Thank u michael. 

I downloaded and install khmer to my machine, the i have include your galaxy plugin in my local instance, but when I try to run this from the web interface i'm getting this error:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/", line 123, in prepare_job
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/", line 702, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/", line 2639, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-i686-ucs4.egg/Cheetah/", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "", line 111, in respond
NotFound: cannot find 'hashsize'
I have tried change parameters, using the default parameters, advanced parameters but it didn't work. Do you know what am i doing wrong?


2013/12/26 Michael R. Crusoe <>
> From: Cristian Alejandro Rojas <>
> Date: December 26, 2013 2:37 AM
> To:
> Subject: [galaxy-dev] Some plugin for digital normalization

> Hello all,
> I've been searching in tool sheds(main and test) for a plugin to do digital normalization of reads, for example Trinity has one script to do this (./util/,  diginorm is another alternative (
> Do you know if there is a galaxy tool ready for this work or should I develop my own?

Hello Cristian,

I am actively working on a wrapper for and the other tools in the khmer suite.

It requires some changes on our end which you can track here:

You can install this branch of khmer via pip

pip install -e

or if you don't have a github account:

pip install -e git+

(Instructions on installing using a virtualenv or on OS X are at: just substitute in the pertinent pip line from above)

I haven't tested it much; doing so is the top of my to-do list for the rest of this week. If you or anyone else is feeling adventurous I would be happy to have the feedback.


Michael R. Crusoe: Software Engineer and Bioinformatician
 @ the Genomics, Evolution, and Development lab; Michigan State University    @biocrusoe

Cristian Alejandro Rojas Quintero
Estudiante Ingeniería de Sistemas 
Universidad Distrital Francisco José de Caldas
Bogotá - Colombia