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gnu: flair: Add missing R packages.

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* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2.
[inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman,
and r-rlang.
[arguments]: Add phase "wrap-executable".
This commit is contained in:
Ricardo Wurmus 2022-10-27 18:19:48 +02:00
parent 302eae2fc3
commit 176a501360
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GPG key ID: 197A5888235FACAC
1 changed files with 18 additions and 1 deletions
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19
gnu/packages/bioinformatics.scm
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@ -17043,13 +17043,30 @@ module capable of computing base-level alignments for very large sequences.")
(lambda _ (lambda _
(apply invoke "pip" "--no-cache-dir" "--no-input" (apply invoke "pip" "--no-cache-dir" "--no-input"
"install" "--no-deps" "--prefix" #$output "install" "--no-deps" "--prefix" #$output
(find-files "dist" "\\.whl$"))))))) (find-files "dist" "\\.whl$"))))
(add-after 'install 'wrap-executable
(lambda _
(for-each
(lambda (script)
(wrap-program script
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
(find-files (string-append #$output "/bin"))))))))
(propagated-inputs (propagated-inputs
(list python-mappy (list python-mappy
python-ncls python-ncls
python-pybedtools python-pybedtools
python-pysam python-pysam
python-rpy2
python-tqdm)) python-tqdm))
;; Used by rpy2
(inputs
(list r-minimal ;for R_LIBS_SITE
r-deseq2 ;for runDE
r-drimseq ;for runDS
r-ggplot2 ;runDS, runDU
r-lazyeval ;for rpy2
r-qqman ;for runDE
r-rlang)) ;for rpy2
(native-inputs (native-inputs
(list python-pypa-build python-setuptools)) (list python-pypa-build python-setuptools))
(home-page "https://flair.readthedocs.io/en/latest/") (home-page "https://flair.readthedocs.io/en/latest/")