diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
1 files changed, 27 insertions, 26 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ce1c1e8394..0a4c68e8c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |