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gnu: snakemake-7: Patch tibanna command line.

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* gnu/packages/python-xyz.scm (snakemake-7)[arguments]: Remove store reference
in tibanna command line.

Change-Id: I339f4c3133a0e687723a53277818749a8e5fc97a
This commit is contained in:
Ricardo Wurmus 2024-03-19 15:01:38 +01:00
parent 7286a4569d
commit 26aa8fc87e
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GPG key ID: 197A5888235FACAC
1 changed files with 16 additions and 1 deletions
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17
gnu/packages/python-xyz.scm
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@ -12963,7 +12963,22 @@ Python style, together with a fast and comfortable execution environment.")
"")
(("\"-m snakemake\"")
(string-append "\"" #$output
"/bin/snakemake" "\"")))))
"/bin/snakemake" "\""))
;; The snakemake command produced by format_job_exec contains
;; references to /gnu/store. Prior to patching above that's
;; just a reference to Python; after patching it's a reference
;; to the snakemake executable.
;;
;; In Tibanna execution mode Snakemake arranges for a certain
;; Docker image to be deployed to AWS. It then passes its own
;; command line to Tibanna. This is misguided because it only
;; ever works if the local Snakemake command was run inside
;; the same Docker image. In the case of using Guix this is
;; never correct, so we need to replace the store reference.
(("tibanna_args.command = command")
(string-append
"tibanna_args.command = command.replace('"
#$output "/bin/snakemake', 'python3 -m snakemake')")))))
(add-after 'unpack 'patch-version
(lambda _
(substitute* "setup.py"