Running your own gfServer

• If you want to run your own blat server you need a lot of spare memory on the machine
• You need two servers, one for protein queries, one for normal DNA queries.

* Add something like this to a startup file of your server, e.g. /etc/rc.d/rc.local:
 gfServer start blatMachine 33333 -stepSize=5 -log=/var/log/blatServerCi1.log /gbdb/ci1/ci1.2bit
 gfServer start blatMachine 33334 -trans -log=/var/log/blatServerCi1Trans.log /gbdb/ci1/ci1.2bit

• Add the server to hgCentral

 update hgcentral.blatServers set host = "localhost", port=33333 where db="ci1" and isTrans=0;
 update hgcentral.blatServers set host = "localhost", port=33333 where db="ci1" and isTrans=1;

• If you're not running a protein server, remove its entry from hgCentral

 delete from hgcentral.blatServers where db="ci1" and isTrans=1;

• Tell the browser where to find the 2bit file:

 update dbDb set nibPath = "" where name="ci1";

• On RedHat you might need SELinux permissions:

 sudo chcon --type=httpd_sys_content_t /gbdb/ci1/ci1.2bit