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
> Subject: Re: [galaxy-dev] CloudMan: Command not found
> From: dannonba...@me.com
> Date: Wed, 13 Jun 2012 21:05:02 -0400
> CC: email@example.com
> 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
> 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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