Post-Release-Checklist: Difference between revisions

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== Post Release Checklist for Known Genes ==
== Post Release Checklist for UCSC Genes ==


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


* Update the metadata in hgcentral:
* Update the metadata in hgcentral:
Line 19: Line 19:
:: Also, include the new assembly in this file: /goldenPath/proteinDB/proteinsYYMMDD/database/README.txt (and edit it out of the previous 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.




[[Category:Browser_QA]]
[[Category:Browser_QA]]

Revision as of 20:21, 28 August 2008

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/hgGeneData/$org/$db/otherOrga.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.