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MTB phylogenetics tutorial #3220
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@cstritt @pvanheus do you think this fits ok to any of the existing GTN topics? https://training.galaxyproject.org/ we try and avoid creating new topics for just a single tutorial, when possible. Maybe visualisation? Sequence analysis feels very NGS-y, but we're trying to expand it, maybe there? |
So I see two issues here:
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@hexylena , @pvanheus , many thanks for the helpful comments! I'll start working on them today. |
That can make sense to me. The thing we try and avoid is topics with a single tutorial, but with our discussed covid phylogeny, yeah, that makes more sense. Evolution it is. |
First round of revisions for the MTB phylogenetics tutorial
Just one more thought here - there really is not much of a workflow for this tutorial because it follows on from previous work. Its not a stand-alone. I understand the desire to note make the "transmission" tutorial too long, but perhaps add a workflow that illustrates the process from VCF to phylogeny at least? |
Co-authored-by: Helena <hxr@hx42.org>
Co-authored-by: Helena <hxr@hx42.org>
Co-authored-by: Helena <hxr@hx42.org>
Co-authored-by: Helena <hxr@hx42.org>
@pvanheus , This was indeed a weighty omission. I now address it in the alignment part, and added a section at the end about rescaling and dating the tree. I use the |
On the linting errors:
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@pvanheus, to create a new topic: https://training.galaxyproject.org/training-material/topics/contributing/tutorials/create-new-topic/tutorial.html (and I am realising I forgot to add instructions for faq folder there, but I can help too) |
So the only thing which remains to be done on our side is to create the 'evolution' topic and move both tutorials there, right? As far as I can see this would only involve renaming the existing folder ('phylogenetics') and modify the corresponding metadata.yml. I'm not sure, though, how both tutorials can be moved there, given that they are both in open pull requests |
@cstritt yes, @hexylena and I will deal with the renaming and moving this morning. We will merge it as draft tutorials, so that it will be accessible for your course next week, and afterwards we can polish all the last things. (We have been thinking for a while already to rename metagenomics topic to "microbial analysis" so then it could fit there as well) |
@cstritt You might be able to install in via conda (using the terminal tab in Rstudio) ..I'm testing it now and will add it to the instructions in the tutorial if it works 👍 |
ok @cstritt, it appears to work if you install via conda 👍 ..it does give a warning that the package was built with R 4.1.2 while the Rstudio runs 4.1.0. It probably won't be a problem, but maybe good to test I will merge this now |
@cstritt here are the links to your tutorials: https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/tutorial.html (I've also put them on the course program page) |
Excellent, thanks a lot for the great support! |
This is a second tutorial for the planned Galaxy workshop on WGS of M. tuberculosis (see request #3211). It covers the interpretation and inference of phylogenetic trees.