Conda conflicts install issue with latest qiime2-2020.11 (mac OSX)

[pma]

Dear Qiimers,

I have been trying to install the latest qiime build (qiime2-2020.11) on my mac (Catalina OS).

After running the conda update I installed via

wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-osx-conda.yml
conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-osx-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2020.11-py36-osx-conda.yml

After a very long

Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

Here is the output (its very long and I could not capture all of it because i did not activate the iunlimited scroll history on this term) Hope it is of interest. qiime conda install output - Pastebin.com

Please note that I could install the previous build qiime2-2020.8 without problems on the same system.

Many thanks for your help,

PM

[llenzi (Luca)]

Hi @pma
I think you may have run in the same isse discussed here:

Instalation qiime 2020.11 Found conflicts! Looking for incompatible packages

Hello everyone! I am trying to install the latest version of QIIME2 (qiime2-2020.11) on Ubuntu 20.04, but some conflicts appear: $ conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml Collecting package metadata (repodata.json): done Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining conflict for bioconductor-s4vectors r-waldo r-permute r-rematch2 r-crayon bioconductor-rhtslib…

They (thanks dev team ) rebuilt the file during last ours, so if you download new copies of the environment files the issue should be fixed
Hope it solve the problem for you as well!
Luca

[pma]

Thanks @llenzi !

I could install on my side by downgrading python to python=3.6.11 in the environment file (I saw it was python=3.6.11 in the linux and tried) and surprisingly it worked.
I will however rebuild the environment freshly using the new files you provide just to be sure.

For the record I switched to qiime2-2020.11 because I could not install empress within qiime2-2020.08 GitHub - biocore/empress: A fast and scalable phylogenetic tree viewer for microbiome data analysis because of some nasty numpy issues. I can now in qiime2-2020.11

Many thanks !

PM

[thermokarst]

Hi @pma!

@pma

downgrading python to python=3.6.11

That is certainly an option, but one reason why I would suggest you not manually tamper with the contents of the environment file is because of testing and verification. We rigorously test and verify QIIME 2, the interfaces, and all of the core plugins - after testing, the precise versions of the packages we confirmed with are recorded in the environment file. If you manually change the env, then you are opting into untested conditions. I don't really expect there to be any issues with your particular manual edits, but just wanted to provide a little context and food for thought (and provide a little warning for anyone else who might come across this discussion).

Thanks!