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gnu: Remove ribodiff.

* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
Maxim Cournoyer 2022-04-29 13:35:20 -04:00
parent 9f4c958d62
commit 98c4f97d18
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1 changed files with 0 additions and 46 deletions

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@ -840,52 +840,6 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
provides the Ribotaper pipeline.")
(license license:gpl3+)))
(define-public ribodiff
(package
(name "ribodiff")
(version "0.2.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ratschlab/RiboDiff")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
;; This test fails because of the matplotlib plotting backend.
(add-after 'unpack 'disable-plot-test
(lambda _
(substitute* "src/ribodiff/functional_test_te.py"
(("pl\\.make_plots\\(data, opts\\)") "#"))))
;; 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"))))))))
(inputs
(list python2-numpy python2-matplotlib python2-scipy
python2-statsmodels))
(native-inputs
(list python2-mock python2-nose))
(home-page "https://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
(package
(name "bioawk")