@@ -2390,59 +2390,60 @@ (define-public python-plastid
(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
* 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. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++---------------- 1 file changed, 27 insertions(+), 26 deletions(-)