Hi @gregcaporaso
I read the documentation and preprint of q2-boots and would like to use it in q2-amplicon-2024.10.
I assumed that q-boots could be installed in an activated q2-amplicon-2024.10 conda environment, but this install command did not work:
PackagesNotFoundError: The following packages are not available from current channels:
- //raw.githubusercontent.com/qiime2/q2-boots/main/environment-files/q2-boots-qiime2-amplicon-2024.10.yml
I 'adopted' the install instructions from the q2-library portal, where an installation into a separate env is described. Is it possible to add this plugin to an existing environment via conda install?
After installing the standalone version, I have seen that most of the q-amplicon plugins are also available. Is q2-boots a full 'amplicon' distribution?
Thanks for your interest in q2-boots! Happy to clarify what's going on here - the install instructions for q2-boots are for a conda environment, rather than a single package install within an existing environment. It's not that q2-boots is a full amplicon distribution, but our install instructions provide it within an environment that also contains the amplicon distribution (as it will be commonly used with many plugins that are also contained within that distribution).
You can absolutely install q2-boots as a single package within an existing environment - which it sounds like you were able to do? But please follow up if that's not the case, and you need additional help getting that installed!
I have tried to do this with conda install as described above, but I received the error.
From my basic knowledge of conda, I assumend that the install instructions on the new library page conda env create -n q2-boots-2024.10.beta will create a new environment rather than installing it into an existing environment. That was the reason why I changed it to conda install to add boots to an existing q2-amplicon-2024.10 distributiion. Please correct me if I am wrong.
Best,
I ask because those use conda env create/update as opposed to conda install, and the command you shared is a conda install command. As far as I can tell, conda install doesn't accept -f to specify a remote environment file (while conda env create does). Both accept --file for this.
I just tested a fresh install and updating an amplicon-2024.10 environment, and both worked for me using the instructions on the q2-boots library page. Can you try copy/pasting whichever of those you prefer (fresh install or update), and let us know if you're still having issues? Our intention is to support both options.
Thanks for your interest in q2-boots! And apologies to all for any confusion as we roll out our new library website!
Hi @gregcaporaso and @lizgehret
Thank you for your help, I was too much attracted by the "To learn how to install" link on the main q2-boots library page, and did completely overlook the top right corner!
After a clean re-install of q2-amplicon-2024.10, I was able to 'update' with q2-boots.
The reason, why I had to start over with a new amplicon installation is due to the third-party plugins gemelli and empress, where I have to use a workaround to get them installed (see: Qiime2 Library Compatibility - #8 by colinbrislawn).
After q2-amplicon and q2-boots, I was able to get q2-gemelli and q2-empress also running.
The new library website is great (including the videos!), I just have to get used to it!
Best,
Thanks for pointing that out - I'll update that now. I suspect we'll have outdated references like this scattered throughout the stand-alone plugins as we make the transition - don't hesitate to let us know if you discover anything else like that!
