I'm trying to run a Snakemake workflow in a new lab - the Snakefile already exists. For context we are using LSF submission system.
If I run snakemake <options>
at the command line, it all runs locally, despite the bsub
arguments being provided in the Snakefile.
This is obviously an issue when using Kraken2 (or similar) since the databases all seem to get loaded locally and then cause RAM issues.
I do not want to use memory-map.
What is the proper way to do this in 8.27? The documentation online is very unclear and some of the "official" documentation doesn't even work (e.g., --executor lsf
isn't available, only --executor <local,dryrun,touch>
)
There is
--executor lsf
in the docs, only--executor cluster-generic
. I'm looking at: https://snakemake.readthedocs.io/en/stable/getting_started/migration.html#id1If you're looking at https://github.com/BEFH/snakemake-executor-plugin-lsf, you may have to add the plug-in (I've never done that, I don't know what it even means).