These are chat archives for nextflow-io/nextflow
beforeScript = singularity exec '../singularity/img_prod' source /opt/anaconda2/bin/activate R342but it doesn't work. Or how to activate an environment for the whole script?
beforeScript = "source /opt/anaconda2/bin/activate R342"I get the following error:
CondaEnvironmentNotFoundError: Could not find environment: R342. But the environment is present when I open a singularity shell and type
conda info --envs.
singularity exec '../singularity/img_prod' conda info --envs
runOptions = '--cleanenv --containall'; maybe it mess up with the nextflow environments?
modulestuff on some HPC systems is far less usable IMHO than docker
Is it possible to use a singularity sandbox images with nextflow?
nextflow run -with-singularity /path/to/your/sandboxit should work fine I guess
-with-singularitytasks run in the container and NF outside
singularity exec /path/to/folder-sandbox toolnameI guess