Setting up your Linux Environment - dkoes/docs GitHub Wiki

These instructions may apply equally well to the Linux Subsystem for Windows.

For Mac, you should use MacPorts for installing packages.

Conda

If you are using an older version of conda (such as the anaconda currently loaded by default on the cluster), be sure to switch to the mamba solver in your base environment:

conda install -n base conda-libmamba-solver
conda config --set solver libmamba

Install prerequisites

Some common packages.

apt-get install build-essential git wget libopenbabel-dev libboost-all-dev libeigen3-dev libgoogle-glog-dev libprotobuf-dev protobuf-compiler libhdf5-serial-dev libatlas-base-dev python-dev cmake librdkit-dev python-pip imagemagick

Some common python packages:

sudo pip install matplotlib scipy scikit-learn scikit-image protobuf psutil numpy seaborn jupyter plumbum MDAnalysis biopython Pillow prody py3dmol pandas cython

We highly recommend using a terminal session manager such as tmux (our group's tutorial is here).

Environment

In your .bashrc configure the history:

HISTCONTROL=ignoredups
export PROMPT_COMMAND="history -a"
shopt -s histappend
export HISTSIZE=1000000