Okay, we fixed that problem, but another tool is now having the same problem. Now I am trying to run cufflinks and I am getting that same error, but this time there is yet another layer of abstraction because the XML is calling a python script. It seems like the LD_LIBRARY_PATH is correct right up until the python wrapper script gets called and then for some reason the environment is not being passed to the script. This seems like a problem with Popen somewhere in galaxy where it is not passing the environment to the subprocess?....

- Nik.

On Tue, Jan 27, 2015 at 4:33 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:

Hi John,

Thanks for your reply. Our sys admin figured out the problem.... we had to use the "environment_setup_file" option to load the modules and we had to fix some shell issues where galaxy was using the dash shell instead of bash. Anyways, it's fixed for now!

- Nik.

On Mon, Jan 26, 2015 at 6:43 AM, John Chilton <jmchilton@gmail.com> wrote:
Had some idea but they were all dead ends. How are you sourcing the
modules - in Galaxy's environment, using an environment file, using
Galaxy dependencies (env.sh files) or using Galaxy's modules support?
Do you have an example of such a module that sets LD_LIBRARY_PATH?

One thing to check is the Galaxy's .bashrc file - make sure it isn't
resetting LD_LIBRARY_PATH somehow.

-John

On Fri, Jan 23, 2015 at 9:34 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
> Hi all,
>
> So we have forked the stable branch of galaxy and are making our own
> modifications. We are running galaxy on Ubuntu 14.04.1 LTS and we're using
> modules to load the underlying software, i.e. set environment variables.
> This works just fine for PATH, JAVA_JAR_PATH, PYTHONPATH, etc., however,
> LD_LIBRARY_PATH is not being passed to the tools. When a tool (such as
> cuffdiff) tries to access LD_LIBRARY_PATH, it is empty. We've checked to
> make sure that loading the cufflinks module correctly updates the
> LD_LIBRARY_PATH, however, when it is used in galaxy, all the other
> environment variables are set properly, but not LD_LIBRARY_PATH. Does anyone
> have any ideas on why this would happen and how to fix it?
>
> - Nik.
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
>

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--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)