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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-16 11:19:45 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-21 10:46:23 +0200 |
| commit | dbf4ed7c91adf3ebbc45f00a9f24a5f1647e570e (patch) | |
| tree | b38aa1c224cbb9b90c7620279b0d653f47115594 | |
| parent | 44fd6ef137f4aa7b9eb9c999e57b450432c4e915 (diff) | |
| download | patches-dbf4ed7c91adf3ebbc45f00a9f24a5f1647e570e.tar patches-dbf4ed7c91adf3ebbc45f00a9f24a5f1647e570e.tar.gz | |
gnu: Add subread.
* gnu/packages/bioinformatics.scm (subread): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 39 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4fd9459350..7fc6af3c4e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1386,6 +1386,45 @@ 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") |