Commit f9efe8de authored by Chris Hines's avatar Chris Hines
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Update docs/conda.md

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Conda on M3
===========
conda (anaconda and miniconda) are great ways to create a python environment.
Unfortunately for some reason they edit your `.bashrc` file creating a situation where MASSIVE desktops no longer work. We provide a wrapper script to help create conda environments without this unforunate side effect
Creating a Conda environment
=============================
Please open a connection to M3 (you might use the strudel2 terminal to do this, or a native terminal) and follow these steps
```
$ cd <minicondapath>
# Install miniconda
$ module load conda-install
$ conda-install <minicondapath>
```
replacing `<minicondapath>` with an actual directory. By default we set `<mincondapath>` to `/scratch/<projectid>/<username>/miniconda`
Using the default JupyterLab environement
=========================================
The conda-install script (by default) sets up a jupyter environment and makes it available by strudel2.
You can use this immediately by selecting the approperiate option on strudel2
If you want to add additional packages to the jupyter lab environment
```
source <minicondapath>/bin/activate
conda activate jupyterlab
conda install <packagename>
```
Creating other (non-Jupyter-non-Strudel2) environments
======================================================
```
source <minicondapath>/bin/activate
conda create <environmentname>
conda activate <environmentname>
```
Stopping conda
==============
```
(jupyterlab) [chines@m3-login2 ~]$ conda deactivate
(base) [chines@m3-login2 ~]$ conda deactivate
```
Note that the first deactivate, deactivates the current environement. The second deactivate deactivates conda entirely (at which point you will have to return the the instruction to `source <minicondapath>/bin/activate`)
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