I have a couple questions about the IGV integration with Galaxy:
This site at Princeton seems to imply there's a setup process for IGV visualization of BAM files from Galaxy, but @bgruening mentioned the IGV integration ships with galaxy by default. I don't see the icon in my galaxy currently, but that might be just because I haven't labeled them as BAM files. Which is right? Do I need to follow that tutorial from Princeton?
One of the requirements of our group is to be pretty good about privacy. We don't want to have a URL from galaxy ending in access to a bam file that should be private. @bgruening mentioned that if you click the "view in IGV" button, the link to that file is only available in your localhost, but I'm not sure I understand what that means, and can't find any obvious documentation about that. Could you explain (or better yet: link to documentation for) how the IGV integration works and what happens when you click that hypothetical "display in IGV" button?
One of the major issues our collaborators are having now is that we are using an unsecured link to our bam files, but we update the link each month for security reasons. But that means each month our collaborators need to set up new "session files" and they'd rather have a stable link. Does galaxy provide a static link, to those bam files, preserving the session files each time you use IGV?
By default, this setup is not required. In the case of the linked
configuration, they have setup authentication through apache in
their proxy. This rule simply allows unauthenticated access to these
files. IGV runs as a Java webstart application on the user’s local
machine, and does not have access to the authenticated session that
is performed within the user’s web browser during login to Galaxy.
For the link to become visible for BAM files, you’ll need to have
the datatype set as BAM for the dataset and should have the dbkey
properly set. Whether or not you should follow the Princeton
tutorial depends upon the configuration of your Galaxy instance.
When user clicks the 'display' link, the user is sent with URL as a query parameter to the IGV site (usually http://www.broadinstitute.org/igv/projects/current/igv.php) along with genome build information, or in some cases a JNLP file is created directly by Galaxy and sent to the user's machine. User needs to open JNLP with javaws (manually or through browser). IGV is launched as a Java webstart application, so the link from
Galaxy is sent to the application running on the user's computer.
The user’s computer must be able to access the URL. You can e.g.
lock this down to a set of IPs in your proxy configuration, instead
of the allow all used in the Princeton configuration.
The links are stable as long as you do not change the ‘id_secret’ in
galaxy.ini. You should set this value when you first configure your
Galaxy instance. Changing this value will effectively invalidate any
links that contain a Galaxy object ID in them.