diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 24 |
1 files changed, 17 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82d4e84b6c..4e850ab562 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3572,20 +3572,26 @@ e.g. microbiome samples, genomes, metagenomes.") (define-public python-pairtools (package (name "python-pairtools") - (version "1.0.2") + (version "1.1.0-fix") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/open2c/pairtools") - (commit (string-append "v" version)))) + (commit (string-append "pairtools-v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs")))) - (build-system python-build-system) + "0983vw4kb6frjncsnml4ahw3l7sixg1paz80s119iah2i086cw06")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-setup.py + (lambda _ + ;; __NUMPY_SETUP__ is undefined. + (substitute* "setup.py" + ((".*__builtins__.__NUMPY_SETUP.*") "")))) (add-after 'unpack 'fix-references (lambda _ (substitute* '("pairtools/cli/header.py" @@ -3598,7 +3604,11 @@ e.g. microbiome samples, genomes, metagenomes.") (with-directory-excursion "/tmp" (invoke "pytest" "-v")))))))) (native-inputs - (list python-cython python-pytest)) + (list python-cython + python-pytest + python-pytest-cov + python-setuptools + python-wheel)) (propagated-inputs (list htslib ; for bgzip, looked up in PATH samtools ; looked up in PATH |