List Configuration
To review the configuration values of PersephoneShell, run the command
PS> list config
Database Connection:
name in config file: prod
database url: prod.persephonesoft.com:3306/production
username: main
sequence storage: type=Filesystem config(path)=/data/prod/sequences
Search index for current connection:
url: http://localhost:8983/solr/
core name: prod
multiple threads: True
File location settings for current connection:
file storage: /data/prod/filestorage
sequence storage: /data/prod/sequences
BLAST db storage: /data/prod/BlastDB
BLAST settings:
BLAST binary directory: /data/prod/NCBIBlast/bin
BLASTP parameters (orthologs): -evalue 1e-5 -max_target_seqs 5 -max_hsps 3 -word_size 4 -threshold 99 -num_threads 8
Other settings:
temp directory: /HDD4Gb/Temp
data directory: /HDD4Gb/Bio
user config directory:
ortholog finder: DIAMOND
DIAMOND parameters: -e 1e-5 --max-target-seqs 5 --max-hsps 2
BLAST: installed
DIAMOND: installed
MINIMAP2: installed
SWISSPROT: installed
MaxFeaturesOnTrackToGroup: 400,000
The most interesting value here is the setting for data directory which can be referenced by $DATA in the INI files.