picrust2 qiime2-2019.10 install error

Community Plugin Support
1

Hello @gmdouglas ,

I am trying to install q2-picrust2 in a qiime2-2019.10 environment. I created a fresh qiime2 environment and then the ran the following command while in the 2019.10 env as stated in the picrust2 tutorial:

conda install q2-picrust2=2019.10 -c conda-forge -c bioconda -c gavinmdouglas

I then received the following conflict error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.

Conda then searched for the conflicts and returns an extremely long list of conflicts.

Can you advise me on what I can try to fix this?

Thank you,
Zach

9

Hey @Zach_Burcham,

I’m not sure what is causing this issue (it occurred with the previous plugin release as well after a couple of months). I can confirm that the actual packages required are not incompatible and that this version of the plugin did originally work with QIIME2 2019.10. I’m not sure what factors are changing to the conda channels (or elsewhere) that are creating issues.

You might be able to install the plugin manually (see: https://github.com/gavinmdouglas/q2-picrust2). Alternatively, you could simply install the standalone picrust2 version and export your data to use the tool (https://github.com/picrust/picrust2/wiki/Installation).

I will troubleshoot this issue though and post here if I figure it out!

Best,

Gavin

10

Hi @gmdouglas ,

Thank you for the reply! I was troubleshooting this a little bit last night and it seems that the issue is when I use the qiime2 environment on my Mac. I was able to install the picrust2 plugin with no problems on our linux cluster but was getting the above error doing the same thing with my qiime2 environment on my Mac.

Thanks,
Zach

11

That’s useful to know - thanks Zach!

12

Hello Gavin, thank you for the help on this tool! I am also getting this error exactly, currently on Mac tested:

conda install q2-picrust2=2019.10 -c conda-forge -c bioconda -c gavinmdouglas

on both qiime2-2019.10 and qiime2-2020.2 and getting the same error, unfortunately.

Any more advice?

13

Sorry I’m still not sure what’s causing this issue, but I’ll post here when it is resolved.

14

No problem at all! You mentioned before that you might be able to install the plugin manually (see: https://github.com/gavinmdouglas/q2-picrust2).

If this is possible, I would love to give it a try on my set-up (Mac, miniconda3, qiime2-2019.10) but I am unsure how to manually install the plugin. Would you have instructions for this?

15

Hi @dann818,

You can try running these commands to install the plugin manually:

Best,

Gavin

1 Like
16

Sorry for the late reply, this worked for me! Thank you Gavin. Summary of what I did for future reference if others need it.

Using MacOSX…

  1. Performed a clean install of miniconda3
  2. Installed qiime2-2019.10, and activated
  3. Installed picrust2 from source (https://github.com/picrust/picrust2/wiki/Installation), skipped the “conda activate picrust2”, instead performed the “pip install --editable .” (with qiime2-2019.10 activated) while still in the “picrust2-2.3.0-b” directory.
  4. Then followed the rest of the instructions to install q2-picrust2 plugin manually within the environment
  5. “qiime picrust2 --help” now provides me with information describing the plugin

Best,
Daniel

2 Likes