test pipeline for singularity

[sivasubramanics]

Dear Team,
The tool looks quite promising on paper, and I am looking forward to use it on a plant transcriptome data. Unfortunately, I am getting lost with the large and complicated user manual given. Provided that I am trying to run this tool using singularily, there is not proper instruction provided for the DB locations, and reference locations. Also "- - data-generate flag during Configuration to configure it locally" basically throwing error that the "EggNOG DIAMOND database was not found at: /entap/eggnog4.clustered_proteins.dmnd". I would highly recommend a clean installation and setting up the DBs for a vanilla run on a transcriptome data.

1. Can we generate the dmnd indices using the --config?
2. Can we update the .ini file using the --config flag upon indexing?
3. a simple batch file with a test pipeline explaining how to prepare the databases?
4. If --data-generate is not downloading and indexing the databases, then what we can expect from the option. Its not clear.

Thanks,

Best,
Siva