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: dannonba...@me.com
> Date: Wed, 13 Jun 2012 21:05:02 -0400
> CC: galaxy-dev@lists.bx.psu.edu
> To: josenavasmol...@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
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