This is likely a stupid question, but I have spent hours now trolling the forum and the web for answers and nothing seems to work for me.
I am VERY new to coding and trying to figure out how to use jupyter notebooks in conjunction with Qiime2.
I have natively installed Qiime2 (v. 2021.4) on my mac via conda.
In terminal, I am running the following:
" (base) [email protected] ~ % conda activate qiime2-2021.4
(qiime2-2021.4) [email protected] ~ % cd Desktop/qiime_files
(qiime2-2021.4) [email protected] qiime_files % jupyter notebook
[I 09:55:17.816 NotebookApp] Serving notebooks from local directory: /Users/shannonwilson/Desktop/qiime_files
[I 09:55:17.816 NotebookApp] Jupyter Notebook 6.3.0 is running at:
[I 09:55:17.817 NotebookApp] http://localhost:8888/?token=3917a6c50b78741ee9d61792cffb2872307ec9a6679853dc
[I 09:55:17.817 NotebookApp] or http://127.0.0.1:8888/?token=3917a6c50b78741ee9d61792cffb2872307ec9a6679853dc
[I 09:55:17.817 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 09:55:17.824 NotebookApp]
To access the notebook, open this file in a browser: file:///Users/shannonwilson/Library/Jupyter/runtime/nbserver-5571-open.html Or copy and paste one of these URLs: http://localhost:8888/?token=3917a6c50b78741ee9d61792cffb2872307ec9a6679853dc or http://127.0.0.1:8888/?token=3917a6c50b78741ee9d61792cffb2872307ec9a6679853dc "
I run the command "Import qiime2" and there is no response to the code in the notebook. I however tried to proceed.
I am then trying to run the "moving pictures" tutorial in the jupyter notebook browser. However, I get the following when I try to make a directory for it (e.g. mkdir qiime2-moving-pictures-tutorial
I received the error:
"File "", line 1
SyntaxError: invalid syntax"
After backing up, resetting my Kernal and terminal completely, I then tried running:
"jupyter serverextension enable --py qiime2 --sys-prefix" in terminal after activating the environment and changing my directory to my desktop (I like to have the files logged there as well) and before launching jupyter as well as in jupyter itself. The same errors are still happening.
So, after that long-winded explination, here is my question:
- Obviously, its a user error. Do you guys have some guidance on how best to run Jupyter notebook with qiime2? The only tutorials I have found are using CyVerse, and they are only using outdated versions/I know theres a better way.
- Could I be having these issues because I am trying to change the directory to have all files and copies saved to my desktop? this has not been an issue when I have been running qiime alone.
- Would this be a better question for the jupyter folks? I figure I would try here first as you guys are FAR more helpful!
Thanks so much for any guideance you can provide to a brand new user!