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(license license:expat))) -(define-public snakemake - (package - (name "snakemake") - (version "5.32.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/snakemake/snakemake") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm")))) - (build-system pyproject-build-system) - (arguments - (list - #:test-flags - '(list - ;; We have no TES support. - "--ignore=tests/test_tes.py" - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - "--ignore=tests/test_tibanna.py" - ;; It's a similar story with this test, which requires access - ;; to the Google Storage service. - "--ignore=tests/test_google_lifesciences.py") - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'tabulate-compatibility - (lambda _ - (substitute* "snakemake/dag.py" - (("\"job\": rule,") - "\"job\": rule.name,")))) - (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)))) - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable PYTHONPATH set, cluster execution will fail. We fix - ;; this by calling the snakemake wrapper instead. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda _ - (substitute* "snakemake/executors/__init__.py" - (("\\{sys.executable\\} -m snakemake") - (string-append #$output "/bin/snakemake"))))) - (add-before 'check 'pre-check - (lambda _ (setenv "HOME" "/tmp")))))) - (propagated-inputs - (list python-appdirs - python-configargparse - python-datrie - python-docutils - python-gitpython - python-jinja2 - python-jsonschema - python-nbformat - python-networkx - python-psutil - python-pulp - python-pyyaml - python-ratelimiter - python-requests - python-toposort - python-wrapt)) - (native-inputs - (list git-minimal - python-wrapper - python-pytest - python-pandas - python-requests-mock - python-setuptools - python-wheel)) - (home-page "https://snakemake.readthedocs.io") - (synopsis "Python-based execution environment for make-like workflows") - (description - "Snakemake aims to reduce the complexity of creating workflows by -providing a clean and modern domain specific specification language (DSL) in -Python style, together with a fast and comfortable execution environment.") - (license license:expat))) - (define-public python-pyqrcode (package (name "python-pyqrcode")