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 <najo...@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 <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. >>> >>> -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) >> > > > > -- > 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)
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