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metagenlab / zAMP

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
https://zamp.readthedocs.io/en/latest/
MIT License
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AttributeError with snakemake <7.32.4 #36

Closed farchaab closed 2 months ago

farchaab commented 3 months ago

Error :

AttributeError in file zAMP/Snakefile, line 11:
can't set attribute 'singularity_args'
 File "zAMP/Snakefile", line 11, in <module>

line:

## When using singularity
if "--use-singularity" in sys.argv:
    ### Bind the directory of the database to the singularity containers.
    workflow.singularity_args += f' -B {config["tax_DB_path"]}:{config["tax_DB_path"]}'
valscherz commented 3 months ago

Hi,

Probably that changing that could do the trick?

### Bind the directory of the database to the singularity containers.
    workflow.deployment_settings.apptainer_args += f' -B {config["tax_DB_path"]}:{config["tax_DB_path"]}'

But I guess that other version related issues would come up...

valscherz commented 3 months ago

Indeed, it seems to work ef2d1666d066bd4d22843fda66db715afaad4c4b

But there a few python semantics and tools (with related conda/docker/singularity containers) to be updated as well. I have started to do some, but not finished yet.

valscherz commented 2 months ago

Now fixed a bully working with https://github.com/metagenlab/zAMP/tree/UpdateTools, waiting for your testing