Alrighty, it’s looking like we have a couple of conda installs which is messing everything up. Also, it looks like your macqiime is nicely tucked away, so we shouldn’t need to worry about hurting it.
That is a lot of Pythons! It looks like these are all set in your
.bash_profile, so we’ll edit that in a minute.
Do you have a particular reason you would need this to be set? I HIGHLY recommend not setting
$PYTHONPATH as it is really hard to keep track of and causes a mess. Based on some of your other directories in
$PATH we should be able to remove this.
If you have a text-editor you can use that, otherwise we’ll just go with
We need to removed everything that says something like:
# added by Anaconda/Miniconda/Python installer
There will likely also be a line that sets your
PYTHONPATH, remove that as well (or at least comment it out with a
# character in front).
Once you’ve done that, open a new terminal and type:
and post that here again. Ideally we should see something like:
which would be correct.
Assuming all of that goes well, you should also remove your
$HOME/anaconda directory and then re-install miniconda (this will edit your bash_profile again, but that’s ok this time).
Finally you should be able to install QIIME 2 from the normal conda instructions.
Let me know if that makes sense, or if you need help!