module 'collections' has no attribute 'Iterable'

[chaochaowong]

Hi, I am very excited about using uORF-tools along with snakemake and conda. I have followed the instruction for installation on ReadMe.md and the User Guide. While running

% snakemake --use-conda -s uORF-Tools/Snakefile --configfile uORF-Tools/config.yaml --directory ${PWD} -j 20 --latency-wait 60

I've encountered the error message:

AttributeError in line 33 of /Users/cwon2/CompBio/uORFs-project/uORF-Tools/Snakefile:
module 'collections' has no attribute 'Iterable'
  File "/Users/cwon2/CompBio/uORFs-project/uORF-Tools/Snakefile", line 33, in <module>

It comes to my attention that the current conda(4.10) ships the latest version of Python (3.10). Since Iterable is no longer supported by Python 3.10 and creating environment of snakemake 5.4.5 would create the error above. If snakemake version 5.4.5 is the only version you recommend to run uORF-Tools, perhaps mention it in ReadMe.md and suggest creating the snakemake environment with Python3.7: conda create -c conda-forge -c bioconda -n snakemake snakemake==5.4.5 python==3.7.11

Thanks,
Chao-Jen

[NastiaSkuba]

Hi, I had the same issue.

For me adding

import collections
collections.Iterable = collections.abc.Iterable

in the beginning of Snakefile worked.