Sorry for the late answer. 

Thank you so much Michael.

I have tested the plugin and everything now works fine!

Cheers

2013/12/29 Michael R. Crusoe <mcrusoe@msu.edu>

You are doing nothing wrong Cristian, it was my error.

I've updated the tool definition file; it is now at https://github.com/ged-lab/khmer/blob/output_naming1/scripts/normalize-by-median.xml

And I've updated the code base. You'll need to run the following to update your installation

pip install -e git+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

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 https://github.com/ged-lab/khmer/pull/237#issuecomment-31307144

On Thu, Dec 26, 2013 at 10:53 PM, Cristian Alejandro Rojas <alejandro.0317@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
    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 <mcrusoe@msu.edu>

> From: Cristian Alejandro Rojas <alejandro.0317@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+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  mcrusoe@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

--

Michael R. Crusoe: Software Engineer and Bioinformatician  mcrusoe@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