This would most likely be done by a systems administrator. The databases and fasta and BLAST software need to be set up on the remote machine. Once this is done the commands that are sent from the Artemis/ACT client to the remote machine are controlled by a 'j2ssh.properties' file, see below for example of this file. This needs to be put in the CLASSPATH for Artemis/ACT or the one in the distribution (lib/j2ssh/j2ssh.properties) modified.
The j2ssh.properties file also hold default information. For example default parameters can be set for the login prompt, the working directory (for searches when sequences are opened on the local side) and any extra directories (other than the users home directory) to display in the file manager.
# # # Configuration file for using SSH file management and # database searches. # # # default login options port=2222 host=localhost # # # Generic default options # blastp=blastall -p blastp blastx=blastall -p blastx tblastx=blastall -p tblastx blastn=blastall -p blastn fasta=fasta33_t -B -S -q -b 100 -H -l /data/fasta/pubseqgbs fastx=fastx33_t -B -S -q -b 40 -H -l /data/fasta/pubseqgbs # # # default working directory wdir=/scratch # # # aliases used for fasta %uniprot=%U %uniprot_archaea=%A %uniprot_bacteria=%B %uniprot_eukaryota=%E %uniprot_viruses=%V %uniprot_rest=%R %malaria=%M %kineto_aa=%K default_db=%uniprot_bacteria # # # remote directories to use as roots in the file manager remotedir.PD=/nfs/pathdata remotedir.YP=/nfs/disk222/yeastpub # local directories to use as roots in the file manager localdir.PD=/nfs/pathdata localdir.YP=/nfs/disk222/yeastpub