gnu: Remove ribodiff.
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
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@ -840,52 +840,6 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
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provides the Ribotaper pipeline.")
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provides the Ribotaper pipeline.")
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(license license:gpl3+)))
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(license license:gpl3+)))
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(define-public ribodiff
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(package
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(name "ribodiff")
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(version "0.2.2")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ratschlab/RiboDiff")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:phases
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(modify-phases %standard-phases
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;; This test fails because of the matplotlib plotting backend.
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(add-after 'unpack 'disable-plot-test
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(lambda _
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(substitute* "src/ribodiff/functional_test_te.py"
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(("pl\\.make_plots\\(data, opts\\)") "#"))))
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;; Generate an installable executable script wrapper.
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(add-after 'unpack 'patch-setup.py
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(lambda _
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(substitute* "setup.py"
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(("^(.*)packages=.*" line prefix)
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(string-append line "\n"
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prefix "scripts=['scripts/TE.py'],\n"))))))))
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(inputs
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(list python2-numpy python2-matplotlib python2-scipy
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python2-statsmodels))
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(native-inputs
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(list python2-mock python2-nose))
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(home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
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(synopsis "Detect translation efficiency changes from ribosome footprints")
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(description "RiboDiff is a statistical tool that detects the protein
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translational efficiency change from Ribo-Seq (ribosome footprinting) and
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RNA-Seq data. It uses a generalized linear model to detect genes showing
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difference in translational profile taking mRNA abundance into account. It
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facilitates us to decipher the translational regulation that behave
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independently with transcriptional regulation.")
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(license license:gpl3+)))
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(define-public bioawk
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(define-public bioawk
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(package
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(package
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(name "bioawk")
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(name "bioawk")
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