Conda Environments
Conda Environments
For reproducible research it is advisable to keep the software versions you use consistent. An easy way of ensuring this is by creating a Conda environment, where you can explicitly say which versions are necessary to run your pipeline:
Downloading Anaconda
To build a conda environment, you will need the Anaconda Python distribution. You can download this at the following link:
Creating a Conda Environment
Once you have downloaded Anaconda, go to your terminal (Terminal for Macs and Mobaxterm is recommended for PC). Now in the terminal create your environment with the desired version of python:
conda create -n yourenvname python=3.8
Once created you can activate your environment like so:
conda acvitate yourenvname
Installing Tools
To install tools in your conda environment use the following syntax:
conda install yourpackage
Check out a list of available tools here:
!!! info "Anaconda Packages
Or if there is no available conda package you can also try installing these tools with pip:
pip install yourpackage
To see what's installed in your conda environment use:
conda list
Deactivating An Environment
When you are finished using your environment, deactivate the environment with:
conda deactivate
Installing A Conda Environment From a File
When you run an analysis using a conda environment, you can pass that environment onto others by exporting the tool versions to a yml file with the following command:
conda env export -n yourenvname -f yourenvname.yml --no-builds
Here we add no --no-builds because the environment you build is often specific to the machine you built it on. If you build the environment on Mac and want others to use it on a PC or linux platform it is advisable you export it without the "build" information your specific machine used.