snakemake[slurm] --use-conda doesn't successfully override Liam's QIIME conda environment on cheaha
If runs
snakemakeslurm --use-conda
from @liamvdp account, we see that the deseq rule first loads the snakemake-local conda environment, but still pulls it's R exe from the QIIME environment, and thus fails, as the "rjson" package is not available in that R.
However, if we activate the local conda env on the command-line (with QIIME conda environment already active, then run vanilla snakemake, it works.
conda activate ./.snakemake/conda/...
which R # validate we're getting the local version
snakemake # works
We think when running snakemakeslurm --use-conda
the conda load should have over-ridden his account settings.
Help? @jelaiw