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/__init__.py",
line 123, in prepare_job
    job_wrapper.prepare()
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
702, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
2639, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", 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/Template.py",
line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1388113247_46_38074.py",
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?

Cheers!


2013/12/26 Michael R. Crusoe <mcru...@msu.edu>

> > From: Cristian Alejandro Rojas <alejandro.0...@gmail.com>
> > Date: December 26, 2013 2:37 AM
> > To: galaxy-dev@lists.bx.psu.edu
> > 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/normalize_by_kmer_coverage.pl),  diginorm is another
> alternative (http://ged.msu.edu/papers/2012-diginorm/).
> >
> > 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 normalize-by-median.py and the
> other tools in the khmer suite.
>
>
> https://github.com/ged-lab/khmer/blob/galaxy-integration/scripts/normalize-by-median.xml
>
> It requires some changes on our end which you can track here:
>
> https://github.com/ged-lab/khmer/pull/237
>
> You can install this branch of khmer via pip
>
> pip install -e git+...@github.com:ged-lab/khmer.git@output_naming1
> #egg=khmer
>
> or if you don't have a github account:
>
> pip install -e git+
> https://github.com/ged-lab/khmer.git@output_naming1#egg=khmer
>
> (Instructions on installing using a virtualenv or on OS X are at:
> https://khmer.readthedocs.org/en/latest/install.html 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.
>
> Cheers!
>
> --
> Michael R. Crusoe: Software Engineer and Bioinformatician  mcru...@msu.edu
>  @ the Genomics, Evolution, and Development lab; Michigan State University
> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670    @biocrusoe
>



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