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| author | Ricardo Wurmus <rekado@elephly.net> | 2017-06-28 16:22:55 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-06-28 16:49:20 +0200 |
| commit | e61bc976f6f3020f4420dabc6e582e1a8c9e4b75 (patch) | |
| tree | 4fc6ba3435e0e42ed2bb8396998ad05f45b1c2d9 | |
| parent | 03b055a1163cbfbd0cc5e931a71a74a7fec6a4d9 (diff) | |
| download | patches-e61bc976f6f3020f4420dabc6e582e1a8c9e4b75.tar patches-e61bc976f6f3020f4420dabc6e582e1a8c9e4b75.tar.gz | |
gnu: snakemake: Fix cluster execution.
* gnu/packages/python.scm (snakemake)[arguments]: Add build phase
"call-wrapper-not-wrapped-snakemake".
| -rw-r--r-- | gnu/packages/python.scm | 14 |
1 files changed, 13 insertions, 1 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6150a8798f..6e1e289e90 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6032,7 +6032,19 @@ of the structure, dynamics, and functions of complex networks.") (build-system python-build-system) (arguments ;; TODO: Package missing test dependencies. - '(#:tests? #f)) + '(#:tests? #f + #:phases + (modify-phases %standard-phases + ;; 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* (#:key outputs #:allow-other-keys) + (substitute* "snakemake/executors.py" + (("\\{sys.executable\\} -m snakemake") + (string-append (assoc-ref outputs "out") + "/bin/snakemake"))) + #t))))) (propagated-inputs `(("python-wrapt" ,python-wrapt) ("python-requests" ,python-requests))) |