> 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.


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+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.


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