On Thu, Jan 29, 2015 at 5:02 AM, Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> wrote:

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
<najoshi@ucdavis.edu
<mailto:najoshi@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
<nate@bx.psu.edu
<mailto:nate@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
<najoshi@ucdavis.edu
<mailto:najoshi@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
<najoshi@ucdavis.edu
<mailto:najoshi@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
<najoshi@ucdavis.edu
<mailto:najoshi@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
<jmchilton@gmail.com
<mailto:jmchilton@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
<najoshi@ucdavis.edu
<mailto:najoshi@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)

___________________________________________________________
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/

___________________________________________________________
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:
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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 (w)