gnu: Add sjcount.
* gnu/packages/bioinformatics.scm (sjcount): New variable.
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@ -13164,3 +13164,54 @@ (define-public r-diversitree
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include Markov models of discrete and continuous trait evolution and constant
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rate speciation and extinction.")
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(license license:gpl2+)))
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(define-public sjcount
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;; There is no tag for version 3.2, nor is there a release archive.
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(let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
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(revision "1"))
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(package
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(name "sjcount")
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(version (git-version "3.2" revision commit))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pervouchine/sjcount-full.git")
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(commit commit)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; requires a 1.4G test file
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#:make-flags
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(list (string-append "SAMTOOLS_DIR="
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(assoc-ref %build-inputs "samtools")
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"/lib/"))
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#:phases
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(modify-phases %standard-phases
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(replace 'configure
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "makefile"
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(("-I \\$\\{SAMTOOLS_DIR\\}")
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(string-append "-I" (assoc-ref inputs "samtools")
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"/include/samtools"))
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(("-lz ") "-lz -lpthread "))
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#t))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(for-each (lambda (tool)
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(install-file tool
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(string-append (assoc-ref outputs "out")
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"/bin")))
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'("j_count" "b_count" "sjcount"))
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#t)))))
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(inputs
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`(("samtools" ,samtools-0.1)
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("zlib" ,zlib)))
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(home-page "https://github.com/pervouchine/sjcount-full/")
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(synopsis "Annotation-agnostic splice junction counting pipeline")
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(description "Sjcount is a utility for fast quantification of splice
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junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This
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version does count multisplits.")
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(license license:gpl3+))))
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