[LEGACY] Conda Environment Setup

This repository contains a legacy conda environment configuration that was previously used in the Simoes-Costa Lab to standardize software environments across users.

It is preserved for reference but is no longer the recommended approach for setting up computational environments in the lab.

Status

⚠️ Archived repository maintained for historical reference.

Current Infrastructure

Updated environment management strategies and computational infrastructure are maintained in the active repositories of the Simoes-Costa-Lab organization.

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Maintained for archival purposes.

Conda Setup

A repository containing an automatic installation of two different conda environments (py27 and py37) for easy user setup.

Installation guide (Only first time!)

Clone the repository, make the script executable, and then run it.

git clone https://github.com/Simoes-Costa-Lab/conda_setup/
cd conda_setup
chmod +x ./install.sh
./install.sh

Reload your shell

Update guide

Update the repository, then update the environment.

cd conda_setup
git pull
conda env update -n py37 --file py37environment.yml #can --prune if you want.
conda env update -n py27 --file py27environment.yml

Exporting an update guide

Update packages for each environment

conda update --all
pip list --outdated --format=freeze | grep -v '^\-e' | cut -d = -f 1 | xargs -n1 pip install -U 
conda activate py27
conda update --all
pip list --outdated --format=freeze | grep -v '^\-e' | cut -d = -f 1 | xargs -n1 pip install -U 

Write out the environment to a file

conda env export -n py37 > py37environment.yml
conda env export -n py27 > py27environment.yml

Then upload this to github, don't forget to update the prefix with $HOME.