diff --git a/docs/setup/package-managers/micromamba.md b/docs/setup/package-managers/micromamba.md index 6225254..0bf1a2c 100644 --- a/docs/setup/package-managers/micromamba.md +++ b/docs/setup/package-managers/micromamba.md @@ -59,6 +59,82 @@ Strict channel priority helps keep dependency resolution more predictable. ::: +## Computational Workstations & Shared Environments + +On shared computational workstations (e.g. `kmer`), micromamba is often pre-installed with a shared conda root. + +### Verify installation + +```sh +micromamba --version +micromamba info +``` + +Make sure the root prefix is set correctly (example): + +```text +/home/ndemo/.conda +``` + +### Create a personal environment + +```sh +micromamba create -n test python=3.12 numpy scipy -y +``` + +Activate and verify it: + +```sh +micromamba activate test +which python +python --version +``` + +The expected path should look like: + +```text +/home/ndemo/.conda/envs/test/bin/python +``` + +Deactivate when done: + +```sh +micromamba deactivate +``` + +### Create and use shared environments (managed by root) + +On shared servers, system administrators can create environments in a shared location (e.g. `/data/conda/shared_envs/`) that all users can activate. + +::: warning +Only root/administrators can create or update shared environments. +::: + +As root: + +```sh +micromamba create \ + -p /data/conda/shared_envs/scientific \ + -c conda-forge \ + python=3.12 numpy scipy pandas matplotlib \ + -y +``` + +As any user, you can activate it directly by path: + +```sh +micromamba activate /data/conda/shared_envs/scientific +``` + +To add packages to a shared environment, only the administrator can do so: + +```sh +micromamba install \ + -p /data/conda/shared_envs/scientific \ + scikit-learn -y +``` + + ## Core Workflow ::: warning