Genbank updates: Difference between revisions
From genomewiki
Jump to navigationJump to search
No edit summary |
(change procedure due to switch to git) |
||
| Line 11: | Line 11: | ||
~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs | ~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs | ||
~/kent/src/hg/makeDb/genbank/etc/rr.dbs | ~/kent/src/hg/makeDb/genbank/etc/rr.dbs | ||
and commit. Please remove the name, don't comment it out, git keeps the file edit history. | |||
-> ssh hgwbeta | -> ssh hgwbeta | ||
-> cd /genbank | -> cd ~/kent/src/hg/makeDb/genbank | ||
-> | -> git pull | ||
-> make etc-update-rr | |||
-> cd to /cluster/data/genbank/data/ftp/${assembly} | -> cd to /cluster/data/genbank/data/ftp/${assembly} | ||
-> remove /cluster/data/genbank/data/ftp/${assembly} | -> remove /cluster/data/genbank/data/ftp/${assembly} | ||
Revision as of 00:46, 16 June 2010
To disable genbank updates to an assembly:
In addition to removing the assembly name from the hgwbeta.dbs and rr.dbs files, the files here need to be removed:
/cluster/data/genbank/data/ftp/
Otherwise the genbank files will keep reappearing.
So, to disable a genome:
-> on hgwdev remove the assembly name from these files:
~/kent/src/hg/makeDb/genbank/etc/hgwbeta.dbs
~/kent/src/hg/makeDb/genbank/etc/rr.dbs
and commit. Please remove the name, don't comment it out, git keeps the file edit history.
-> ssh hgwbeta
-> cd ~/kent/src/hg/makeDb/genbank
-> git pull
-> make etc-update-rr
-> cd to /cluster/data/genbank/data/ftp/${assembly}
-> remove /cluster/data/genbank/data/ftp/${assembly}
-> remove files on hgdownload by sending a push request to drop this directory and its contents:
/usr/local/apache/htdocs/goldenPath/${assembly}