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: dannonba...@me.com
> Date: Wed, 13 Jun 2012 21:32:24 -0400
> CC: galaxy-dev@lists.bx.psu.edu
> To: josenavasmol...@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: 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
> > > > ___________________________________________________________
> > > > 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:
> > > > 
> > > > http://lists.bx.psu.edu/
> > >
> 
                                          
___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to