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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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error in createIndices: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'? #991

Closed sunta3iouxos closed 6 months ago

sunta3iouxos commented 6 months ago

I am on the latest developmental brach as created by cloning the github here and using the instruction on It is not related to #932 I am trying to create the indices/indexes for the mm39 and I stabled on the following error:

(/scratch/tgeorgom/mamba/snakepipes_devel) [tgeorgom@cheops1:~]$ 13:28:14$createIndices -o assemblies/mm39 --genomeURL /home/tgeorgom/assemblies/mm39/mm39.fa.gz --gtfURL  /home/tgeorgom/assemblies/mm39/mm39.knownGene.gtf.gz  -j 10 --tools 'all' --blacklist /home/tgeorgom/assemblies/mm39/mm39.excluderanges.bed --ignoreForNormalization /home/tgeorgom/assemblies/mm39/ignorefornormalisation.ext mm39 Traceback (most recent call last):
  File "/scratch/tgeorgom/mamba/snakepipes_devel/bin/snakemake", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/scratch/tgeorgom/mamba/snakepipes_devel/lib/python3.11/site-packages/snakemake/__init__.py", line 2522, in main
    parser = get_argument_parser()
             ^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/tgeorgom/mamba/snakepipes_devel/lib/python3.11/site-packages/snakemake/__init__.py", line 1469, in get_argument_parser
    lp_solvers = pulp.list_solvers(onlyAvailable=True)
                 ^^^^^^^^^^^^^^^^^
AttributeError: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'?
Error: snakemake returned an error code of 1, so processing is incomplete!

Any idea? Thank you

WardDeb commented 6 months ago

How exactly did you install the requirements ? This seems a mismatch between snakemake & pulp versions

sunta3iouxos commented 6 months ago

This is what I did

mamba create -n snakepipes_devel python=3.11 pip
#1710858972
mamba activate snakepipes_devel
#1710858983
pip install --upgrade .
#1710859427
snakePipes config --condaEnvDir /scratch/tgeorgom/mamba/snakepipes_devel/envs/
#1710859440
snakePipes createEnvs
sunta3iouxos commented 6 months ago

How exactly did you install the requirements ? This seems a mismatch between snakemake & pulp versions

This is related to: https://github.com/snakemake/snakemake/issues/2606

I fixed it by doing:

pip install --upgrade pulp==2.7.0