I wanted to use the full version of MicrobeAnnotator on HPC. I know it is not designed for HPC contrary to DRAM, but still, I thought it would not be a big problem.
However I needed therefore to use Shifter to open my docker image on the HPC. Sadly, one thing is that currently Shifter overwrites the tmp file of the image, which is then later used in the following command:
Therefore to use Microbeannotator on the HPC of my faculties, I will have to rewrite the script, and I guess the same goes for anyone wanted to use it on a HPC that uses Shifter as it is currently. Unless I am missing something.
So my question is: Would it be consistent with the design of MicrobeAnnotator to make changes? (Using for instance the output directory instead of tmp)
Hi,
Thank you for the great tool!
I wanted to use the full version of MicrobeAnnotator on HPC. I know it is not designed for HPC contrary to DRAM, but still, I thought it would not be a big problem.
However I needed therefore to use Shifter to open my docker image on the HPC. Sadly, one thing is that currently Shifter overwrites the tmp file of the image, which is then later used in the following command:
/root/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64 -o /tmp/tmpkdo_yr5mTCQMLIM8AQDAQIFT2AZE --tblout /tmp/tmpwqeg0z2e/tbl.txt --domtblout /tmp/tmpwqeg0z2e/domtbl.txt /scratch/user/microbeannotator_db_light/kofam_data/profiles/common_1.model /scratch/user/genomes/mygenome.fa
Therefore to use Microbeannotator on the HPC of my faculties, I will have to rewrite the script, and I guess the same goes for anyone wanted to use it on a HPC that uses Shifter as it is currently. Unless I am missing something.
So my question is: Would it be consistent with the design of MicrobeAnnotator to make changes? (Using for instance the output directory instead of tmp)