Genome Browser in a box config

Release

The Gbib is a Ubuntu 14 (=supported until late 2019) 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.

Updating a box

On the box, the update is started by /root/updateBrowser.sh.

By default, it updates the box to "release" state, which is the one on hgdownload, but can also update to "devbox", "alpha", or "beta" states, these can be prepared by developers or QA during testing, see Gbib release

The script updates various directories on the box:

1. cgi-bin: from hgdownload (or from hgwdev, if alpha/beta/devbox state)
2. htdocs: from hgdownload (or from hgwdev, if alpha/beta/devbox state)
3. mysql: always from hgdownload
4. additional files from a "push" directory on our servers: e.g. additional icons and the tableListAdd.*.tab files in /root. Depending on state, from hgdownload or hgwdev
5. html patches: Remove menu items, change some text. Static.
6. some mysql tables (via hgMirror): remove some tracks from search, hide some tracks, load /root/tableListAdd.* etc. Calls hgMirror for this.

Protected tracks have no state and are not updated.

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), as hgMirror includes all local post-rsync database changes.

The track tables are added manually to the box once by developers and are not changed by updateBrowser.sh.

OMIM is a copy of the OMIM tables (copied in Apr 2014).

The HGMD table is a pointer to a bigbed file on hgdownload. Our binaries include code to add a password when this file is loaded via https.

Auto updates

The updateBrowser.sh script is called by cron every five minutes. This can be changed with autoUpdatesOff and autoUpdatesOn as user "browser" (see ~browser/.bashrc).

The updateBrowser.sh script checks if a flagfile on hgdownload has changed relative to a local file. If it has not been changed, then the script just stops.

Pushing files into the box

If a CGI release requires other files, outside the cgi-bin directory, or special software on the box, these files have to be pushed into the box.

To push a file into the box, on hgwdev, copy it into /usr/local/apache/gbib/push/ in many cases you will have to create the right subdirectory. Note that /usr/local/apache/gbib/push/ is the "root" of the box. After each update, the box will rsync from /usr/local/apache/gbib/push/ into /.

You can test if this works by running as qateam on hgwdev

 boxPrepare beta 

and then on the box

 updateBrowser beta

If it works, tell the pushers to push the push directory onto hgdownload. On the next update of the box (usually Sunday), all boxes will pull the push directory into their root directory.

If an update requires an ubuntu package, you will have to add "apt-get install" commands to updateBrowser.sh.