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gnu: snakemake: Fix cluster execution.
* gnu/packages/python.scm (snakemake)[arguments]: Add build phase "call-wrapper-not-wrapped-snakemake".
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1 changed files with 13 additions and 1 deletions
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@ -6032,7 +6032,19 @@ (define-public snakemake
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(build-system python-build-system)
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(arguments
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;; TODO: Package missing test dependencies.
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'(#:tests? #f))
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'(#:tests? #f
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#:phases
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(modify-phases %standard-phases
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;; For cluster execution Snakemake will call Python. Since there is
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;; no suitable PYTHONPATH set, cluster execution will fail. We fix
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;; this by calling the snakemake wrapper instead.
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(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* "snakemake/executors.py"
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(("\\{sys.executable\\} -m snakemake")
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(string-append (assoc-ref outputs "out")
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"/bin/snakemake")))
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#t)))))
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(propagated-inputs
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`(("python-wrapt" ,python-wrapt)
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("python-requests" ,python-requests)))
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