gnu: Add fasttree.
* gnu/packages/bioinformatics.scm (fasttree): New variable.
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@ -780,6 +780,65 @@ analysis (from RNA-Seq), transcription factor binding quantification in
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ChIP-Seq, and analysis of metagenomic data.")
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(license license:artistic2.0)))
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(define-public fasttree
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(package
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(name "fasttree")
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(version "2.1.8")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://www.microbesonline.org/fasttree/FastTree-"
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version ".c"))
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(sha256
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(base32
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"0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
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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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#:phases
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(modify-phases %standard-phases
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(delete 'unpack)
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(delete 'configure)
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(replace 'build
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(lambda* (#:key source #:allow-other-keys)
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(and (zero? (system* "gcc"
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"-O3"
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"-finline-functions"
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"-funroll-loops"
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"-Wall"
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"-o"
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"FastTree"
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source
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"-lm"))
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(zero? (system* "gcc"
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"-DOPENMP"
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"-fopenmp"
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"-O3"
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"-finline-functions"
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"-funroll-loops"
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"-Wall"
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"-o"
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"FastTreeMP"
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source
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"-lm")))))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out")
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"/bin")))
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(mkdir-p bin)
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(copy-file "FastTree"
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(string-append bin "/FastTree"))
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(copy-file "FastTreeMP"
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(string-append bin "/FastTreeMP"))
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#t))))))
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(home-page "http://www.microbesonline.org/fasttree")
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(synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
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(description
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"FastTree can handle alignments with up to a million of sequences in a
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reasonable amount of time and memory. For large alignments, FastTree is
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100-1,000 times faster than PhyML 3.0 or RAxML 7.")
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(license license:gpl2+)))
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(define-public fastx-toolkit
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(package
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(name "fastx-toolkit")
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