Ensembl QA

There are periodic updates to all Ensembl Genes tracks in all dbs. Here is a list of things to do in addition to the regular QA you would do normally for a track:

• Run 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.

• All Ensembl builds are documented in the single file:

   src/hg/makeDb/doc/makeEnsembl.txt

• If it is the first assembly, however, it will rather be documented in the assembly.txt make document.

   /kent/src/hg/makeDb/doc/nameAssembly.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
  • The latest entry in the hgFixed.trackVersion table should have "current" in the dateReference field and the previous entry needs to have the dateReference field updated to whatever month the last Ensembl release was dated.
  • Before you push the hgFixed.trackVersion table (2017 NOTE - likely QA should NOT push the entire table as there may be rows in this table that are in development and should not yet be on the rr. Check with an engineer if you have a row that needs to get to the rr), check (using the compareWholeTable.csh script) that you aren't pushing changes that aren't ready to go out yet. For instance, if there are changes to an unrelated track, you will need to check with the person who made the changes to see if it is okay to push the changes. If it is not, the timing of the push should be coordinated or the trackVersion table should be edited on hgwbeta to exclude the changes that are not ready to go out.
  • Hiram has said to not worry about pushing entries for the COSMIC track in the hgFixed.trackVersion table. The COSMIC track is otto updated on the RR, but the version number updates in hgFixed.trackVersion table aren't automatically pushed to the RR. Hiram said he expects these COSMIC version number updates to be pushed along with the Ensembl Genes updates. (From Hiram's comment in Redmine #11675 note-74)

• Note: You also need to update the blastTabs if the zebrafish assembly used in hgGene got new Ensembl Genes. Talk to Brooke or Mary if this is case.

• Note: See the issue from this RM MLQ regarding a missing joiner rule. The ensemblToGeneName table should be linked to ensGene.