Incorrect download_eggnog_data.py arguments

[biobakery]

Incorrect download_eggnog_data.py arguments

[WiscEvan]

Ah, I see this is part of the excluding those dependencies that have licenses. section.

I resolved this by conda install -c bioconda eggnog-mapper -y and re-running.

Enumerating these (dependencies that have licenses) in the README.md may be helpful?

[WiscEvan]

Scratch that, it appears eggnogg-mapper requires python 2.7 for the conda installation and is not up-to-date with the argparse parser in download_eggnogg_data.py. It appears they have commented this out on their master branch:

https://github.com/eggnogdb/eggnog-mapper/blob/4c2b55e80770ccddc98cf3f3ace2d01052811ba4/download_eggnog_data.py#L58-L59

However, when running biobakery_workflows_databases --install isolate_assembly --location $LOCATION I now receive:

Downloading eggnog mapper databases
usage: download_eggnog_data.py [-h] [-D] [-y] [-f] [-s] [-q] [--data_dir]
                               dbs [dbs ...]
download_eggnog_data.py: error: too few arguments
Unable to install database. Error running command: download_eggnog_data.py --data_dir $LOCATION/eggnog_mapper/ -y

Perhaps either @eggnogdb/eggnog-mapper should resolve the conda installation or biobakery_workflows_databases.py should be updated?