Re: [galaxy-dev] Pass Working Directory from xml

[Daniel Blankenberg]

Hi Todd,

Can you just pass in “.”?


   the_tool.py -o ‘.'


Thanks for using Galaxy,

Dan


On Dec 11, 2015, at 4:00 PM, Todd Oakley  wrote:

> Greetings,
>I feel this must be simple, but I cannot find it.
> 
> I'm making a wrapper for a tool that requires the output directory to be 
> specified on the command line of a python script (otherwise it uses the path 
> of the input file for the multiple output files). How can I pass the working 
> directory to the tool from the xml file?
> 
> 
>the_tool.py -o $DIRECTORY_WHERE_GALAXY_RUNS_THE_TOOL
> 
> This is similar to from_work_dir in the outputs -- but I need the path of 
> the directory that does not include any file names.
> 
> 
> Thanks!
> 
> Todd Oakley, UCSB
> ___
> 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/

[galaxy-dev] Pass Working Directory from xml

[Todd Oakley]

Greetings,
I feel this must be simple, but I cannot find it.

I'm making a wrapper for a tool that requires the output directory to be 
specified on the command line of a python script (otherwise it uses the 
path of the input file for the multiple output files). How can I pass 
the working directory to the tool from the xml file?



the_tool.py -o $DIRECTORY_WHERE_GALAXY_RUNS_THE_TOOL

 This is similar to from_work_dir in the outputs -- but I need the 
path of the directory that does not include any file names.



Thanks!

Todd Oakley, UCSB
___
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/