Deploying the khmer project tools on Galaxy

This document is for people interested in deploying the khmer tools on the Galaxy platform.

We are developing the support for running all the khmer scripts in Galaxy.

Install the tools & tool description

In the administrative interface select “Search and browse tool sheds” under the heading “Tool sheds”. Click on “Galaxy test tool shed” and search for khmer. Click on the “khmer” button and choose “Preview and install”. Click the “Install to Galaxy” button at the top. At the bottom of the next page click the “Install” button.

Single Output Usage

For one or more files into a single file:

  1. Choose ‘Normalize By Median’ from the ‘khmer protocols’ section of the ‘Tools’ menu.
  2. Compatible files already uploaded to your Galaxy instance should be listed. If not then you may need to set their datatype manually.
  3. After selecting the input files specify if they are paired-interleaved or not.
  4. Specify the sample type or show the advanced parameters to set the tablesize yourself. Consult Setting khmer memory usage for assistance.
comments powered by Disqus