Question: RGenetics and Genome Diversity
0
gravatar for tra
3.7 years ago by
tra50
United States of America
tra50 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
ADD COMMENTlink modified 3.7 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.7 years ago by tra50

This page seems to be out of date.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by tra50
1
gravatar for Martin Čech
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 COMMENTlink written 3.7 years ago by Martin Čech ♦♦ 4.9k
1
gravatar for Daniel Blankenberg
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 COMMENTlink 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 REPLYlink modified 3.7 years ago • written 3.7 years ago by fubar1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour