On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian <mheydar1@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: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial

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!