On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian <mheyd...@jhmi.edu>wrote:

> Hi Dannon,
> Thanks for this information. Will the ENA SRA button be enabled on the
> next update of Cloudman?

I'll check to make sure there wasn't a good reason to remove it (couldn't
find one in my first pass, and it's available on main, so it should be in
the cloud), but yes.

Is there a protocol (or help page) available for how to re-enable tools in
> the 'tool_conf.xml'?

With everything headed to the toolshed, hopefully this is a thing of the
past very soon.  The only documentation I found on the wiki is here:

In short, you'll need to:

1) ssh to your cloud galaxy instance
2) navigate to /mnt/galaxy/galaxy-app
3) open tool_conf.xml in your favorite editor, and add the line below,
exactly, in the Get Data section (the first one, begins on line 3):

 <tool file="data_source/ebi_sra.xml" />

4) Close down ssh,
5) In a web browser, go to the cloud admin panel and click restart for the
Galaxy service.

> One of the great things about Galaxy Cloudman is that someone who doesn't
> know programming (myself and many other biologists and clinicians) can
> seamlessly use the platform. Unfortunately, when trivial issues arise where
> the solution is to insert a line or two of code in the universe of Galaxy
> Cloudman people like me are stymied and really don't even know where to
> start.  I know it requires work at some level, but a tutorial on "how to
> find your 'tool_conf.xml'" (or "dummies guide to quick Cloudman fixes")
> would likely be helpful to many end users (including myself).

We definitely do try to make it as ready-to-go out of the box as possible,
but that's a great idea.  I'll try to document this better.

> Thanks again, Dannon!

Anytime, thanks for your patience and for using Galaxy/Cloudman!
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