> From: Cristian Alejandro Rojas <firstname.lastname@example.org>
> 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?
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 firstname.lastname@example.org: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 email@example.com
@ the Genomics, Evolution, and Development lab; Michigan State University
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe