Updating blat servers

• 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 dev, beta, RR. Select the assembly of interest, put in DNA or protein as needed and hit submit. 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 steps 4-5 for beta and the RR.