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.
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
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
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