diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 32 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38b9fe6cf6..9c18737ade 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3985,26 +3985,44 @@ HMMs).") (define-public htseq (package (name "htseq") - (version "0.12.3") + (version "2.0.2") + ;; Sources on pypi do not include everything needed to run the tests. (source (origin - (method url-fetch) - (uri (pypi-uri "HTSeq" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/htseq/htseq") + (commit (string-append "release_" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b")))) + "1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19")))) (build-system python-build-system) - (native-inputs - (list python-cython)) - ;; Numpy needs to be propagated when htseq is used as a Python library. + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Avoid rebuilding the extension. Everything is built during the + ;; 'install phase anyway. + (delete 'build) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v"))))))) (propagated-inputs - (list python-numpy)) - (inputs - (list python-pysam python-matplotlib)) - (home-page "https://htseq.readthedocs.io/") - (synopsis "Analysing high-throughput sequencing data with Python") + (list python-matplotlib + python-numpy + python-pysam)) + (native-inputs + (list python-cython + python-pandas + python-pytest + python-scipy + swig)) + (home-page "https://github.com/htseq") + (synopsis "Framework for analyzing high-throughput sequencing data") (description - "HTSeq is a Python package that provides infrastructure to process data -from high-throughput sequencing assays.") + "This package provides a framework to process and analyze data from +high-throughput sequencing (HTS) assays") (license license:gpl3+))) (define-public java-htsjdk |