From e61bc976f6f3020f4420dabc6e582e1a8c9e4b75 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 28 Jun 2017 16:22:55 +0200 Subject: gnu: snakemake: Fix cluster execution. * gnu/packages/python.scm (snakemake)[arguments]: Add build phase "call-wrapper-not-wrapped-snakemake". --- gnu/packages/python.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) (limited to 'gnu') 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))) -- cgit v1.2.3