Conda problems when installing new qiime2 release

It seems like although miniconda is installed and some conda commands work, conda update conda throws up an error. How do I solve this? And how do I get miniconda to update (I tried ‘conda update conda’ and ‘sudo apt-get install …’)

(qiime2-2018.2) [email protected]:~$ conda info

 active environment : qiime2-2018.2
active env location : /home/qiime2/miniconda/envs/qiime2-2018.2
        shell level : 1
   user config file : /home/sara/.condarc

populated config files :
conda version : 4.4.7
conda-build version : not installed
python version : 3.6.3.final.0
base environment : /home/qiime2/miniconda (read only)
channel URLs : https://repo.continuum.io/pkgs/main/linux-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/linux-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/linux-64
https://repo.continuum.io/pkgs/pro/noarch
package cache : /home/qiime2/miniconda/pkgs
/home/sara/.conda/pkgs
envs directories : /home/sara/.conda/envs
/home/qiime2/miniconda/envs
platform : linux-64
user-agent : conda/4.4.7 requests/2.18.4 CPython/3.6.3 Linux/4.4.0-112-generic ubuntu/16.04 glibc/2.23
UID:GID : 1002:1003
netrc file : None
offline mode : False

(qiime2-2018.2) [email protected]:~$ conda update conda

PackageNotInstalledError: Package is not installed in prefix.
prefix: /home/qiime2/miniconda/envs/qiime2-2018.2
package name: conda

(qiime2-2018.2) [email protected]:~$

And how do I solve the problem of getting a clash between the qiime2-provided miniconda and the miniconda I installed under /home/qiime2? I have two users, one admin (‘qiime2’) and one normal (‘sara’) - got a bit too enthusiastic on the qiime2 account and installed miniconda “again” and now I get solving environment messages when I run things as ‘qiime2’. No problems as ‘sara’.

Thanks!

Hi @SaraR, I might not entirely understand your question, so apologies for that, but if you want to update conda, you need to do that in the base (formerly called root) environment, so basically don’t have your QIIME 2 environment activated when you run that conda update conda command:

(qiime2-2018.2) [email protected]:~$ source deactivate
[email protected]:~$ conda update conda

Don’t worry, we don’t provide a anaconda/miniconda installation — that is why one of the first steps in the Native Install guide is to install miniconda — basically it is BYOMC (bring your own miniconda)! If you already have it, then you are good to go.

Hmm, something sounds weird here — maybe it makes sense to uninstall miniconda and reinstall one system-wide instance? Either way, if you are still having issues, you might want to seek help on the miniconda support channels, they are probably better equipped to help debug issues with their software (but we are certainly willing to give it a try, too!).

Good luck and please let us know what you wind up doing! :t_rex:

Hi and thanks!

This bit solved part of the issue, as I hadn’t realised I had to do the source deactivate bit first:

if you want to update conda, you need to do that in the base (formerly called root) environment, so basically don’t have your QIIME 2 environment activated when you run that conda update conda command:

I have also removed everything related to miniconda3 that I installed now. But I am still getting that “solving environments” and a twirling stick (|/) when calling conda, even if it does work after a while.

I am using Qiime2 in Virtualbox as provided by qiime2, so most things are the way they were set up in that. I might have (probably?) installed miniconda last time I tried to update qiime2 back in January using the native install instructions. Could installing miniconda while having qiime2 activated be causing these problems, or does that not have anything to do with it?

Either way, if you are still having issues, you might want to seek help on the miniconda support channels, they are probably better equipped to help debug issues with their software (but we are certainly willing to give it a try, too!).
After my experience with Bio-Linux and similar bioinformatics-bundle-provided-as-tweeked-distros-in-a-VB, I’ve found that the “normal” communities often can’t help as things in the bundle aren’t necessarily where they would normally be in an ordinary setup, and I’m not experienced enough at Linux to bridge the gap.

Hi @SaraR!

That’s normal conda behavior – the “twirling stick” is an indicator that the conda command is still running. Depending on the command and your system specs, it can take awhile to complete.

If you’re using the QIIME 2 VirtualBox, you don’t need to install Miniconda or a QIIME 2 conda environment – those are already set up for you. Probably the easiest way forward is to download the latest QIIME 2 VirtualBox image since it sounds like the current VirtualBox image you’re using has a clobbered Miniconda install and/or QIIME 2 conda environment. Let us know if that fixes the issue!

Hi @jairideout

So it seems like everything is actually working as it should. That’s good! :slight_smile:

I set up the QIIME2 in VB last year, but since the new releases are so frequent and I didn’t want to risk loosing what I’ve got in there (I’m also using it as my go to Ubuntu now, since Bio-Linux is stuck an older version) so Evan suggested using the native install instructions to update.

I think between your, @thermokarst and google I’ve managed to get this to work. (Until next time…)

Thank you!

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