Hi Greg,

In order to install custom tools you'll need to SSH into a running instance, 
install your tool and make any modifications to Galaxy you need in order to use 
it, and then use the "Persist changes to file system" option in the Cloudman 
administration panel.  By default, Cloudman discards and simply recreates from 
snapshot the galaxyTools and galaxyData volumes when an instance is relaunched, 
but this persistence command will make a snapshot specific to your instance 
that will be used going forward.

Here's a wiki link for more info: 
http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud

Let me know if you have any other questions, and good luck!

-Dannon



On Jan 6, 2012, at 7:28 PM, Greg Edwards wrote:

> Hi Folks,
> 
> I could use some help on adding a tool to the cloud version of Galaxy. The 
> Cloud startup process creates, among other things, 
> /mnt/galaxyTools/galaxy-central which has tools_conf.xml, and subdir tools 
> etc. This seems not accessible before starting the cloud. I assume I need to 
> add my tool into the structure as per a local Galaxy instance, and then get 
> Galaxy to restart, or re-read it's config ? Would appreciate some advice 
> there.
> 
> Just as background .. I have got a custom proteomics Perl script running ok 
> under a local version of Galaxy on Mac. Added in to tools_conf.xml, tools 
> etc. Made several mods to the Perl to stop any writing to stderr except for 
> fatal show-stopper errors, everyone seems to hit that one, and other small 
> things to make it play better with Galaxy. Also quite familiar with AWS EC2, 
> have been using that for a while.
> 
> I have Galaxy Cloudman running well, start/stop extra servers etc. Using the 
> free t1.micro AMI for now, slowish but ok for testing. Or a Spot Instance of 
> m1.large when I'm impatient.
> 
> I couldn't find the answer in a search of Galaxy archives, apologies if it's 
> there, or obvious in some other way.
> 
> Thanks!
> 
> -- 
> Greg Edwards,
> Port Jackson Bioinformatics Consulting.
> gedwar...@gmail.com
> 
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___________________________________________________________
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