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'> 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 normalizationHello Cristian,
> 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?
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