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 <http://www.gnu.org/software/bash/manual/bashref.html#Bash-Startup-Files> 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
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/ aebrenne@uci.edu On Wed, Sep 11, 2013 at 10:18 AM, Ryan Davis <rrdavis@ucdavis.edu> wrote:
Hi,****
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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<http://www.gnu.org/software/bash/manual/bashref.html#Bash-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****
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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. =======================================================================
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.
participants (4)
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Adam Brenner -
Guest, Simon -
James Taylor -
Ryan Davis