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gnu: tetoolkit: Update to 2.2.1b.

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* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse.  Replace python2-pysam with python-pysam.
[home-page]: Update URL.
This commit is contained in:
Maxim Cournoyer 2022-04-29 13:35:30 -04:00
parent d29d50a556
commit 3d63c5f1ba
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GPG key ID: 1260E46482E63562
1 changed files with 27 additions and 26 deletions
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53
gnu/packages/bioinformatics.scm
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@ -2391,59 +2391,60 @@ high-throughput sequencing data – with an emphasis on simplicity.")
(define-public tetoolkit
(package
(name "tetoolkit")
(version "2.0.3")
(version "2.2.1b")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mhammell-laboratory/tetoolkit")
(url "https://github.com/mhammell-laboratory/TEtranscripts")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807"))))
"1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; not guaranteed to work with Python 3
#:phases
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'make-writable
(add-after 'unpack 'adjust-requirements
(lambda _
(for-each make-file-writable (find-files "."))
#t))
(substitute* "setup.py"
;; This defunct dependency isn't required for Python 3 (see:
;; https://github.com/mhammell-laboratory/TEtranscripts/issues/111).
((".*'argparse'.*") ""))))
(add-after 'unpack 'patch-invocations
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("bin/TEtranscripts"
"bin/TEcount")
(("'sort ")
(string-append "'" (which "sort") " "))
(string-append "'" (search-input-file inputs "bin/sort") " "))
(("'rm -f ")
(string-append "'" (which "rm") " -f "))
(("'Rscript'") (string-append "'" (which "Rscript") "'")))
(string-append "'" (search-input-file inputs "bin/rm") " -f "))
(("'Rscript'")
(string-append "'" (search-input-file inputs "bin/Rscript")
"'")))
(substitute* "TEToolkit/IO/ReadInputs.py"
(("BamToBED") (which "bamToBed")))
(("BamToBED")
(search-input-file inputs "bin/bamToBed")))
(substitute* "TEToolkit/Normalization.py"
(("\"Rscript\"")
(string-append "\"" (which "Rscript") "\"")))
#t))
(string-append "\"" (search-input-file inputs "bin/Rscript")
"\"")))))
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure the executables find R packages.
(let ((out (assoc-ref outputs "out")))
(for-each
(lambda (script)
(wrap-program (string-append out "/bin/" script)
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
'("TEtranscripts"
"TEcount")))
#t)))))
(for-each (lambda (script)
(wrap-program script
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
(list (search-input-file outputs "bin/TEtranscripts")
(search-input-file outputs "bin/TEcount"))))))))
(inputs
(list coreutils
(list bash-minimal
coreutils
bedtools
python2-argparse
python2-pysam
python-pysam
r-minimal
r-deseq2))
(home-page "https://github.com/mhammell-laboratory/tetoolkit")
(home-page "https://github.com/mhammell-laboratory/TEtranscripts")
(synopsis "Transposable elements in differential enrichment analysis")
(description
"This is package for including transposable elements in differential