frattalab / frattalab/rna_seq_single_steps
Some submit scripts do not use the conda environment
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- Python
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Description
This definitely applies to `submit_samtools_stats.sh` & `submit_sort_pull.sh` but possible others too.
The snakemake commands don't include `--use-conda` as so rely on dependencies being available in $PATH for the pipeline to run. Since both of these just use samtools this is somewhat likely (at least in my case), but this is a bug waiting to happen and defeats the point of having a conda environment.
I suggest also adding a `--conda-prefix` call to our general conda env space to save every new user from doing a local install.
TL;DR: update the submit scripts to ensure they include `--use-conda` and `--conda-prefix "/
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