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Question: Running custom tool in Galaxy
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gravatar for cdean11
2.8 years ago by
cdean11 • 20
cdean11 • 20 wrote:

In my tool's XML file I have the following line:

<command>path_to_foo_exe/foo -input1 $input1 -input2 $input2 -output $output2</command>

I don't want to specify the full path of the program's executable in the command tag. How can I execute my program using:

<command>foo -input1 $input1 -input2 $input2 -output $output2</command>

Note: the executable is in the same directory as my tool's XML file.
galaxy • 714 views
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modified 2.8 years ago by danielfortin86 • 110 • written 2.8 years ago by cdean11 • 20
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gravatar for danielfortin86
2.8 years ago by
danielfortin86 • 110
United States
danielfortin86 • 110 wrote:

You can use the "$__tool_directory__" variable:

<command>$__tool_directory__/foo -input1 $input1 -input2 $input2 -output $output2</command>

As long as your xml is in the same directory as foo, this should work.

 
ADD COMMENT • link written 2.8 years ago by danielfortin86 • 110
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