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Inherit from snakemake-7. --- gnu/packages/python-science.scm | 19 ++++++++ gnu/packages/python-xyz.scm | 83 --------------------------------- 2 files changed, 19 insertions(+), 83 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 5acead6523..509e77b765 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -4602,6 +4602,25 @@ (define-public snakemake-7 python-setuptools python-wheel)))) +(define-public snakemake-6 + (package + (inherit snakemake-7) + (name "snakemake") + (version "6.15.5") + (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 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai")))) + (build-system pyproject-build-system) + (propagated-inputs + (modify-inputs (package-propagated-inputs snakemake-7) + (delete "python-retry" "python-yte"))))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 740e6cfd33..fa73a189ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14999,89 +14999,6 @@ (define-public snakemake Python style, together with a fast and comfortable execution environment.") (license license:expat))) -(define-public snakemake-6 - (package - (inherit snakemake) - (name "snakemake") - (version "6.15.5") - (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 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai")))) - (build-system pyproject-build-system) - (arguments - (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. - - ;; XXX: There is another instance of sys.executable on line 692, but - ;; it is not clear how to patch it. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "snakemake/executors/__init__.py" - (("\\{sys.executable\\} -m snakemake") - (string-append #$output "/bin/snakemake"))))) - (add-after 'unpack 'tabulate-compatibility - (lambda _ - (substitute* "snakemake/dag.py" - (("\"job\": rule,") - "\"job\": rule.name,")))) - (add-after 'unpack 'patch-version - (lambda _ - (substitute* "setup.py" - (("version=versioneer.get_version\\(\\)") - (format #f "version=~s" #$version))) - (substitute* '("snakemake/_version.py" - "versioneer.py") - (("0\\+unknown") #$version)))) - (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") - (invoke "pytest"))))))) - (propagated-inputs - (list python-appdirs - python-configargparse - python-connection-pool - python-datrie - python-docutils - python-filelock - python-gitpython - python-jinja2 - python-jsonschema - python-nbformat - python-networkx - python-psutil - python-pulp - python-pyyaml - python-py-tes - python-ratelimiter - python-requests - python-smart-open - python-stopit - python-tabulate - python-toposort - python-wrapt)) - (native-inputs - (list git-minimal - python-wrapper - python-pytest - python-pandas - python-requests-mock - python-setuptools - python-wheel)))) - (define-public python-pyqrcode (package (name "python-pyqrcode")