Gbib development

This page is for developers, it's not relevant for QA. The QA page is Genome_Browser_in_a_box_config.

The devbox listens to http on 1236 and for ssh on 1237.

Box-specific development can happen on the devbox, a development version of the browserbox with git, gcc etc. For testing during development, a special command on the box can pull in the CGIs that were compiled on the devbox.

(sidenote: All virtual machines live in qateam/VirtualBox VMs/. The central virtualbox xml config file where they are registered is ~/.config/VirtualBox/VirtualBox.xml )

To start the devbox, you need to login as qateam onto hgwdev.

From hgwdev, you can then connect to the box with "ssh devbox". This works, because of the .ssh/config file:

 Host devbox
 Hostname localhost
 Port 1237
 User browser

You can start and stop browserbox-dev with the aliases devStart and devStop.

typical development cycle

start browserbox-dev:

 devStart

connect + git pull + compile:

 ssh devbox
 compileCgis

You can now test the CGIs on port 1236 of hgwdev. You can also hack on the /home/browser/kent directory and e.g. run makes in there.

Typically, you will need to add hReplaceGbdb instead of cloneString at places where files in /gbdb are opened.

To do a more realistic test, the alpha binaries can also be put into the final browserbox.

To copy the alpha binaries into the browserbox: Copy them from the devbox to alpha distribution rsync server directory (this command is defined in qateam's .bashrc) by running this command as qateam on hgwdev while the devbox is running (this will ssh into the devbox and rsync the binaries onto hgwdev):

 boxUpdateAlpha

Now start the browserbox and pull the alpha binaries from the rsync server:

 boxStart
 ssh box
 updateBrowser alpha

You can now use the alpha CGIs on port 1234 of hgwdev or use ssh port forwarding to access them from localhost:1234.

When you're done: stop the development box:

 devStop

Pushing your changes to hgwdev

Direct - easier: set username for kent repo:

 cd kent
 git remote set-url origin ssh://YOURUSERNAME@hgwdev.cse.ucsc.edu/data/git/kent.git/
 git push
 # Don't forget to set it back to the public repo.
 git remote set-url origin git://genome-source.cse.ucsc.edu/kent.git

Indirect: simply rsync or scp to copy into your own homedir on hgwdev and commit there:

 rsync file USER@hgwdev:kent/PATH/FILE
 logout