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| To disable genbank updates to an assembly:
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| In addition to removing the assembly name from the hgwbeta.dbs and rr.dbs files, the files here need to be removed:
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| /cluster/data/genbank/data/ftp/
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| Otherwise the genbank files will keep reappearing.
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| So, to disable a genome:
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| -> on hgwdev remove the assembly name from these files:
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| ~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs
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| ~/kent/src/hg/makeDb/genbank/etc/rr.dbs
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| and commit. Please remove the name, don't comment it out, git keeps the file edit history.
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| -> ssh hgwbeta
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| -> cd ~/kent/src/hg/makeDb/genbank
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| -> git pull
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| -> make etc-update-rr
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| -> cd to /cluster/data/genbank/data/ftp/${assembly}
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| -> remove /cluster/data/genbank/data/ftp/${assembly}
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| -> remove files on hgdownload by sending a push request to drop this directory and its contents:
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| /usr/local/apache/htdocs/goldenPath/${assembly}
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| ==Some extra notes about Genbank tables==
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| The current list of Genbank tables (curated by Mark Diekhans) is located at hgwdev:/cluster/data/genbank/etc/genbank.tbls (also located at hgwbeta:/genbank/etc/genbank.tbls). All tables in the list up to 'gbLoaded' must exist; those after 'gbLoaded' are optional. To get a list of those tables included in a database (using hg18 as an example), do:
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| hgsql -N -e 'SHOW TABLES' hg18 | egrep -f /cluster/data/genbank/etc/genbank.tbls (hgwdev)
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| hgsql -N -e 'SHOW TABLES' hg18 | egrep -f /genbank/etc/genbank.tbls (hgwbeta)
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| The two tables 'gbCdnaInfo' and 'gbStatus' are main tables that should contain all entries for a database.
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| [[Category:Browser QA]]
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