Sorry for the late answer.
Thank you so much Michael.
I have tested the plugin and everything now works fine!
2013/12/29 Michael R. Crusoe <mcru...@msu.edu>
> You are doing nothing wrong Cristian, it was my error.
> I've updated the tool definition file; it is now at
> And I've updated the code base. You'll need to run the following to update
> your installation
> pip install -e git+...@github.com:ged-lab/khmer.git@output_naming1
> or if you don't have a github account:
> pip install -e git+
> To be able to use diginorm inside Galaxy Workflows we are only supporting
> diginorming into a single file at this time.
> There is a chaining method where multiple files can be processed
> sequentially but until Galaxy supports proper collections a cleaner
> integration will have to wait.
> Interested parties can follow along at
> On Thu, Dec 26, 2013 at 10:53 PM, Cristian Alejandro Rojas <
> alejandro.0...@gmail.com> wrote:
>> 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
>> File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in
>> 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
>> return str( Template( source=template_text, searchList=[context] ) )
>> 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?
>> 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: email@example.com
>>> > 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.
>>> It requires some changes on our end which you can track here:
>>> You can install this branch of khmer via pip
>>> pip install -e git+...@github.com:ged-lab/khmer.git@output_naming1
>>> 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:
>>> 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.
>>> Michael R. Crusoe: Software Engineer and Bioinformatician
>>> @ the Genomics, Evolution, and Development lab; Michigan State
>>> http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
>> *Cristian Alejandro Rojas Quintero*
>> *Estudiante Ingeniería de Sistemas *
>> *Universidad Distrital Francisco José de Caldas*
>> Bogotá - Colombia
> 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
*Cristian Alejandro Rojas Quintero*
*Estudiante Ingeniería de Sistemas *
*Universidad Distrital Francisco José de Caldas*
Bogotá - Colombia
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