KnownGene build

Initialize work directory

• Create and cd into work directory of the form /hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
• Start a screen.
• Copy buildEnv.sh from previous build on this db

Setting environment variables

The environment variables used in the build are set in the script buildEnv.sh. All the other scripts assume that this script has been sourced in the current shell.

Adding IsPcr server

After building /gbdb/$db/targetDb/${db}KgSeq${curVer}.2bit, which happens in the buildCore.sh script run at the beginning of the process, ask cluster-admin to start an untranslated, -stepSize=5 gfServer on /gbdb/$db/targetDb/${db}KgSeq${curVer}.2bit

 to cluster-admin

 Hey my friends,
 
 Could you please start an untranslated -stepSize=5 production gfserver
 with this 2bit file?
 
 hgwdev:/gbdb/mm39/targetDb/mm39KgSeq13.2bit
 
 thanks!
 brian

On hgwdev, insert new records into blatServers and targetDb, using the host (field 2) and port (field 3) specified by cluster-admin. Identify the blatServer by the keyword "$db"Kg with the version number appended

cluster-admin will say something like this:

 Starting untrans gfServer for mm39KgSeq13 on host blat1b port 17921

Add this info to blatServers and targetDb tables in hgcentral.

  hgsql hgcentraltest -e \
     'INSERT into blatServers values ("mm39KgSeq13", "blat1c", 17921, 0, 1,"");'
  hgsql hgcentraltest -e \
           'INSERT into targetDb values("mm39KgSeq13", "GENCODE Genes", \
                    "mm39", "kgTargetAli", "", "", \
                             "/gbdb/mm39/targetDb/mm39KgSeq13.2bit", 1, now(), "");'