I have generated a VCF detailing the SNPs in 18 individuals from a population. In a pilot study, I had previously used some of the Genome Diversity tools to generate the genotypes for the samples and then visualized their relatedness to each other using a phylogenetic tree. I would like to do this type of analysis again but these tools are now deprecated. Are there any tools available on galaxy to replace these? I saw in a previous post that MiMod was suggested but I don’t believe this has the functionality I’m looking for. Any guidance is appreciated.
Genome Diversity tools have been deprecated for several years now (at least 5). The good news is that those were based on R packages that you can directly use in
RStudio within Galaxy.
- Q&A (at the prior Galaxy biostars forum): RGenetics and Genome Diversity
- Bioconductor package/vingette: Bioconductor - GeneticsPed
- Search the GTN training site with the keyword “rstudio” for tutorials: https://training.galaxyproject.org/
Hope that helps!
Maybe the answer from Jen can help you dealing with your issue coding inside Galaxy, but in case you are searching “classical”" Galaxy tools who can made the job, maybe you can give more informations about the “steps” you want to follow and/or what you have as input, what you want as output. Sorry but I don’t know (or remember the Genome Diversity tools…
Thank you @yvanlebras!! – those are the Genome Diversity tools The EU server doesn’t have them marked as deprecated but I’m pretty sure there are some usage issues.
@Danielle_Ireland You can certainly try the tools at EU – then if you run into problems, consider other options, including posting back what it is that you want to do that other tools won’t. I personally don’t know of any exact replacements except by using R directly, but others might, especially Yvan!
Note: I recall that there were some datatype handling problems (the “gd” formats associated with this tool suite – can’t find the issue ticket, was probably pre-Github). This issue ticket is a different example of known problems (tools not containerized). All this means that any error message could be difficult to interpret (data/parameter issues versus bugs/technical issues). And this is the original Galaxy “page” that was associated with the tools/publication – I wouldn’t expect much of it to work anymore as-is after ~8 years and the known tools issues, but perhaps helpful as a general guide still https://usegalaxy.org/u/webb/p/aye-aye.
Thank you @jennaj and @yvanlebras! Yes, @yvanlebras those are the exact tools I had been using previously on usegalaxy and was hoping to use now. I had used them ~ 2 years ago and must not have realized they were deprecated at the time. I will try to move forward with the R packages to see if this will work for my data.
I appreciate both your help,
2 posts were split to a new topic: Interactive environments (Rstudio, Jupyter): Issue at Usegalaxy.org Nov 4 2021 status “pending fix”