guix_mirror_bot pushed a commit to branch master
in repository guix.
commit f731d71846a6df8aab13e1639ae685f0d4cc3874
Author: Kjartan Oli Agustsson <kjartan...@outlook.com>
AuthorDate: Wed Jun 18 21:05:42 2025 +0000
gnu: tetoolkit: Run guix style
* gnu/packages/bioinformatics.scm (tetoolkit): Run guix style.
Change-Id: I5f4c6a647a41a9d60e5bc1d2b4fbee045626dc12
Signed-off-by: Sharlatan Hellseher <sharlata...@gmail.com>
---
gnu/packages/bioinformatics.scm | 110 +++++++++++++++++++++-------------------
1 file changed, 57 insertions(+), 53 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6e42e1a45e..6b45c48a7a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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
