Recommended Track Sets

This page describes the Recommended Track Sets feature (http://redmine.soe.ucsc.edu/issues/25601). This includes the process of making a new track set and releasing to the RR.

This setting is controlled by an hg.conf setting:

vim /usr/local/apache/cgi-bin/hg.conf
# Recommended track sets
browser.recTrackSets=on

Without this setting, the feature will be unavailable.

Initial steps - Dev

In order to make a new track set, you will want to start with a session. This can be made on any user. For example, I will start with the following session on dev:

• User: Lou
• Session name: SNVs Clinical

Note: When there is a space in the name, that gets encoded to %20. So the way this session is actually stored is SNVs%20Clinical

Here is an example of looking up the user/name of this session of hgCentralTest:

$ hgsql -e "select sessionName from namedSessionDb where userName='Lou' and sessionName like 'SNV%'" hgcentraltest
+-----------------+
| sessionName     |
+-----------------+
| SNVs%20Clinical |
+-----------------+

Once you have the session, you will want to transfer it to the View user. The credentials for this GB user can be found in the following file:

ssh qateam@hgwdev
grep -A 1 "View" googleHangoutStepsPassword

In order to transfer the session, log in as the View user and use the Restore Settings option to load a session from the original user, in this case user Lou and session name SNVs Clinical. Once you load the session, save it under the same name. Now the same session should exist under the View identity.

The next step is to add the session to the recommended track sets .tab file. This is the file that holds all the sessions that pop up in the recommended track sets menu. The file is in the following location:

~/kent/src/hg/htdocs/inc/recTrackSets.hg19.tab

Note that currently track sets only exist for hg19, but the file for any other db would follow the same format except with the respective assembly db in the file name.

This file is under version control, so you will want to pull in changes before editing. This is a tab-separated file, and has the following format: label, userName, sessionName, description. It is important to separate the fields with a tab, or it may break the database hgTracks. In vim, a tab character can be added with ctrl+v then tab. The vim command :set list will display the file tabs shown as ^I (so you can check your work). For the above example, the session would be added with the following entry:

Clinical SNVs   View    SNVs%20Clinical Assess potential disease contributions of single nucleotide variants in coding regions

The description provided will show up in the recommended track sets menu, and the order of the file will reflect the order in the menu. At this point a make on the htdocs directory can be done, and the new session should show up on dev. At the moment, sessions should all belong to the View user. Once complete, do not forget to commit and push the changes.

Beta

Once a make beta is done on htdocs with an updated .tab file, the track set should appear on the respective database on beta. However, clicking on it will lead to an error if the session has not been transferred to beta under the View user.

The following steps describe how to take the session from dev to beta, which will then be the same in the RR + mirrors:

• Login to the View user on dev, load the session of interest, go back to hgSession, and Save current settings to a local file
• Login to the View user on beta, Restore Settings using Use settings from a local file:, and upload the file from the previous step
• Make a new session with the same name from the uploaded file. The session from dev and beta should be identical - user (view), name, and contents

At this point the track set should load without issues from beta. Keep in mind if the title or user names are different, then they will not match the .tab file, and the track set will yield an error.