switch tool_conf.xml

[Franziska D]

Hi Brad & colleagues, 

Firstly, thanks a lot for setting up this awesome tool for the research community! 

As a linux novice, I have a really basic question & I apologies for bothering you with this -- but maybe it will help other people that are similarly clueless...

Basically, I am running your galaxy/cloudbiolinux ami via biocloudcentral and everything is working very well - the only thing is that I actually would like some extra tools on galaxy, e.g. tophat2 (which i see in the command line is already installed) and deseq2. 

My question is: how do i start a different galaxy instance, ideally through the web-browser "access galaxy" link or from the command line? I can see that there are different tool_conf.xml files already uploaded and that all the different tophat2 versions are there. I simply do not know how to use them...

I assume once I can do that, I can also add new tools like deseq2 through editing the relevant tool_conf file?

Thank you and all the best, 

Fran

[Enis Afgan]

Hi Fran,

If you ssh into your instance, it should be possible to change the symlink path for tophat (in /mnt/galaxy/tools/tophat) so the 'default' directory points to tophat2 (possibly installing tophat2 if it is not already there). This also needs to be matched with the tophat2 wrapper in Galaxy, which can be installed via the Tool Shed right from the Galaxy Admin panel. Alternatively, you can manually edit /mnt/galaxy/galaxy-app/tool_conf.xml and add a tophat2 entry for the wrapper you've installed manually in /mnt/galaxy/galaxy-app/tools/.

Hope this helps,

Enis

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[Franziska D]

Hi Enis, 

Thanks a lot for your super-fast reply! I will have a go!

Best wishes,

Fran

[Franziska D]

Hi Enis, 

It's me again - sorry...

I went for a seemingly simpler way of adding tools to the Galaxy instance in the end: I simply added my account name to admin user panel and then added the tools through the galaxy toolshed on the web interface. They install fine, but now it seems that they don't consistently show up in the tool panel: sometimes they show after I refresh and then they disappear again...any idea of what I am doing wrong? 

Thanks!

[Dannon Baker]

Hey Fran,

Using the cloudman admin console, restart the galaxy service after installing a tool.  Galaxy now runs multiple web processes by default and this will force them all to reload (and you'll see a consistent toolbox).  There's a fix in the works for this, but for now restarting is the simplest way forward.

-Dannon

[Franziska D]

Hi Dannon, 

Wow thanks, that was superquick!

All the best, 
Fran