Genome Browser in a box config: Difference between revisions
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QA release instructions [[Gbib release]] | == Release == | ||
The Gbib is a Ubuntu 13 VirtualBox VM with apache, mysql and the genome browser (see [[Preparing_VirtualBox_images]]). | |||
It has a special hg.conf, uses the tableList tables in all organism DBs and loads most files from hgdownload on the fly. | |||
For QA release instructions, see [[Gbib release]] | |||
Development for the Gbib is a different business and described in [[Gbib development]]. | |||
== Protected tracks == | |||
protected tracks are tracks that are not on hgdownload but are available from the box. Currently these are OMIM and hgmd, but will hopefully include LOVD and decipher one day. | |||
These tracks are missing from the tableList table in hg19, so their tableList info is in /root/tableListAdd.hg19.tab and is added to tableList after each rsync. This is done by hgMirror, (is called from updateBrowser.sh), because hgMirror includes all post-rsync code now. | |||
The track tables are added manually to the box once and are not updated with normal auto updates. | |||
OMIM are just the normal tables, in a copy form hgwbeta from Apr 2014. | |||
The HGMD table is just a pointer to a bigbed file on hgdownload. Our binaries include code to add a password when this file is loaded via https. | |||
Revision as of 13:09, 25 April 2014
Release
The Gbib is a Ubuntu 13 VirtualBox VM with apache, mysql and the genome browser (see Preparing_VirtualBox_images). It has a special hg.conf, uses the tableList tables in all organism DBs and loads most files from hgdownload on the fly.
For QA release instructions, see Gbib release
Development for the Gbib is a different business and described in Gbib development.
Protected tracks
protected tracks are tracks that are not on hgdownload but are available from the box. Currently these are OMIM and hgmd, but will hopefully include LOVD and decipher one day.
These tracks are missing from the tableList table in hg19, so their tableList info is in /root/tableListAdd.hg19.tab and is added to tableList after each rsync. This is done by hgMirror, (is called from updateBrowser.sh), because hgMirror includes all post-rsync code now.
The track tables are added manually to the box once and are not updated with normal auto updates.
OMIM are just the normal tables, in a copy form hgwbeta from Apr 2014.
The HGMD table is just a pointer to a bigbed file on hgdownload. Our binaries include code to add a password when this file is loaded via https.
