Post-Release-Checklist

Post Release Checklist for UCSC Genes

This page capture the things to remember after the release of UCSC Genes for the new assembly.

• Update the metadata in hgcentral:

set hgNearOk and hgPbOk = 1 in the dbDb table.

change defaultDb to the new assembly.

add a record in the gdbPdb table that points the assembly to the recent protein database.

• Check to see if otherOrgs.ra file is updated for this assembly in:

kent/src/hg/hgGene/hgGeneData/$org/$db/otherOrgs.ra

• For human, mouse and rat ask for a push of:

/usr/local.apache/htdocs/knownGeneList/$db/*

from hgwdev --> /usr/local/apache/htdocs/knownGeneList/

/usr/local/apache/htdocs/knownGeneLists.html (update this file to point to the new assembly)

from hgwdev --> /usr/local/apache/htdocs/

on all 8 RR machines and MGC

• Add the link to the protein database /goldenPath/proteinDB/proteinsYYMMDD/database/ in:

downloads.html file

Also, include the new assembly in this file: /goldenPath/proteinDB/proteinsYYMMDD/database/README.txt (and edit it out of the previous file).

• Alert Ensembl:

Please e-mail this information to Glenn Proctor <glenn@ebi.ac.uk> and cc Ewan Birney <birney@ebi.ac.uk>. They would like UCSC Gene IDs, and coordinates and/or sequences. One problem is that they handle randoms differently to us and display individual scaffolds instead of an artificially created random chromosome like we do. We might also send them the knownToEnsembl table, too.