Hello Tim,
The tools in the Galaxy distribution should all be executable from the command line. Each tool config ( the tool's xml file ) includes a tag set like the follwoing that defines the command:
<command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
Running this tool from the command line would simply be:
python wiggle_to_simple.py <input file> < output file>
Of course, you will need to have all tool dependencies installed and available in your path. for a list of tool dependencies, see our wiki at http://g2.trac.bx.psu.edu/wiki/ToolDependencies.
Greg Von Kuster Galaxy Development Team
Tim Yu wrote:
hi!
First, kudos to the galaxy team, it is really fantastic, and I'm really enjoying using it.
Auestion: are any of the tools that are available in galaxy available for download (or extraction from the galaxy distribution), to be used from the command line?
The Operate on Genomic Intervals: intersect and subtract tools are proving very useful, and I'd like to integrate them into some custom workflows we are running in our lab.
Thank you very much! T
Tim Yu, MD, PhD Assistant in Neurology, MGH Research Fellow, Neurogenetics, BIDMC and CHB _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user