Ensembl QA

There are periodic updates to all Ensembl Genes tracks in all dbs.

• A good script to run that checks many things is checkEnsembl.sh.
  • This script doesn't even seem to be isntalled for me. Maybe it is worth investigating?

• An even better script (in that it runs) is qaEnsGenes.csh
  • Run it before you push to beta, as it compares dev to beta. You'll lose that comparison if you push too soon. Not that I ever did that.

• All Ensembl builds are documented in the single file:

   src/hg/makeDb/doc/makeEnsembl.txt

• You can find all ensembl gene builds in:

   /hive/data/genomes/<db>/bed/ensGene.NN/

where NN is the ensembl version number.

• To get the links to go to the correct place at Ensembl, you will have to check for the appropriate rows in trackVersion table in hgFixed database
  • Basically, lines from trackVersion need to be copied over into the different hgFixed dbs as you go along.
    • You can also manipulate the dates so the current version says 'current'. However, that does not seem to be a rule. Look in hgFixed. You'll see.