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(s):
                                 1) 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:
                    filestorage: /data/prod/filestorage
               sequence storage: /data/prod/sequences
               blast db storage: /data/prod/BlastDB

Blast settings:
         blast binary directory: /data/prod/NCBIBlast/bin
               blast parameters: -evalue 1e-5 -max_target_seqs 5 -max_hsps 3 -word_size 4 -threshold 99 -num_threads 8

Other settings:
                 temp directory: /HDD4Tb/Temp
                 data directory: /HDD4Tb/Bio
          user config directory:

The most interesting value here is the setting for data directory which can be referenced by $DATA in the INI files.