Hi,
our galaxy is behind a firewall which seems to imply that many of the nice possibilities to use online services which download data from galaxy do not work, e.g. phinch or the UCSC browser.
Has anybody ideas for (or experience with) workarounds?
Maybe you can elaborate about these firewall issues first ? What do you mean by "do not work" ? Did you get in touch with your security team ?
For instance, biom files can be visualised at phinch. If a user clicks the link "view biom at Phinch" a new website is opened: http://www.bx.psu.edu/~dan/Phinch/index.html?biomURL=http%3A%2F%2Fbioinf2-de... so the phinch website tries to download the biom file from our local Galaxy bioinf2-dev which is behind the firewall. Similar mechanism is at work to visualize annotations at the UCSC genome browser. There is no way that our security team will open the firewall for galaxy which runs on a head node of our compute cluster.
For instance, we have a local own cloud which we might exploit, i.e., upload the data to OC and modify the link.
What kind of integration are you intending with ownCloud exactly ?
I was just thinking that one could create a tool that uploads the data set to OC, makes it publicly accessible via a link, and redirects to a website (essentially replacing the link to the galaxy by the one to OC). Cheers, Matthias