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