Python

conda

  • conda is a package manager that saves a lot of headache in terms of installation and preventing conflicts between applications
  • can install anaconda or miniconda. Anaconda is pretty bloated, so I recommend minconda. Use installation instructions at https://docs.conda.io/en/latest/miniconda.html
  • lots of good info for using conda at https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
    • Each “environment” is isolated, so that you can keep apps that conflict with each other separate.
  • Do not install lots of applications on servers like baron1. For a shared system, it is better for me to install it once for everybody to use (with conda, everyone would have their own copy of the app, which is innefficient).
    • However, conda would still be useful for python packages in your home directory

pip (package installer for Python)

  • pip is a package manager for python
  • conda can do almost everything pip can. However, one thing pip can do is install directly from github, which is useful for CFMM’s pybruker package (see below)

pybruker

  • used for reading bruker enhanced dicoms
  • see gitlab.com/cfmm/bruker/pybruker for more info
  • use the following:
    pip install pydicom
    pip install git+https://gitlab.com/cfmm/bruker/pybruker 
  • Pip may give a warning that the installed executables are not on the path. If so, add the path to ~/.bashrc using the below template (you will need to change the path to whatever pip tells you):
    # Path for executables installed by pip
    export PATH="/path/to/add:$PATH"