me
/
guix
Archived
1
0
Fork 0
Code

gnu: snakemake-7: Fix cluster execution bug 

* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Revise the patch for
the cluster execution script

Signed-off-by: Marius Bakke <marius@gnu.org>
master
Konrad Hinsen 2022-08-25 20:17:55 +02:00 committed by Marius Bakke
parent 52aa21cc9a
commit 5831155175
No known key found for this signature in database
GPG Key ID: A2A06DF2A33A54FA
1 changed files with 5 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
gnu/packages/python-xyz.scm
View File

@ -9739,15 +9739,14 @@ Python style, together with a fast and comfortable execution environment.")
;; 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")))))
(("self\\.get_python_executable\\(\\),")
"")
(("\"-m snakemake\"")
(string-append "\"" (assoc-ref outputs "out")
"/bin/snakemake" "\"")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?