gnu: Add bits.
* gnu/packages/bioinformatics.scm (bits): New variable.
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@ -5539,6 +5539,52 @@ biology. EMBOSS also integrates a range of currently available packages and
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tools for sequence analysis into a seamless whole.")
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(license license:gpl2+)))
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(define-public bits
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(let ((revision "1")
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(commit "3cc4567896d9d6442923da944beb704750a08d2d"))
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(package
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(name "bits")
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;; The version is 2.13.0 even though no release archives have been
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;; published as yet.
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(version (string-append "2.13.0-" revision "." (string-take commit 9)))
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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/arq5x/bits.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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"17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no tests included
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-after 'unpack 'remove-cuda
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(lambda _
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(substitute* "Makefile"
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((".*_cuda") "")
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(("(bits_test_intersections) \\\\" _ match) match))
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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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(copy-recursively
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"bin" (string-append (assoc-ref outputs "out") "/bin"))
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#t)))))
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(inputs
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`(("gsl" ,gsl)
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("zlib" ,zlib)))
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(home-page "https://github.com/arq5x/bits")
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(synopsis "Implementation of binary interval search algorithm")
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(description "This package provides an implementation of the
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BITS (Binary Interval Search) algorithm, an approach to interval set
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intersection. It is especially suited for the comparison of diverse genomic
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datasets and the exploration of large datasets of genome
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intervals (e.g. genes, sequence alignments).")
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(license license:gpl2))))
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(define-public piranha
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;; There is no release tarball for the latest version. The latest commit is
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;; older than one year at the time of this writing.
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