I needed to run a few samples through the metagenomic biobakery workflow, and was sad to see that LSF was not supported (although perhaps it was at some point?). I have hacked together a solution where I’ve created a new runner class based heavily on the SGE profile, which seems to be working well enough for my purposes.
Would you be interested in a PR? I’d definitely appreciate the teams input to make sure the changes I’m proposing are on the right track.
Alternatively, if Anadama is being depreciated in favor of tools that already support multiple backends (snakemake, nextflow, wdl, etc), i would be happy to help with the transition.
Hey Nick, I followed your PR. Did you finally made it work. I’m hesitating to create a neat snakemake for metaphlan and humann. what do you think?
Hi Silas! Yes, I got it working enough to do what I needed (comparing some of our samples to the HMP2 results). Its not perfect, but I’m happy to help you try to run it. Code is here (sorry, I realized this morning i forgot to commit the actual lsf.py file).
Our lab has done what you described with putting all these together with snakemake. Happy to give you access to that repo as well!