LD_LIBRARY_PATH not exporting to galaxy

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LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
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
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Re: LD_LIBRARY_PATH not exporting to galaxy

John Chilton-4
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 <[hidden email]> 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/
___________________________________________________________
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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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]> 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
> <a href="tel:530.752.2698" value="+15307522698">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)

___________________________________________________________
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/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> <a href="tel:530.752.2698" value="+15307522698" target="_blank">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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> <a href="tel:530.752.2698" value="+15307522698" target="_blank">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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> <a href="tel:530.752.2698" value="+15307522698" target="_blank">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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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:
  http://galaxyproject.org/search/mailinglists/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> <a href="tel:530.752.2698" value="+15307522698" target="_blank">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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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)

___________________________________________________________
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/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> <a href="tel:530.752.2698" value="+15307522698" target="_blank">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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Wolfgang Maier
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
> <[hidden email]
> <mailto:[hidden email]>> 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
>     <[hidden email]
>     <mailto:[hidden email]>> 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
>         <[hidden email]
>         <mailto:[hidden email]>> 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
>             <[hidden email]
>             <mailto:[hidden email]>> 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
>                 <[hidden email]
>                 <mailto:[hidden email]>> 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
>                     <[hidden email]
>                     <mailto:[hidden email]>>
>                     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
>                         <[hidden email]
>                         <mailto:[hidden email]>> 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)
>                          >
>                          >
>                         ___________________________________________________________
>                          > 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 <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:
  http://galaxyproject.org/search/mailinglists/
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
It is a regular system installation. Just for a sanity check, I checked the md5 hash with the same version of my local python and it is the same. Also, as a sanity check, I ran the tests on my local machine and python got the LD_LIBRARY_PATH variable just fine, both as a regular user and as root. I thought that maybe it was an apparmor thing, but usually that logs when it denies an application, and I didn't find anything in the logs.
- Nik.

On Thu, Jan 29, 2015 at 5:02 AM, Wolfgang Maier <[hidden email]> 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
<[hidden email]
<mailto:[hidden email]>> 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
    <[hidden email]
    <mailto:[hidden email]>> 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
        <[hidden email]
        <mailto:[hidden email]>> 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
            <[hidden email]
            <mailto:[hidden email]>> 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
                <[hidden email]
                <mailto:[hidden email]>> 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
                    <[hidden email]
                    <mailto:[hidden email]>>
                    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
                        <[hidden email]
                        <mailto:[hidden email]>> 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
                         > <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">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
                    <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)




                --
                Nikhil Joshi
                Bioinformatics Analyst/Programmer
                UC Davis Bioinformatics Core
                http://bioinformatics.ucdavis.edu/
                najoshi -at- ucdavis -dot- edu
                <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)




            --
            Nikhil Joshi
            Bioinformatics Analyst/Programmer
            UC Davis Bioinformatics Core
            http://bioinformatics.ucdavis.edu/
            najoshi -at- ucdavis -dot- edu
            <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">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
    <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)




--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)


___________________________________________________________
Please keep all replies on the list by using "reply all"
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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)

___________________________________________________________
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Re: LD_LIBRARY_PATH not exporting to galaxy

Nikhil Joshi-2
We finally figured it out. It was because we are running our galaxy on port 80, so we needed to give python the permission to bind to port 80. We used setcap to do this, however, if one is giving permission to bind to a privileged port, setcap make it so that LD_LIBRARY_PATH is removed from the passed environment variables. That nearly drove us all crazy, but it works now! :)
- Nik.

On Thu, Jan 29, 2015 at 3:24 PM, Nikhil Joshi <[hidden email]> wrote:
It is a regular system installation. Just for a sanity check, I checked the md5 hash with the same version of my local python and it is the same. Also, as a sanity check, I ran the tests on my local machine and python got the LD_LIBRARY_PATH variable just fine, both as a regular user and as root. I thought that maybe it was an apparmor thing, but usually that logs when it denies an application, and I didn't find anything in the logs.
- Nik.

On Thu, Jan 29, 2015 at 5:02 AM, Wolfgang Maier <[hidden email]> 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
<[hidden email]
<mailto:[hidden email]>> 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
    <[hidden email]
    <mailto:[hidden email]>> 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
        <[hidden email]
        <mailto:[hidden email]>> 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
            <[hidden email]
            <mailto:[hidden email]>> 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
                <[hidden email]
                <mailto:[hidden email]>> 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
                    <[hidden email]
                    <mailto:[hidden email]>>
                    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
                        <[hidden email]
                        <mailto:[hidden email]>> 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
                         > <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)
                         >
                         >
                        ___________________________________________________________
                         > Please keep all replies on the list by using
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                    --
                    Nikhil Joshi
                    Bioinformatics Analyst/Programmer
                    UC Davis Bioinformatics Core
                    http://bioinformatics.ucdavis.edu/
                    najoshi -at- ucdavis -dot- edu
                    <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)




                --
                Nikhil Joshi
                Bioinformatics Analyst/Programmer
                UC Davis Bioinformatics Core
                http://bioinformatics.ucdavis.edu/
                najoshi -at- ucdavis -dot- edu
                <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)




            --
            Nikhil Joshi
            Bioinformatics Analyst/Programmer
            UC Davis Bioinformatics Core
            http://bioinformatics.ucdavis.edu/
            najoshi -at- ucdavis -dot- edu
            <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)

            ___________________________________________________________
            Please keep all replies on the list by using "reply all"
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    --
    Nikhil Joshi
    Bioinformatics Analyst/Programmer
    UC Davis Bioinformatics Core
    http://bioinformatics.ucdavis.edu/
    najoshi -at- ucdavis -dot- edu
    <a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 <tel:<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698> (w)




--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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:
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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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
<a href="tel:530.752.2698" value="+15307522698" target="_blank">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
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