FORUMInstalling QIIME2
NickB asked 2 years ago

I am totally new to CC and also to bioinformatics. I’m a software developer and starting to learn bioinformatics. I have played with QIIME2 on a VM on my personal computer to learn the basics. Currently, I have a job that has been running for the last 7 days which is the reason why I opened a CC account.
Now I’m trying to install QIIME2 on the Graham node, but I get an invalid syntax error when trying to pip install.
Here are the steps I have done :

  • loaded the python/3.7 module ok
  • created my virtual env ok
  • activated my virtual env  ok
  • pip upgrade ok
  • installed numpy ok
  • Trying to install QIIME not ok!
    • command pip install qiime

Am I missing something?
Thank you

2 Answers
jrosner Staff answered 2 years ago

Hi NickB,
I believe there might be an issue with trying to install within a conda environment on the system.
But for this, I would recommend enlisting the help of the Compute Canada support team.  I believe they’ve dealt with this issue before and can help get you sorted.
I will submit a ticket on your behalf to and you should get a response fairly soon.

jshleap Staff answered 2 years ago

Hello everyone, you can find the QIIME2 installing instructions at