gnu: Add ribodiff.

* gnu/packages/bioinformatics.scm (ribodiff): New variable.
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Ricardo Wurmus 2017-01-16 11:56:00 +01:00
parent e84efc50d7
commit 769fc6bb18
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@ -468,6 +468,47 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
provides the Ribotaper pipeline.") provides the Ribotaper pipeline.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public ribodiff
(package
(name "ribodiff")
(version "0.2.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/ratschlab/RiboDiff/"
"archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
;; Generate an installable executable script wrapper.
(add-after 'unpack 'patch-setup.py
(lambda _
(substitute* "setup.py"
(("^(.*)packages=.*" line prefix)
(string-append line "\n"
prefix "scripts=['scripts/TE.py'],\n")))
#t)))))
(inputs
`(("python-numpy" ,python2-numpy)
("python-matplotlib" ,python2-matplotlib)
("python-scipy" ,python2-scipy)
("python-statsmodels" ,python2-statsmodels)))
(home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
(synopsis "Detect translation efficiency changes from ribosome footprints")
(description "RiboDiff is a statistical tool that detects the protein
translational efficiency change from Ribo-Seq (ribosome footprinting) and
RNA-Seq data. It uses a generalized linear model to detect genes showing
difference in translational profile taking mRNA abundance into account. It
facilitates us to decipher the translational regulation that behave
independently with transcriptional regulation.")
(license license:gpl3+)))
(define-public bioawk (define-public bioawk
(package (package
(name "bioawk") (name "bioawk")