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 <jmchil...@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 <najo...@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)
> >
> > ___________________________________________________________
> > 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/
>



-- 
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/

Reply via email to