Ecogenomics/APP

Merged database versions

fangly opened this issue · 1 comments

fangly commented

When using a custom database, e.g. the 'MERGED' database:
1/ it does not seem that APP checks that the hardcoded database files are available prior to continuing its work
2/ there is no way to specify which version of the merged database to use, though apparently, one can specify a couple of different Greengenes database versions

Ideally, APP should have a config file that lets people provide a database, instead of hardcoding file paths.
Cheers,
Florent

fangly commented

Besides, there are some obsolete variables in AppConfig.pm

Merged DBs (GG Bacteria + Archaea with Silva Eukaryotes)

our $MERGED_TAX_tax_file = "/srv/whitlam/bio/db/merged_gg_silva/merged_gg_silva_taxo.txt";
our $MERGED_TAX_blast_file = "/srv/whitlam/bio/db/merged_gg_silva/merged_gg_silva.fna";

... and probably other ones.

These files exist on our system, and yet were not used. I suggest removing all these unused variables.