Dannon, Thanks. I can't believe I didn;t see that, I've read the Cloud setup page a dozen times while getting familiar with Cloudman. I guess you skip what you don;t need at the time :=( Greg On Sat, Jan 7, 2012 at 11:20 PM, Dannon Baker <dannonbaker@me.com> wrote:

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. gedwards2@gmail.com

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-- Greg Edwards, Port Jackson Bioinformatics Consulting. gedwards2@gmail.com