Question: Command Line Access To Galaxy Tools
gravatar for Tim Yu
10.1 years ago by
Tim Yu20
Tim Yu20 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 • 2.9k views
ADD COMMENTlink modified 10.1 years ago by Greg Von Kuster840 • written 10.1 years ago by Tim Yu20
gravatar for Greg Von Kuster
10.1 years ago by
Greg Von Kuster840 wrote:
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: $input $out_file1 Running this tool from the command line would simply be: python < 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 Greg Von Kuster Galaxy Development Team
ADD COMMENTlink written 10.1 years ago by Greg Von Kuster840
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