Hi,
I have recently installed the newest update of qiime2, 2021.11. I am trying to run qiime2 as a module within ipython. To do so I activate the qiime2 conda environment and enter ipython.
When trying to load qiime2 in ipython (e.g. qiime2.plugins.feature_table.actions as feature_table_actions) I get the error "No module named 'qiime2'
I think I am missing something fundamental
Thanks for any help in advance.
Let's make sure that the correct conda environment is activated by running qiime info and also check that ipython is installed in your environment with conda list.
It sounds like somehow a different install of ipython is coming first in your path, so go ahead and run which ipython as well?
Hi @Keegan-Evans, thank you for your reply.
qiime info
System versions
Python version: 3.8.12
QIIME 2 release: 2021.11
QIIME 2 version: 2021.11.0
q2cli version: 2021.11.0
Installed plugins
alignment: 2021.11.0
composition: 2021.11.0
cutadapt: 2021.11.0
dada2: 2021.11.0
deblur: 2021.11.0
demux: 2021.11.0
diversity: 2021.11.0
diversity-lib: 2021.11.0
emperor: 2021.11.0
feature-classifier: 2021.11.0
feature-table: 2021.11.0
fragment-insertion: 2021.11.0
gneiss: 2021.11.0
longitudinal: 2021.11.0
metadata: 2021.11.0
phylogeny: 2021.11.0
quality-control: 2021.11.0
quality-filter: 2021.11.0
sample-classifier: 2021.11.0
taxa: 2021.11.0
types: 2021.11.0
vsearch: 2021.11.0
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(qiime2-2021.11) maurice@Mossy-Machine:~$ which ipython
/home/maurice/.local/bin/ipython.
Does this indicate that ipython is coiming for the wrong place?
Thank you for your assistance.
Yes, it looks like ipython is coming from a local install rather than your conda environment. Most likely this location is coming before your conda path in your system path($PATH). Fixing this will be specific to your system. From your command line it looks like you are on a linux machine, in which case, you might have a sys admin who should be able to help you resolve this(and may be the one who has to do it for you, depending on how the permissions are set up). The good news is that your QIIME2 install and conda environment look good!
If this is your personal machine, you will have to fix it yourself. You could view your current path with echo $PATH. The path is reset every time your terminal starts up, with its configuration coming from a file(most likely called .bashrc or .zshrc depending on your terminal and stored in your home directory). Here is a general guide to setting your path and here are some conda docs related to getting your path setup. You generally want conda to set its path itself with conda init rather than setting this manually. However, you may end up needing to make changes to the other ipython install using information from the first link.
It is worth noting that the path is read left to right, meaning that the command will be run from the first place that it is found in your path starting from the beginning. I wish I had more specific advice that I could give you, but since this seems to be a system configuration issue(rather than a QIIME 2 specific issue), it is hard be more specific advice at this point. Hopefully I have given you enough here to get you headed in the right direction; feel free to comment again here with any other questions you might have or other issues that you run into 
Yes, I think you are very much correct. I can call ipython specifically using directly with /home/maurice/anaconda3/bin and import qiime. You are correct, I am using Linux (ubuntu) and it is my own.
Thanks for your help. I will look at the links you have provide and consider changing my paths variables.
Thanks for the assistance, greatly appreciated. I am running the qiime2 Artifact API just fine now.
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