Question: Running custom tool in Galaxy
0
gravatar for cdean11
2.3 years ago by
cdean1120
cdean1120 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 • 584 views
ADD COMMENTlink modified 2.3 years ago by danielfortin86100 • written 2.3 years ago by cdean1120
2
gravatar for danielfortin86
2.3 years ago by
United States
danielfortin86100 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 COMMENTlink written 2.3 years ago by danielfortin86100
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