To answer your questions from above, in case it can help with this new problem, we are sourcing the modules from an "env.sh" script whose full path is the value of the "environment_setup_file" option. This fixed our first problem, but not this second one. We created the modules ourselves for each of the programs.

- Nik.

On Tue, Jan 27, 2015 at 6:45 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:

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)

--

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

___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/