Since there are so many surprising new details in your last mail, maybe it would help if you could tell where you got your Python from. Is it a regular system installation or a toolshed installed version inside Galaxy (which may use its own env.sh to manipulate paths) ?

Best,
Wolfgang
On 29.01.2015 11:02, Nikhil Joshi wrote:
Ok, a little more progress. This is really strange. It seems that it is
only python that is not getting LD_LIBRARY_PATH, and it only doesn't get
it if it is being invoked by a user (i.e. not root). If root invokes
python then it gets the variable no problem. If the galaxy user invokes
it, it does not get it. However, if the galaxy user invokes perl and
prints LD_LIBRARY_PATH, it is there?!?!? I should mention that this
Galaxy is being run on an Amazon AMI. Is there some weird security thing
where *specifically* python does not get LD_LIBRARY_PATH?

- Nik.

On Wed, Jan 28, 2015 at 4:33 PM, Nikhil Joshi
<najo...@ucdavis.edu
<mailto:najo...@ucdavis.edu>> wrote:

    Well we are using the "environment_setup_file" option in our
    galaxy.ini file. Supposedly we can point to a shell script that will
    be sourced before running each job. In this script we load all of
    the environment variables using modules. The paths are all correct
    after this runs. However, the python script that is run (from the
    XML for the cufflinks tool) does not inherit these environment
    variables correctly. Below is the content of our env.sh script:

    #!/bin/bash
    . /etc/profile.d/modules_sh.sh
    module load meta/galaxy

    This definitely loads the environment properly. And here is the
    cufflinks line from the XML:

        <command interpreter="python">
             cufflinks_wrapper.py
                 --input=$input
    ..... etc.

    This cufflinks wrapper fails because it cannot actually run
    cufflinks because it cannot find a library that it needs, because
    the LD_LIBRARY_PATH is empty within its environment. I actually
    edited the XML to echo the load path to a file before the python
    script runs and the path was fine, but still the python script
    doesn't inherit it properly.

    - Nik.

    On Wed, Jan 28, 2015 at 6:16 AM, Nate Coraor
    <n...@bx.psu.edu
    <mailto:n...@bx.psu.edu>> wrote:

        Hi Nik,

        Is there any chance that $LD_LIBRARY_PATH is being set in the
        parent shell but not exported?

        --nate

        On Wed, Jan 28, 2015 at 7:04 AM, Nikhil Joshi
        <najo...@ucdavis.edu
        <mailto:najo...@ucdavis.edu>> wrote:

            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
            <mailto: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
                <mailto: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
                    <mailto: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
                        <mailto: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 <tel: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 <tel: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 <tel: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 <tel: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 <tel: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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