Running your own gfServer

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  • If you want to run your own blat server you need a lot of spare memory on the machine. You may also want to review our mailing list archives for gfServer troubleshooting advice.
  • 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=33334 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