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Running snakemake does not recognize mamba

Open AmitMY opened this issue 4 years ago • 1 comments

Following the instructions on the README, I get to the make dry-run step, and snakemake errors it does not know mamba.

To fix, I had to additionally

export PATH=$(conda info --base)/bin/:$PATH 

(where conda info --base is the same as CONDA_PATH in the Makefile)

AmitMY avatar Apr 21 '22 08:04 AmitMY

This issue happens because of a conflict with preinstalled conda. We should modify the Makefile so that it always uses our mamba installation for snakemake.

evgenyrp avatar Apr 21 '22 21:04 evgenyrp