Re: [galaxy-dev] PATH and local jobs

[James Taylor]

> Another vote for the excellent modules system from us at AgResearch.  I think 
> it's the only sane way to manage PATH, etc, when you have multiple versions 
> of tools installed.
> http://modules.sourceforge.net/
> I know I've said this before here.  Tell all your friends. ;-)

Galaxy's dependency injection works in a similar way, without
requiring all the external dependencies. We don't need unload since we
compose a unique environment for every tool execution. This is much
cleaner that loading everything into the environment before running
Galaxy, we want tools to be executed with as clean an environment as
possible.
___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] PATH and local jobs

[Guest, Simon]

> From: galaxy-dev-bounces ... On Behalf Of Adam Brenner
> On our HPC setup, we use the modules system but its the same issue you are
> running into.

Another vote for the excellent modules system from us at AgResearch.  I think 
it's the only sane way to manage PATH, etc, when you have multiple versions of 
tools installed.
http://modules.sourceforge.net/
I know I've said this before here.  Tell all your friends. ;-)
 
> A number of methods exists for setting up the correct path, for you, I
> believe the easiest would be one of the two:
> 
> 
> 1) In your init script: source (or setup) PATHS as you have them in your
> .bash_profile.
> /etc/init.d/galaxy
> 
> OR
> 
> 2) Within Galaxy, edit universe_wsgi.ini and look for:
> environment_setup_file
> and create a file that will setup the correct $PATH for you.


We use (2), which is better than (1), as it will continue to work when you 
start running your jobs on a cluster, whereas the PATH you set in (1) will not 
be picked up on the cluster (as far as I remember from our early experience).

cheers,
Simon


===
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
===

___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] PATH and local jobs

[Adam Brenner]

Ryan,

On our HPC setup, we use the modules system but its the same issue you are
running into.

A number of methods exists for setting up the correct path, for you, I
believe the easiest would be one of the two:


1) In your init script: source (or setup) PATHS as you have them in your
.bash_profile.
/etc/init.d/galaxy

OR

2) Within Galaxy, edit universe_wsgi.ini and look for:
environment_setup_file
and create a file that will setup the correct $PATH for you.


You can also invoke the Tool Dependency options for each specific tool you
load as shown in[1].

[1]: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu


On Wed, Sep 11, 2013 at 10:18 AM, Ryan Davis  wrote:

> Hi,
>
> ** **
>
> We have a local server running Galaxy and a majority of the tools work
> correctly (bowtie, BWA, samtools and etc…).  I am having issues with some
> of the FASTX-Toolkit tools.  I am starting Galaxy with an init script on
> Centos 6 and the tools are in my $PATH and work at the command line, just
> not in Galaxy.  The wiki suggest to “set $PATH in the startup file or
> use.” 
>
> It leaves me hanging and don’t know what the other option is.  Can someone
> share with me their workaround?
>
> ** **
>
> Here is the wiki page:
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>
> ** **
>
> Here is the section I am hoping will help:
>
> ** **
> Local Jobs
>
> Changes to $PATH can be persisted by setting them in your shell's startup
> file(s).  This typically means ~/.bash_profile for bash, but please see
> the bash documentation on startup 
> files
>  or the *INVOCATION* section of the bash(1) man page to understand the
> intricacies of how that file is read.  Of particular importance, if you are
> starting Galaxy in a method other than manual invocation from a shell
> prompt (with sh run.sh) such as with an init script, it is likely that
> your startup file will not be read.  In this instance, you should set
> $PATH in the startup file or use.
>
> ** **
>
> ** **
>
> Thanks!
>
> Ryan
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/