diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2022-05-20 14:43:52 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-05-20 14:43:52 +0200 |
| commit | 8d32ec335b35948d190b3fee3b561f19b9ed24ff (patch) | |
| tree | 60b81c9a0d12665b76da6791778dcf1fdf93a7be | |
| parent | 5fd82d7bbd30e17fa1e542037dd48e34a0a1c776 (diff) | |
| download | guix-patches-8d32ec335b35948d190b3fee3b561f19b9ed24ff.tar guix-patches-8d32ec335b35948d190b3fee3b561f19b9ed24ff.tar.gz | |
gnu: Add snakemake-7.
* gnu/packages/python-xyz.scm (snakemake-7): New variable.
| -rw-r--r-- | gnu/packages/python-xyz.scm | 73 |
1 files changed, 73 insertions, 0 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 96a739f90e..738dfd61cd 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10262,6 +10262,79 @@ Python style, together with a fast and comfortable execution environment.") python-pandas python-requests-mock)))) +(define-public snakemake-7 + (package + (inherit snakemake-6) + (name "snakemake") + (version "7.7.0") + (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 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) + (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") + ;; 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"))))))) + (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-retry + python-smart-open + python-stopit + python-tabulate + python-toposort + python-wrapt + python-yte)) + (native-inputs + (list git-minimal + python-wrapper + python-pytest + python-pandas + python-requests-mock)))) + (define-public python-pyqrcode (package (name "python-pyqrcode") |