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
On Tue, Jan 27, 2015 at 4:33 PM, Nikhil Joshi <najo...@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 <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.
>> On Fri, Jan 23, 2015 at 9:34 PM, Nikhil Joshi <najo...@ucdavis.edu>
>> > 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
>> > 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
>> > 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
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
UC Davis Bioinformatics Core
najoshi -at- ucdavis -dot- edu
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