Computer Resources at TSRI.
Yates group members can use computer resources at TSRI for database searches. First, one needs to obtain an
account to use a cluster. For this, send an email to William Young at
wyoung@scripps.edu.
run_ms2
To use run_ms2 on LINUX cluster you need to do the following:
Edit your .cshrc file to add /redfish/people/rovshan/bin to your path. If you
do not have a .cshrc file you can copy one from /redfish/people/rovshan/.cshrc to
your home directory.
Copy sequest.job file from /redfish/people/rovshan/sequest.job to a directory where you will start your search from.
You need to edit this file to specify computer resources you want to request. Resource allocation is administered by
RC using PBS. You need to edit the "cd /redfish/people/rovshan/run_sequest" line
to point cd to a directory where you will start search.
sftp ms2 files and sequest.params file to redfish. For this, from redfish type\n
sftp finnigan@gemini
type finnigan password
cd to directory where your ms2 files located on gemini or fields.
mget *.ms2
get sequest.params
quit
The only difference in redfish sequest.params file from the local sequest.params is the database path. Our databases are
located in /redfish/scratch/yates directory which is equivalent of /wfs/dbase directory. So one needs to change /wfs/dbase/ to
/redfish/scratch/yates/ in the sequest.params file.
submit a job by typing qsub sequest.job