Is there a way to install qiime2 in an existing virtual environment already containing a previous version of qiime2, but also a lot of other packages. Otherwise I would have to copy the packages I also use to the other environments each time, some of which do not install easily using conda or pip
Hello!
To avoid conflicts between different dependencies it is better to install a newer version of Qiime2 into a new environment. Most probably you will not be able to install Q2 into already existing environment with bunch of packages installed. And even in case of successful installation there is a high possibility of some hidden issues with different packages/plugins.
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