I am running the 2017.8 Release of Qiime 2 on a Linux Virtual Machine and I want to run the alpha-group-significance plugin but it is not showing up on my Qiime 2 Studio. Therefore, I am assuming this was not available during that release. Is there a way to get that plugin? Or do I need to install another virtual machine with the latest Qiime 2?
There is no elegant way to get a single plugin without just upgrading to the newest version of Qiime. But that might not take downloading a new VM!
In your current VM, you could follow the instructions for natively installing qiime 2 starting with the command
conda update conda. This should be more lightweight than just downloading a new VM because it will only change the software that has been updated.
Let me know what you try…
Thank you for the response.
If I am using Qiime 2 Studio, would I need to activate the conda environment every time I use the user interface or would it do this automatically when I boot Qiime 2 Studio?
Good question… I think you would have to activate the conda environment to use the new software, but I’m not totally sure how the Qiime 2 Studio software is set up.
If you want to always use the conda environment you can add
source activate qiime2-2018.01 to your
.bashrc file so it automatically loads it upon log in. Maybe the qiime developers have other ideas about how to set this up.
Just to clarify, there is no QIIME 2 plugin called
alpha-group-significance. There is however a plugin called
q2-diversity that has an
alpha-group-significance action in it. Is that what you are thinking of? This visualization has been in QIIME 2 since late 2016, so if it isn’t showing up, it is either because it was somehow removed in your local installation, or it could be because of how q2studio handles input verification (protection). Read on for more info…
As far as it “not showing up” in q2studio — the studio doesn’t allow you to select methods that don’t have any available inputs in the current working directory. For example, an action that needs demultiplexed sequences won’t allow you to launch it until you change your working directory to one that has a demultiplexed sequences artifact in it.
Can you please send a screenshot of the issue, if the comments above don’t clear things up?
Hey @thermokarst! Thank you for the response, I appreciate it.
Here is a screenshot of what the q2-diversity plugin has under visualizers:
I do not seem to see alpha-group-significance under that. I did generate the artifacts required for this action and they seem to be present in my working directory:
I also have a metadata file also:
Maybe it got deleted from my local installation as you mentioned? Or am I doing something wrong in terms of artifacts and such?
Thanks for the screenshot @patthehat033 - the action you are looking for is listed as “Alpha diversity comparisons”. This is certainly confusing, and we have an open issue about this, basically the studio shows the action’s short description, but not the actual action name. Hope that helps!
@thermokarst Thank you for the response! I figured that was probably the case but was not sure which action was the correct one.
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