QIIME2 installation using pycharm

Technical Support
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1

Hi community! I'm a relatively new qiime2 and python user.

So far, I have been using qiime2 inside a virtual machine, which is ok but not great.

Since I'm taking a python course and have gotten used to work with pycharm, I'm trying to install the latest version of qiime2 in pycharm.

I use anaconda as my python interperter.

However, I can't get past the wget installation which seemes to be the problem. any ideas on how to solve this?

thanks a lot!

PS C:\Users\USER\PycharmProjects\QIIME2> conda install wget
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done                                   
Solving environment: failed with initial frozen solve. Retrying with flexible solve.  
                                                                                      
PackagesNotFoundError: The following packages are not available from current channels:
                                                                                      
  - wget                                                                              
                                                                                      
Current channels:                                                                     
                                                                                      
PS C:\Users\USER\PycharmProjects\QIIME2> wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml


StatusCode        : 200                     
StatusDescription : OK                      
Content           : channels:               
                      - qiime2/label/r2022.2
                      - conda-forge         
                      - bioconda            
                      - defaults            
                    dependencies:           
                      - _libgcc_mutex=0.1   
                      - _openmp_mutex=4.5   
                      - _r-mutex=1.0.1      
                      - alsa-lib=1.2.3      
                      - argcomplete=2.0.0   
                      - a...
RawContent        : HTTP/1.1 200 OK
                    Connection: keep-alive
                    Strict-Transport-Security: max-age=31536000
                    X-Content-Type-Options: nosniff
                    ...
2

Hi, just a quick update of what I was able to do since I wrote this post and what is my problem now - I was able to wget the file by importing a package with wget command for pycharm.

However, I still couldn't open a conda environment with the qiime file, after trying the instructions here (Configure a conda virtual environment | PyCharm Documentation) and from several forums.

So, if someone here have experience using qiime on pycharm with conda environment that would be great.

Thanks!

3

Hi @kam,

Given this:

It appears you are trying to run QIIME 2 directly within the Windows Command line. QIIME 2 can only be run through the Windows Subsystem for Linux (WSL). You can check out these threads for more details on how to do this:

-Mike

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4

Thanks for the quick guidance!

Turns out using a wsl conda environment is just not possible inside pycharm.

Anyone have a recommendation for a good substitute to pycharm?

6

This may not be entirely correct. Check out:

Thanks to @thermokarst for the tip!

7

Thnak you both.. for my understanding this is not possible, if I have created a conda environment within the wsl interperter

8

My solution to get around this was to have Anaconda installed on both Windows and WSL and then create the Conda environment within Windows. I was then able to activate this environment within WSL with the absolute path to the environment.
(from the same post you linked)

3 Likes
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