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?