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Hardcode path to make_msa.sh means can only run from RFAA main directory #105

Open jjv5 opened 6 months ago

jjv5 commented 6 months ago

In rf2aa/preprocessing.py the path to the make_msa.sh command is prefaced with a "./" :

search_command = f"./{command} {fasta_file} {out_dir} {num_cpus} {ram_gb} {search_base} {template_database}"

this seems to mean jobs can only be run from the RosettaFoldAA directory (where make_msa.sh lives). We are unable to override this path in the base.yaml file because of the prepended cwd.

Can the leading ./ be removed?

jjv5 commented 6 months ago

File is rf2aa/data/preprocessing.py

fglaser commented 1 month ago

Dear all,

Has this issue been solved, or can anybody kindly detail how to run python -m rf2aa.run_inference --config-name protein from a different directory?

Thanks a lot for this wonderful tool.

Fabian

wehs7661 commented 1 month ago

@fglaser see #125. I am not sure if the work has been completed or not or if/when it is going to be merged though.