diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 54 |
1 files changed, 24 insertions, 30 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 540bc121a7..1837ad0bc3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2149,7 +2149,7 @@ databases.") (define-public clipper (package (name "clipper") - (version "1.2.1") + (version "2.0") (source (origin (method git-fetch) (uri (git-reference @@ -2158,40 +2158,34 @@ databases.") (file-name (git-file-name name version)) (sha256 (base32 - "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb")) - (modules '((guix build utils))) - (snippet - '(begin - ;; remove unnecessary setup dependency - (substitute* "setup.py" - (("setup_requires = .*") "")) - #t)))) + "1bcag4lb5bkzsj2vg7lrq24aw6yfgq275ifrbhd82l7kqgbbjbkv")))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:phases + `(#:phases (modify-phases %standard-phases - ;; This is fixed in upstream commit - ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "clipper/src/readsToWiggle.pyx" - (("^sc.*") "")) - #t))))) + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure .gz files are writable so that the + ;; 'reset-gzip-timestamps' phase can do its work. + (let ((out (assoc-ref outputs "out"))) + (for-each make-file-writable + (find-files out "\\.gz$")) + #t)))))) (inputs - `(("htseq" ,python2-htseq) - ("python-pybedtools" ,python2-pybedtools) - ("python-cython" ,python2-cython) - ("python-scikit-learn" ,python2-scikit-learn) - ("python-matplotlib" ,python2-matplotlib) - ("python-pandas" ,python2-pandas) - ("python-pysam" ,python2-pysam) - ("python-numpy" ,python2-numpy) - ("python-scipy" ,python2-scipy))) + `(("htseq" ,htseq) + ("python-pybedtools" ,python-pybedtools) + ("python-cython" ,python-cython) + ("python-scikit-learn" ,python-scikit-learn) + ("python-matplotlib" ,python-matplotlib) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) (native-inputs - `(("python-mock" ,python2-mock) ; for tests - ("python-nose" ,python2-nose) ; for tests - ("python-pytz" ,python2-pytz))) ; for tests + `(("python-setuptools-git" ,python-setuptools-git) + ("python-mock" ,python-mock) ; for tests + ("python-nose" ,python-nose) ; for tests + ("python-pytz" ,python-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") (description |