyfish is a tool for fast, memory-efficient counting of k-mers in +DNA. A k-mer is a substring of length k, and counting the occurrences of all +such substrings is a central step in many analyses of DNA sequence. Jellyfish +is a command-line program that reads FASTA and multi-FASTA files containing +DNA sequences. It outputs its k-mer counts in a binary format, which can be +translated into a human-readable text format using the @code{jellyfish dump} +command, or queried for specific k-mers with @code{jellyfish query}.") + (home-page "http://www.genome.umd.edu/jellyfish.html") + ;; The combined work is published under the GPLv3 or later. Individual + ;; files such as lib/jsoncpp.cpp are released under the Expat license. + (license (list license:gpl3+ license:expat)))) + (define-public macs (package (name "macs") -- 2.1.0