From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Add rsem. Date: Thu, 21 May 2015 15:44:13 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45366) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YvQls-00082f-WF for guix-devel@gnu.org; Thu, 21 May 2015 09:44:28 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YvQlo-00011T-US for guix-devel@gnu.org; Thu, 21 May 2015 09:44:24 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:47761) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YvQlo-000118-Hk for guix-devel@gnu.org; Thu, 21 May 2015 09:44:20 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id E6D5E380DB2 for ; Thu, 21 May 2015 15:44:18 +0200 (CEST) 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 s6QNj698MU_J for ; Thu, 21 May 2015 15:44:12 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 21 May 2015 15:44:12 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-rsem.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 93ac344b82dae538c1610dd3b1195d9dd50c9592 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 21 May 2015 15:43:25 +0200 Subject: [PATCH] gnu: Add rsem. * gnu/packages/bioinformatics.scm (rsem): New variable. --- gnu/packages/bioinformatics.scm | 78 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e1dfda1..7bc5971 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1068,6 +1068,84 @@ files and writing bioinformatics applications.") generated using the PacBio Iso-Seq protocol.") (license license:bsd-3)))) +(define-public rsem + (package + (name "rsem") + (version "1.2.20") + (source + (origin + (method url-fetch) + (uri + (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" + version ".tar.gz")) + (sha256 + (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) + (patches (list (search-patch "rsem-makefile.patch"))) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled copy of boost + (delete-file-recursively "boost") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + ;; No "configure" script. + ;; Do not build bundled samtools library. + (replace 'configure + (lambda _ + (substitute* "Makefile" + (("^all : sam/libbam.a") "all : ")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/")) + (perl (string-append out "/lib/perl5/site_perl"))) + (mkdir-p bin) + (mkdir-p perl) + (for-each (lambda (file) + (copy-file file + (string-append bin (basename file)))) + (find-files "." "rsem-.*")) + (copy-file "rsem_perl_utils.pm" + (string-append perl "/rsem_perl_utils.pm"))) + #t)) + (add-after + 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (prog) + (wrap-program (string-append out "/bin/" prog) + `("PERL5LIB" ":" prefix + (,(string-append out "/lib/perl5/site_perl"))))) + '("rsem-plot-transcript-wiggles" + "rsem-calculate-expression" + "rsem-generate-ngvector" + "rsem-run-ebseq" + "rsem-prepare-reference"))) + #t))))) + (inputs + `(("boost" ,boost) + ("ncurses" ,ncurses) + ("r" ,r) + ("perl" ,perl) + ("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "http://deweylab.biostat.wisc.edu/rsem/") + (synopsis "Estimate gene expression levels from RNA-Seq data") + (description + "RSEM is a software package for estimating gene and isoform expression +levels from RNA-Seq data. The RSEM package provides a user-friendly +interface, supports threads for parallel computation of the EM algorithm, +single-end and paired-end read data, quality scores, variable-length reads and +RSPD estimation. In addition, it provides posterior mean and 95% credibility +interval estimates for expression levels. For visualization, it can generate +BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") + (license license:gpl3+))) + (define-public rseqc (package (name "rseqc") -- 2.1.0