From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add subread. Date: Thu, 16 Apr 2015 11:20:29 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46355) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YifyX-0001WQ-0D for guix-devel@gnu.org; Thu, 16 Apr 2015 05:20:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YifyS-0001dW-Q2 for guix-devel@gnu.org; Thu, 16 Apr 2015 05:20:44 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:60675) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YifyS-0001cw-EE for guix-devel@gnu.org; Thu, 16 Apr 2015 05:20:40 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 8F0C43807B1 for ; Thu, 16 Apr 2015 11:20:38 +0200 (CEST) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id FD1MAa1cE2Mx for ; Thu, 16 Apr 2015 11:20:32 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 16 Apr 2015 11:20:32 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-subread.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 fd34c03a72d280bc623af5edfc2a28a570c26784 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 16 Apr 2015 11:19:45 +0200 Subject: [PATCH] gnu: Add subread. * gnu/packages/bioinformatics.scm (subread): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0fd6c0c..7da6c75 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1444,6 +1444,45 @@ sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) +(define-public subread + (package + (name "subread") + (version "1.4.6-p2") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/subread/subread-" + version "-source.tar.gz")) + (sha256 + (base32 + "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:make-flags '("-f" "Makefile.Linux") + #:phases + (alist-cons-after + 'unpack 'enter-dir + (lambda _ (chdir "src") #t) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (copy-recursively "../bin" bin))) + ;; no "configure" script + (alist-delete 'configure %standard-phases))))) + (inputs `(("zlib" ,zlib))) + (home-page "http://bioinf.wehi.edu.au/subread-package/") + (synopsis "Tool kit for processing next-gen sequencing data") + (description + "The subread package contains the following tools: subread aligner, a +general-purpose read aligner; subjunc aligner: detecting exon-exon junctions +and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic +features; exactSNP: a SNP caller that discovers SNPs by testing signals +against local background noises.") + (license license:gpl3+))) + (define-public shogun (package (name "shogun") -- 2.1.0