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Python error in quantile_norm of module pulp #63

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mrheinnecker opened this issue May 15, 2024 · 0 comments
Open

Python error in quantile_norm of module pulp #63

mrheinnecker opened this issue May 15, 2024 · 0 comments

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@mrheinnecker
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when executing:

cem-run supervoxels --cluster slurm -c 64 -g 12

the follwouing error occurs:
Traceback (most recent call last):
File "/home/rheinnec/miniconda3/envs/cebra1/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home/rheinnec/miniconda3/envs/cebra1/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/rheinnec/miniconda3/envs/cebra1/lib/python3.9/site-packages/snakemake/main.py", line 4, in
main()
File "/home/rheinnec/miniconda3/envs/cebra1/lib/python3.9/site-packages/snakemake/init.py", line 2736, in main
parser = get_argument_parser()
File "/home/rheinnec/miniconda3/envs/cebra1/lib/python3.9/site-packages/snakemake/init.py", line 1607, in get_argument_parser
lp_solvers = pulp.list_solvers(onlyAvailable=True)
AttributeError: module 'pulp' has no attribute 'list_solvers'

according to: snakemake/snakemake#2607

the list_solvers was updated to listSolvers

so i changed the line 1607 of file:
"/home/rheinnec/miniconda3/envs/cebra1/lib/python3.9/site-packages/snakemake/init.py"

from:
lp_solvers = pulp.list_solvers(onlyAvailable=True)
into:
lp_solvers = pulp.listSolvers(onlyAvailable=True)

this seems to fix the problem

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