Updating blat servers

See also: Emergency backup blat servers for the top 5 assemblies here -- Emergency Backup BLAT Servers This below page is not about emergencies.

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There are two places where blat servers are located. Assemblies that are important (eg. human or mouse) and are expected to get a lot of hits are hosted here at UCSC and will have a blat host name like blat#$ (where # is a number and $ is a letter, for example: blat4a). Assemblies that are going to stay on hgwdev (never to be released publicly) will get a blat server also at UCSC, but on a less important server. They will have a blat host name of blatx. Wherever the blat server is hosted, the steps below will allow you to transfer the pointers to a new machine.

• Do a select statement on dev to make sure that everything is where you expect it to be:

hgwdev: hgsql hgcentraltest
mysql> select * from blatServers where host="blat#" ORDER BY port;
+---------+--------+-------+---------+--------+
| db      | host   | port  | isTrans | canPcr |
+---------+--------+-------+---------+--------+
| apiMel1 | blat12 | 17778 |       1 |      0 |
| apiMel1 | blat12 | 17779 |       0 |      1 |
| monDom1 | blat12 | 17786 |       1 |      0 |
| monDom1 | blat12 | 17787 |       0 |      0 |
| caeRei0 | blat12 | 17790 |       1 |      0 |
| caeRei0 | blat12 | 17791 |       0 |      1 |
+---------+--------+-------+---------+--------+

• Get DNA and protein sequences for a gene for given assembly and paste below for future reference:

DNA

protein

• Open 9 windows: BLAT DNA, BLAT protein, PCR for hgwdev, the RR, and genome-euro (we don't check on beta since it doesn't really matter if blat is working there or not). Make sure that all 9 windows function without errors.

Getting into hgcentral database on dev, beta, RR:

DEV: hgwdev: hgsql hgcentraltest
BETA: hgwbeta: hgsql hgcentralbeta
RR: hgwdev: hgsql -h genome-centdb hgcentral 
          
Statements for changing pointers:
        
update blatServers set host='blat#', port=177## where db='xxxXxx#' and isTrans=1;
update blatServers set host='blat#', port=177## where db='xxxXxx#' and isTrans=0;

**Note that the admins will simiply say:
bosTau3
trans port 17786
untrans port 17787

This means put the trans port number for isTrans=1 and the untrans port number for isTrans=0

• Go to hgcentral on dev and change the pointers for the assembly of interest.
• Go back to the browser, hit back for the 3 windows open on dev, and then click re-submit. Check to see if broken. If not, go on; if yes, troubleshoot until solution is found.
• Repeat step 4 for beta and 4-5 for the RR.
• hgcentral changes are synced from the RR to genome-euro via the pullHgcentral script. See the new assembly release page for more info.
• Ask the buildmeister to rebuild the hgCentral.sql file for mirror sites. The file at http://hgdownload.soe.ucsc.edu/admin/ should be updated. Optional: Some mirrors like to get hgcentral tables via ftp or rsync from ftp://hgdownload.soe.ucsc.edu/mysql/hgcentral/. You can request a push from hgnfs1 --> hgdownload if you want to make the hgcentral info available there immediately (otherwise it will be copied there by a weekly rsync).
• Notify the mirrors (on genome-mirror@soe.ucsc.edu) that we have updated our blatServers. An example genome-mirror new hgcentral.sql (blatServers table update) email is here: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome-mirror/xxMcXbuXq9Y/lGW5fJ95NzMJ If you didn't ask for a push of the mysql tables, you can just say that they will be updated over the weekend.

Your changes to the table blatServers will sync to euro (and asia, I think) hourly. To push them sooner, run a script: See: http://genomewiki.ucsc.edu/genecats/index.php/Releasing_an_assembly#Verify_that_everything_is_working_on_genome-euro