BLAT Switch Test Protocol

ID Test Name Action Expected Result
1 Identify test cases Working on RR, use the Refseq track. Follow cross-link to NCBI, obtain nucleotide and protein sequences. Get BLAT results (can use default settings including BLAT's guess). Observe expected BLAT results. If PCR server is also in use, obtain primer sequences (can use STS Markers or look them up in UniSTS). Or simply copy/paste some DNA from GET DNA on our browser about 25 bases long and 1 kb apart. Nucleotide search may have multiple matches; best match should be to Refseq annotation position. Protein match will likely have just one match to coding region of annotation.
2 Test on hgwdev. Change BLAT server in use on hgwdev: hgsql hgcentraltest
  • UPDATE blatServers SET host="$host" WHERE db="$db";
  • UPDATE blatServers SET port ="$port" WHERE db = "$db" AND isTrans = 1;
  • UPDATE blatServers SET port ="$port" WHERE db = "$db" AND isTrans = 0;
  • Execute test cases.
    BLAT results as expected.
    3 Test on hgwbeta Change BLAT server in use on hgwbeta: hgsql hgcentralbeta
    • Use above SQL commands.
    • Execute test cases.
    BLAT results as expected.
    4 Test on RR. Change BLAT server in use on RR: hgsql -h genome-centdb hgcentral
    • Use above SQL commands.
    • Execute test cases.
    BLAT results as expected.
    5 Update mirror site
    http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql
    • cd /cluster/bin/build/scripts
    • source buildEnv.csh
    • buildHgCentralSql.csh
    • buildHgCentralSql.csh real
    • do the push request for /usr/local/apache/htdocs/admin/hgcentral.sql from hgwdev to hgdownload
    6 Cleanup Notify Jorge.