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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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python vs python3 #44

Open sneuensc opened 2 years ago

sneuensc commented 2 years ago

Thank you for the development of MAGpy, it is a great tool.

Using the pipeline with the rule specific conda packages (--use-conda, following your instructions), I had to adapt the call to python in a few rules. Somehow the 'python' symlink was missing and therefore 'python3' had to be called directly. Personally, I solved the issue by not changing the shebang of the scripts, but by calling the python scripts with python in the rules, e.g.: $ python3 script.py

There is also a small error in the readme. To run the pipeline, you have to call $ snakemake -rp -s MAGpy --use-conda without the ‘MAGpy’. I assume that this rule name has changed to ‘all’.

mw55309 commented 1 year ago

I think this is now fixed, please let me know