Ensembl QA: Difference between revisions
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(Removing Category:Browser_QA (it's now in Category:Browser QA tracks)) |
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There are periodic updates to all Ensembl Genes tracks in all dbs. | There are periodic updates to all Ensembl Genes tracks in all dbs. | ||
*A good script to run that checks many things is checkEnsembl.sh. | *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: | *All Ensembl builds are documented in the single file: | ||
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*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 | *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. | |||
[[Category:Browser QA tracks]] | [[Category:Browser QA tracks]] | ||
Revision as of 17:25, 26 July 2010
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.
- Basically, lines from trackVersion need to be copied over into the different hgFixed dbs as you go along.
