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Set up Miniconda on Aguirre Lab machine


Here are instructions for a user of an Aguirre Lab machine to set up Miniconda.

Miniconda is installed in the administrator account, aguirrelab. You should access and use this installation, and can modify it and install packages.

Activate:

$ source /home/aguirrelab/miniconda3/bin/activate

Your console prompt should now be prepended by (base).

Create an environment from your environment.yml. My usual environment is in my dotfiles repo. It is called er and it contains Python 3.8, Tensorflow, Numpy, Pandas, h5py, etc. Your repo may have its own environment.yml, or you can create an environment with commands.

$ conda env create -f environment.yml
$ conda activate er

Your prompt should now be prepended by (er) (or whatever your environment name is).

If you use my .zshrc, every time a new shell is opened, the script conda.sh is called, and if you are in a Tmux session, conda is re-activated.

If you do not use my .zshrc or something similar, update your .zshrc so new shells know the path to Conda:

$ conda init zsh

Check to ensure your path has the miniconda environment version of Python, and that the version is correct:

$ which python
/home/aguirrelab/miniconda3/envs/er/bin/python
  
$ python --version
Python 3.8.3