From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add StringTie. Date: Tue, 2 Feb 2016 15:50:06 +0100 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59999) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aQcHa-0005fc-WA for guix-devel@gnu.org; Tue, 02 Feb 2016 09:50:20 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aQcHW-000479-PZ for guix-devel@gnu.org; Tue, 02 Feb 2016 09:50:18 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:41885) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aQcHW-00046S-DN for guix-devel@gnu.org; Tue, 02 Feb 2016 09:50:14 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 830E5380E9C for ; Tue, 2 Feb 2016 15:50:12 +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 FJKTPX8TUtc3 for ; Tue, 2 Feb 2016 15:50:06 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 2 Feb 2016 15:50:06 +0100 (CET) Content-Disposition: inline; filename="0001-gnu-Add-StringTie.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 a6c40f6e88e612764e50ef567d81ca99b8304103 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 2 Feb 2016 15:45:38 +0100 Subject: [PATCH] gnu: Add StringTie. * gnu/packages/bioinformatics.scm (stringtie): New variable. --- gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 709757b..1e093b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3370,6 +3370,61 @@ features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.") (license license:gpl3+))) +(define-public stringtie + (package + (name "stringtie") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" + "stringtie-" version ".tar.gz")) + (sha256 + (base32 + "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "samtools-0.1.18") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no test suite + #:phases + (modify-phases %standard-phases + ;; no configure script + (delete 'configure) + (add-before 'build 'use-system-samtools + (lambda _ + (substitute* "Makefile" + (("stringtie: \\$\\{BAM\\}/libbam\\.a") + "stringtie: ")) + (substitute* '("gclib/GBam.h" + "gclib/GBam.cpp") + (("#include \"(bam|sam|kstring).h\"" _ header) + (string-append "#include "))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "stringtie" bin) + #t)))))) + (inputs + `(("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "http://ccb.jhu.edu/software/stringtie/") + (synopsis "Transcript assembly and quantification for RNA-Seq data") + (description + "StringTie is a fast and efficient assembler of RNA-Seq sequence +alignments into potential transcripts. It uses a novel network flow algorithm +as well as an optional de novo assembly step to assemble and quantitate +full-length transcripts representing multiple splice variants for each gene +locus. Its input can include not only the alignments of raw reads used by +other transcript assemblers, but also alignments of longer sequences that have +been assembled from those reads. To identify differentially expressed genes +between experiments, StringTie's output can be processed either by the +Cuffdiff or Ballgown programs.") + (license license:artistic2.0))) + (define-public vcftools (package (name "vcftools") -- 2.1.0