file_path passed directly to wrappers

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file_path passed directly to wrappers

Sabrina rodriguez
Dear all,

I am integrating some tools into galaxy and I would like to use some of
the paths from the file "universe_wsgi.ini" (ex:file_path) directly into
my perl wrappers in order for my per script to work in this directory.
For now, I am providing the path in each perl script, manually, which is
not maintainable when we change that path.

Could you please tell me how to pass the file_path variable directly
from the .xml to the .pl script?

Thanks in advance.

Best regards,

SAbrina
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Re: file_path passed directly to wrappers

Nate Coraor (nate@bx.psu.edu)
On Wed, May 13, 2015 at 7:23 AM, Sabrina rodriguez <[hidden email]> wrote:
Dear all,

I am integrating some tools into galaxy and I would like to use some of the paths from the file "universe_wsgi.ini" (ex:file_path) directly into my perl wrappers in order for my per script to work in this directory.
For now, I am providing the path in each perl script, manually, which is not maintainable when we change that path.

Could you please tell me how to pass the file_path variable directly from the .xml to the .pl script?


Hi Sabrina,

Galaxy tools are strongly encouraged to run as self-contained units. Objects that you need to to access (such as other datasets) should be passed to your tool as parameters. If you provide some additional details on what you're trying to accomplish in the file_path directory, we can probably help with some alternative options to directly accessing file_path.

That said, it is possible to access that config value - all of Galaxy's config options are exposed in the tool template using ${__app__.config}, so you'd want to look at ${__app__.config.file_path}.

--nate
 
Thanks in advance.

Best regards,

SAbrina
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and other Galaxy lists, please use the interface at:
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