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gnu: tetoolkit: Run guix style

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* gnu/packages/bioinformatics.scm (tetoolkit): Run guix style.

Change-Id: I5f4c6a647a41a9d60e5bc1d2b4fbee045626dc12
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
This commit is contained in:
Kjartan Oli Agustsson
2025-06-18 21:05:42 +00:00
committed by Sharlatan Hellseher
parent 09a3e09fa8
commit f731d71846
1 changed files with 57 additions and 53 deletions
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110
gnu/packages/bioinformatics.scm
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@@ -5942,61 +5942,65 @@ high-throughput sequencing data – with an emphasis on simplicity.")
(package
(name "tetoolkit")
(version "2.2.1b")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mhammell-laboratory/TEtranscripts")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y"))))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mhammell-laboratory/TEtranscripts")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y"))))
(build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-requirements
(lambda _
(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 "'" (search-input-file inputs "bin/sort") " "))
(("'rm -f ")
(string-append "'" (search-input-file inputs "bin/rm") " -f "))
(("'Rscript'")
(string-append "'" (search-input-file inputs "bin/Rscript")
"'")))
(substitute* "TEToolkit/IO/ReadInputs.py"
(("BamToBED")
(search-input-file inputs "bin/bamToBed")))
(substitute* "TEToolkit/Normalization.py"
(("\"Rscript\"")
(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.
(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 bash-minimal
coreutils
bedtools
python-pysam
r-minimal
r-deseq2))
(native-inputs
(list python-setuptools
python-wheel))
`(#:phases (modify-phases %standard-phases
(add-after 'unpack 'adjust-requirements
(lambda _
(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 "'"
(search-input-file inputs "bin/sort")
" "))
(("'rm -f ")
(string-append "'"
(search-input-file inputs "bin/rm")
" -f "))
(("'Rscript'")
(string-append "'"
(search-input-file inputs
"bin/Rscript") "'")))
(substitute* "TEToolkit/IO/ReadInputs.py"
(("BamToBED")
(search-input-file inputs "bin/bamToBed")))
(substitute* "TEToolkit/Normalization.py"
(("\"Rscript\"")
(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.
(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 bash-minimal
coreutils
bedtools
python-pysam
r-minimal
r-deseq2))
(native-inputs (list python-setuptools python-wheel))
(home-page "https://github.com/mhammell-laboratory/TEtranscripts")
(synopsis "Transposable elements in differential enrichment analysis")
(description