gnu: Add express-beta-diversity.

* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
This commit is contained in:
Ben Woodcroft 2015-10-15 22:53:31 +10:00 committed by Ludovic Courtès
parent 6394fe650e
commit f3674b1c80

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@ -1090,6 +1090,51 @@ analysis (from RNA-Seq), transcription factor binding quantification in
ChIP-Seq, and analysis of metagenomic data.")
(license license:artistic2.0)))
(define-public express-beta-diversity
(package
(name "express-beta-diversity")
(version "1.0.7")
(source (origin
(method url-fetch)
(uri
(string-append
"https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'enter-source (lambda _ (chdir "source") #t))
(replace 'check
(lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
"-u"))))
(add-after 'check 'exit-source (lambda _ (chdir "..") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p bin)
(copy-file "scripts/convertToEBD.py"
(string-append bin "/convertToEBD.py"))
(copy-file "bin/ExpressBetaDiversity"
(string-append bin "/ExpressBetaDiversity"))
#t))))))
(inputs
`(("python" ,python-2)))
(home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
(synopsis "Taxon- and phylogenetic-based beta diversity measures")
(description
"Express Beta Diversity (EBD) calculates ecological beta diversity
(dissimilarity) measures between biological communities. EBD implements a
variety of diversity measures including those that make use of phylogenetic
similarity of community members.")
(license license:gpl3+)))
(define-public fasttree
(package
(name "fasttree")