Hello Enis,

Many thanks for your reply.
I've made some progress: the middle pane view works if I start galaxy with 
--deamon. I have figured out that I can test modifying the tools xml  files 
(e.g. adding options).

Now I am having issues with not being able to unmount /mnt/galaxyTools (step 
3). It keeps complaining that the device is busy. - I check first all my 
windows that I am not accessing that directory
- "lsof" shows nginx processes running under user galaxy. I kill all of them. 
Still can't unmount.
- tried force unmount. Still no luck.

Any ideas?

Isabelle

> -----Original Message-----
> From: Enis Afgan [mailto:eaf...@emory.edu]
> Sent: Friday, March 11, 2011 4:42 PM
> To: Isabelle Phan
> Cc: galaxy-dev@lists.bx.psu.edu; Gowthaman Ramasamy
> Subject: Re: [galaxy-dev] testing updates on Galaxy CloudMan
> 
> Hi
> Isabelle,
> There is nothing special on the instance of Galaxy deployed through CloudMan, 
> so
> any changes performed to the configuration of Galaxy should be tested the same
> way they would be tested if they were installed on a local system. That said, 
> if there
> are system dependencies that need to be satisfied for some of the 
> functionality to
> work, the update is more complicated because it would, most likely, involve 
> creation
> of a new AMI. Especially if the mentioned functionality is not working on the 
> default
> instance of CloudMan, we should work out the issue and release a new CloudMan
> AMI that fixes the underlying problem. I'll test the functionality you 
> mentioned on a
> new instance of Galaxy CloudMan and help you resolving the issues.
> 
> Enis
> 
> 
> On Fri, Mar 11, 2011 at 5:32 PM, Isabelle Phan 
> <isabelle.p...@seattlebiomed.org>
> wrote:
> 
> 
>       I am at step 2 of Galaxy CloudMan deployment.
>       "Now, manipulate Galaxy as desired."
> 
>       How do I test that my updates are working before proceeding to step 3?
> 
>       I assumed I could just type 'run.sh'. This starts Galaxy but:
>       - fasta files do not display in the middle pane
>       - png images generated by e.g. boxplot do not display in the middle pane
>       - saving images does not work (get empty file)
> 
>       I need to know how people are customizing their cloud instance of 
> galaxy. If
> it is NOT possible to test modifications in the usual way PLEASE would 
> somebody
> simply confirm?
> 
>       I really would appreciate a response.
> 
> 
>       Isabelle
>       --
>       Isabelle Phan, DPhil
>       Seattle Biomedical Research Institute
>       +1(206)256 7113 <tel:%2B1%28206%29256%207113>
> 
> 
> 
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