gnu: Add subread.
* gnu/packages/bioinformatics.scm (subread): New variable.
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@ -1386,6 +1386,45 @@ sequences.")
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;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
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(license license:gpl3+)))
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(define-public subread
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(package
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(name "subread")
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(version "1.4.6-p2")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"mirror://sourceforge/subread/subread-"
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version "-source.tar.gz"))
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(sha256
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(base32
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"06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no "check" target
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#:make-flags '("-f" "Makefile.Linux")
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#:phases
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(alist-cons-after
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'unpack 'enter-dir
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(lambda _ (chdir "src") #t)
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(alist-replace
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'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
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(mkdir-p bin)
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(copy-recursively "../bin" bin)))
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;; no "configure" script
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(alist-delete 'configure %standard-phases)))))
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(inputs `(("zlib" ,zlib)))
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(home-page "http://bioinf.wehi.edu.au/subread-package/")
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(synopsis "Tool kit for processing next-gen sequencing data")
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(description
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"The subread package contains the following tools: subread aligner, a
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general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
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and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
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features; exactSNP: a SNP caller that discovers SNPs by testing signals
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against local background noises.")
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(license license:gpl3+)))
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(define-public shogun
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(package
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(name "shogun")
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