Hello, That's wonderful to see 2023.9 now out! I just made a first attempt to install the amplicon distribution on our Linux x86_64 cluster, and received the following error: $ uname -a Linux barnacle2 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux …

I traced the issue. Sorry for the delay. The bionconda usage instructions state to modify ~/.condarc. Those changes appear to be incompatible for QIIME 2 when installing with micromamba, mamba, as well as conda. The installation only worked once I rm'd my ~/.condarc file.

Hey @wasade ! Thanks for reaching out and bringing this to our attention! It looks like there has been some very unfortunate timing with the latest version of conda that seems to be causing some conflicts with conda and mamba in the same environment. We're currently working on a fix for our latest i…

Hi @lizgehret , Thanks, but that's regrettably not viable due to pending compute and associated environment dependencies in place. I'll hold off on 2023.9 until a fix is in place, thanks! Best, Daniel

Hey @wasade , We've reverted our install instructions to just use conda instead of mamba for installing the latest QIIME 2 release. With that being said - I went back through the traceback you provided and noticed that you weren't using the latest version of conda where the install conflicts would h…

Thanks, @lizgehret . Removal of the recommended settings for bioconda, and attempting to use conda env create led to an exception from conda. The mamba env create proceeds, and downloads files, but then throws an exception on install (meaningful stuff below). As a sanity check, I reinstituted the bi…

...finding and deleting the offending corrupt file seems to have begun to restore functionality. I am not going to attempt another 2023.9 install near term though, I cannot risk it breaking my other environments right now.

Hey @wasade , I'm afraid I can't reproduce this issue either. I do notice a few things that seem unusual: [image] wasade: active environment : qiime2-2023.5 active env location : /home/mcdonadt/miniconda3/envs/qiime2-2023.5 Do you by chance have an shell init that auto-loads the las…

Thanks, @ebolyen . The install attempt was occurring while the qiime2-2023.5 env was active, but this hasn't in the past inhibited creation of other environments. The q2 environment is not autoloaded. Makes sense re: the corrupt package. By eye, I couldn't spot the affected issue, and a brief hack o…

Ok, thanks for the info, that all sounds fine. Given it's a recent mamba version, it does seem unlikely that there's an issue with that, but I can't say for certain without comparing strings. I think it would still be safe to create a new (non-base) env with mamba/conda (just like you did with bow…

Hey Daniel, Don’t know if this will help but I just installed on Pop-OS, mamba 1.5.2, conda 23.9.0 and the amplicon/distro seem to install correctly.

just wanted to add the terminal printout to my reply. mamba-terminal.txt (133.8 KB)

QIIME 2 Forum

QIIME 2 2023.9 installation issue

Technical Support

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled