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| author | Ricardo Wurmus <rekado@elephly.net> | 2022-05-20 13:59:38 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-05-20 14:18:12 +0200 |
| commit | 5fd82d7bbd30e17fa1e542037dd48e34a0a1c776 (patch) | |
| tree | 9ecf7f2f190bd4e30cf7cb754b88fd2be0f460bd | |
| parent | 192c7229284b9499257b6b4ac46a17b93ffd0c52 (diff) | |
| download | guix-patches-5fd82d7bbd30e17fa1e542037dd48e34a0a1c776.tar guix-patches-5fd82d7bbd30e17fa1e542037dd48e34a0a1c776.tar.gz | |
gnu: Add snakemake-6.
* gnu/packages/python-xyz.scm (snakemake-6): New variable.
| -rw-r--r-- | gnu/packages/python-xyz.scm | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index cdb6300117..96a739f90e 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10194,6 +10194,74 @@ 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 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 python-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. + + ;; 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 (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") + (invoke "pytest"))))))) + (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)))) + (define-public python-pyqrcode (package (name "python-pyqrcode") |