Hi,
I was wondering whether there is a way to set (or more properly to update) the PATH environmental variable for my Galaxy instance? so that I could simply avoid using the absolute path of the scripts/tools that are defined in the XML(tool) files I created.
thanks, Erick
Erick Antezana wrote:
Hi,
I was wondering whether there is a way to set (or more properly to update) the PATH environmental variable for my Galaxy instance? so that I could simply avoid using the absolute path of the scripts/tools that are defined in the XML(tool) files I created.
Hi Erick,
The $PATH used to run tools is inherited from the environment in which Galaxy is started. So as long as it is set properly beforehand, your tools should be found.
--nate
thanks, Erick _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Erick,
Please see the thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-July/002978.html
where I had issues with the environment and $PATH, it turned out to be my mistake with the shell script I had to start the Galaxy daemon. You shouldn't ever need to specify the full path to your executables in with the <command> tag
hth, Leandro
On Fri, Sep 10, 2010 at 2:47 PM, Nate Coraor nate@bx.psu.edu wrote:
Erick Antezana wrote:
Hi,
I was wondering whether there is a way to set (or more properly to update) the PATH environmental variable for my Galaxy instance? so that I could simply avoid using the absolute path of the scripts/tools that are defined in the XML(tool) files I created.
Hi Erick,
The $PATH used to run tools is inherited from the environment in which Galaxy is started. So as long as it is set properly beforehand, your tools should be found.
--nate
thanks, Erick _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Nate,
should I expect the same behaviour within a SGE environment?
Erick
On 10 September 2010 20:47, Nate Coraor nate@bx.psu.edu wrote:
Erick Antezana wrote:
Hi,
I was wondering whether there is a way to set (or more properly to update) the PATH environmental variable for my Galaxy instance? so that I could simply avoid using the absolute path of the scripts/tools that are defined in the XML(tool) files I created.
Hi Erick,
The $PATH used to run tools is inherited from the environment in which Galaxy is started. So as long as it is set properly beforehand, your tools should be found.
--nate
thanks, Erick _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Erick Antezana wrote:
Nate,
should I expect the same behaviour within a SGE environment?
No, with SGE you would need to make sure that the $PATH is set in the clustered environment. This is done with your shell's startup files or the sge_request(5) file.
--nate
Erick
On 10 September 2010 20:47, Nate Coraor nate@bx.psu.edu wrote:
Erick Antezana wrote:
Hi,
I was wondering whether there is a way to set (or more properly to update) the PATH environmental variable for my Galaxy instance? so that I could simply avoid using the absolute path of the scripts/tools that are defined in the XML(tool) files I created.
Hi Erick,
The $PATH used to run tools is inherited from the environment in which Galaxy is started. So as long as it is set properly beforehand, your tools should be found.
--nate
thanks, Erick _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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Erick Antezana -
Leandro Hermida -
Nate Coraor