Export miniconda2's environments to miniconda3

Question

I used miniconda2 but I had to upgrade to miniconda3. However, how can export miniconda2's environments to miniconda3?

Thank you in advance,

UPDATE

I found here the below script:

for env in $(conda env list | cut -d" " -f1); do 
   if [[ ${env:0:1} == "#" ]] ; then continue; fi;
   conda env export -n $env > ${env}.yml
done

It only picks up the new miniconda3 environments and not the old miniconda2 which are located in a different folder.

> ls -1 /work/miniconda2/envs/
3d-dna
abyss
afterqc
busco4
...

(base)> conda activate /work//miniconda2/envs/busco4
(busco4)>

How can I modify the above script to export from miniconda2 folder?

score 0 · Answer 1 · answered May 20 '22 at 03:35

I'm having a hard time finding a conda YML file that's that old. There's no foolproof way that I'm aware of but here is a way that should satisfice the solution.

Note: This is for linux or mac; you can use findstr for Windows. Or PowerShell.

From your environment:

conda env export --from-history | grep -v "prefix" > your_environment_name.yml

You can view the contents with cat environment.yml. This gives you the libraries -- but not the dependencies -- and no version numbers for anything. I did that because sometimes a dependent library will get dropped for some reason or another. You may need to modify this with the new version of python you want.

I think this works better than conda env export | cut -f 1 -d '=' | grep -v ^prefix because, again, sometimes a dependency will get dropped.

From there

conda env create -f your_environment_name.yml -p /home/user/anaconda3/envs/your_environment_name

Thank you, I updated my question. Is there a way to do it for all environmentss in one go? — user977828, May 20 '22 at 04:13

merv · Answer 2 · 2022-05-22T01:43:11.367

An alternative approach here is to add the previous Miniconda2 package cache (/work/miniconda2/pkgs) and environments directory (/work/miniconda2/envs) to the pkgs_dirs and envs_dirs Conda configuration settings. That way you can simply continuing having them available without having to archive and recreate. There are some details in this answer.

You may need to add back the Miniconda3 locations after this if you would like them to continue to be defaults.

Also, because you installed multiple copies of Conda, you should probably check your ~/.bashrc (and/or ~/.bash_profile) file to remove any previous sections from conda init left by the other version.

Export miniconda2's environments to miniconda3

2 Answers2