Ok, I will change my XML files. I've another question. When I customize my cluster, I can make this customizations permanent through the CloudMan management console. We are trying to customize the Galaxy instance with our tools and then make an AMI public where the users can use our tools through the Galaxy interface. What should I do to create this AMI? Thanks,Jose
Subject: Re: [galaxy-dev] CloudMan: Command not found From: dannonbaker@me.com Date: Wed, 13 Jun 2012 21:32:24 -0400 CC: galaxy-dev@lists.bx.psu.edu To: josenavasmolina@hotmail.com
You can probably modfiy /home/galaxy/.sge_request to make it work for now, but for portability of tools I'd still recommend the <requirements> tag. Changes to .sge_request will not be persisted after shutdown, so you'll have to redo it with each new cluster.
On Jun 13, 2012, at 9:25 PM, Jose Navas wrote:
Hi Dannon,
thank you for your help. I've tried the <requirements> tag option with the 'env.sh' script. I have added ~100 XML files... there isn't any option to modify the environment variables directly? If not I will modify all my XML files....
thanks!
Jose
Subject: Re: [galaxy-dev] CloudMan: Command not found From: dannonbaker@me.com Date: Wed, 13 Jun 2012 21:05:02 -0400 CC: galaxy-dev@lists.bx.psu.edu To: josenavasmolina@hotmail.com
Instead of modifying the environment variables directly, I've found it easier to use Galaxy's built in tool dependency framework. All you'd have to do is add a <requirements type="package"> tag to your custom tools to specify the package directory that needs to be checked at runtime.
See http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies, specifically the "Managed Tool Dependencies" section. Many of the other tools on the cloud volume use the 'env.sh' method discussed there. For example, blast has the 'blast' package requirement, and in the /mnt/galaxyTools/blast/default directory you'll find an 'env.sh' file that configures the environment at runtime.
-Dannon
On Jun 13, 2012, at 8:49 PM, Jose Navas wrote:
Hi Galaxy Team,
I'm modifying my Galaxy CloudMan instance by adding custom tools. I've installed my tools under the /mnt/galaxyTools/tools folder and I've modified the .bashrc files from the sgeadmin and galaxy users to add the needed paths to the PATH and PYTHONPATH variables. When I'm in Galaxy and I try to launch one of my tools, it fails and shows the 'Command not found' error.
Where I should add the paths to make Galaxy now where are my executables?
Whan I log into the isntance through ssh and I use the galaxy user, it knows where are my executables.
What I'm missing?
Thanks, Jose ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: