Running your own gfServer: Difference between revisions
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(Created page with "* 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 someth...") |
(adding link to mailing list archives about gfServer for troubleshooting) |
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* If you want to run your own blat server you need a lot of spare memory on the machine | * 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 [https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/gfServer gfServer troubleshooting advice]. | ||
* You need two servers, one for protein queries, one for normal DNA queries. | * 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: | * Add something like this to a startup file of your server, e.g. /etc/rc.d/rc.local: | ||
Revision as of 22:54, 19 January 2015
- 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=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
