diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 59 |
1 files changed, 34 insertions, 25 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c058c25071..e7236c075c 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -11519,32 +11519,41 @@ Python style, together with a fast and comfortable execution environment.") (file-name (git-file-name name version)) (sha256 (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We - ;; fix this by calling the snakemake wrapper instead. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "snakemake/executors/__init__.py" - (("self\\.get_python_executable\\(\\),") - "") - (("\"-m snakemake\"") - (string-append "\"" (assoc-ref outputs "out") - "/bin/snakemake" "\""))))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - (delete-file "tests/test_tibanna.py") - ;; It's a similar story with this test, which requires access - ;; to the Google Storage service. - (delete-file "tests/test_google_lifesciences.py") - (invoke "pytest"))))))) + (list + #:phases + #~(modify-phases %standard-phases + ;; For cluster execution Snakemake will call Python. Since there is + ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We + ;; fix this by calling the snakemake wrapper instead. + (add-after 'unpack 'call-wrapper-not-wrapped-snakemake + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "snakemake/executors/__init__.py" + (("self\\.get_python_executable\\(\\),") + "") + (("\"-m snakemake\"") + (string-append "\"" #$output + "/bin/snakemake" "\""))))) + (add-after 'unpack 'patch-version + (lambda _ + (substitute* "setup.py" + (("version=versioneer.get_version\\(\\)") + (format #f "version=~s" #$version))) + (substitute* '("snakemake/_version.py" + "versioneer.py") + (("0\\+unknown") #$version)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + ;; This test attempts to change S3 buckets on AWS and fails + ;; because there are no AWS credentials. + (delete-file "tests/test_tibanna.py") + ;; It's a similar story with this test, which requires access + ;; to the Google Storage service. + (delete-file "tests/test_google_lifesciences.py") + (invoke "pytest"))))))) (propagated-inputs (list python-appdirs python-configargparse |