Genbank updates: Difference between revisions
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(New page: 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...) |
(Removed instructions to delete from /cluster/data/genbank/data/ftp (per Braney). Made the instructions generic for enabling and disabling.) |
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To disable genbank updates to an assembly: | To enable/disable genbank updates to an assembly for hgwbeta and the RR: | ||
-> in the source tree, add/remove the assembly name from these files: | |||
~/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. | and commit. (Don't comment out names; remove them. Git keeps the file edit history.) | ||
-> ssh hgwbeta | -> ssh hgwbeta | ||
-> cd ~/kent/src/hg/makeDb/genbank | -> cd ~/kent/src/hg/makeDb/genbank | ||
-> git pull | -> git pull | ||
-> make etc-update-rr | -> make etc-update-rr | ||
If you are disabling updates and you also want to remove the downloads files that are updated by the GenBank process (in the bigZips and multiz* directories on hgdownload), the genbank person will need to remove this assembly from the /cluster/data/genbank/data/ftp directory. The genbank person can also drop the files from hgdownload. | |||
==Some extra notes about Genbank tables== | ==Some extra notes about Genbank tables== | ||
The current list of Genbank tables | The current list of Genbank tables 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: | ||
hgsql -N -e 'SHOW TABLES' hg18 | egrep -f /cluster/data/genbank/etc/genbank.tbls (hgwdev) | hgsql -N -e 'SHOW TABLES' hg18 | egrep -f /cluster/data/genbank/etc/genbank.tbls (hgwdev) | ||
Revision as of 22:33, 2 July 2012
To enable/disable genbank updates to an assembly for hgwbeta and the RR:
-> in the source tree, add/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. (Don't comment out names; remove them. Git keeps the file edit history.)
-> ssh hgwbeta
-> cd ~/kent/src/hg/makeDb/genbank
-> git pull
-> make etc-update-rr
If you are disabling updates and you also want to remove the downloads files that are updated by the GenBank process (in the bigZips and multiz* directories on hgdownload), the genbank person will need to remove this assembly from the /cluster/data/genbank/data/ftp directory. The genbank person can also drop the files from hgdownload.
Some extra notes about Genbank tables
The current list of Genbank tables 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:
hgsql -N -e 'SHOW TABLES' hg18 | egrep -f /cluster/data/genbank/etc/genbank.tbls (hgwdev) hgsql -N -e 'SHOW TABLES' hg18 | egrep -f /genbank/etc/genbank.tbls (hgwbeta)
The two tables 'gbCdnaInfo' and 'gbStatus' are main tables that should contain all entries for a database.
