RGenetics and Genome Diversity

Question: RGenetics and Genome Diversity

3.7 years ago by

tra • 50

United States of America

tra • 50 wrote:

Hi,

I am new to Galaxy and I am trying to find tools to make some population genetics analysis.

If I go through the documentation there is a reference to a RGenetics tool (even a screencast), but I have not been able to find it neither in the main server nor in the toolshed. I have found the "Genome Diversity" entry instead. Can anyone shed light on the current status of both projects, please?

I was also interested in the RGenetics PLINK interface which the screencast shown to be quite promising...

Sorry for the newbie questions, but after much searching it almost seems that RGenetics is deprecated or something...

Many thanks

galaxy popgen rgenetics • 919 views

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modified 3.7 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.7 years ago by tra • 50

This page seems to be out of date.

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by tra • 50

3.7 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

The genome_diversity repository (https://toolshed.g2.bx.psu.edu/view/miller-lab/genome_diversity) contains dozens of tools and is installed at usegalaxy.org in the 'Genome Diversity' section.

RGenetics seems to be an R package (http://cran.r-project.org/web/packages/RGenetics/index.html) and I do not think it is wrapped for use in Galaxy. Example on how to wrap an R package can be seen here: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_rhmm_1_5_0/tool_dependencies.xml

ADD COMMENT • link written 3.7 years ago by Martin Čech ♦♦ 4.9k

3.7 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

The Galaxy RGenetics tools were deprecated and removed. Ross Lazarus (@fubar) may be able to provide additional information on these tools.

ADD COMMENT • link written 3.7 years ago by Daniel Blankenberg ♦♦ 1.7k

Sorry to say there has been no grant support for RGenetics microarray/plink development since 2010 which is probably when that screencast was made.

As Martin points out, Rgenetics is also the name of a BioC package which appeared recently for writing and integrating Galaxy tools based on R packages. It doesn't make a lot of sense to wrap it for use within Galaxy IMHO because it's designed for R hackers working in R. The existing Galaxy equivalent (more or less) is the Tool Factory tool to generate new Galaxy tools from scripts (R/Perl/Python/Bash)

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by fubar ♦ 1.1k

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