In its current implementation, PersephoneShellServer is a standalone application that runs a REST API web server. It must be executed on a system that has direct access to both the Persephone database and the file system used by the application.

The configuration file PersephoneShellServer.exe.config supplied with the application contains several fields that need to be modified before launching the server. This part is similar to the configuration of PersephoneShell (see the file psh.exe.config in the PersephoneShell folder):

...  
<connectionStrings>
    <add name="Default" providerName="MySql.Data.MySqlClient" connectionString="encrypted connection string" />
  </connectionStrings>
  <ConnectionSettings>
    <Connection Name="Default">
      <FileStorage Path="/Data/FileStorage/small" />
      <BlastDbStorage Path="/Data/blastdb/small" />
      <SequenceStorage Path="/Data/Sequences/small" />
      <SearchIndex ServerUrl="http://localhost:8983" CoreName="small" MultiThreads="true" />
    </Connection>
  </ConnectionSettings>
...

Please note that unlike psh.exe.config, SearchIndex is now specified inside the section <ConnectionSettings>. You can use the same encrypted connection string from the corresponding section of psh.exe.config.