Conda Cheatsheet¶

Command line package and environment manager Learn to use conda in 30 minutes at bit.ly/tryconda

Getting Started¶

Setting up Conda on your machine¶

When using tllihpcmind6, initialize Conda by source ~/.bashrc

$ source ~/.bashrc

$ which conda
/gpfs/mskmind_ess/<YOUR_USER_NAME>/miniconda/bin/conda

$ conda update conda

$ conda --version

$ conda --help

$ conda list

Creating a Virtual Environment¶

A virtual environment can be defined and created through an environment.yml file. For example, the Conda environment conda-env-cdm can be created with this snippet included in environment.yml

name: conda-env-cdm
channels:
  - pytorch
  - nvidia
  - conda-forge
dependencies:
   - python == 3.10
   - pandas
   - pyyaml
   - requests
   - setuptools_scm
   - setuptools
   - pip
   - pip: 
       - git+https://github.com/clinical-data-mining/msk_cdm.git
   - minio

Conda Basics¶

conda info: Verify conda is installed, check version number
conda update conda: Update conda to the current version
conda install PACKAGENAME: Install a package included in Anaconda
spyder: Run a package after install, example Spyder*
conda update PACKAGENAME: Update any installed program
COMMANDNAME --help: Command line help
- conda install --help

Using Environments¶

conda create --name py35 python=3.5: Create a new environment named py35, install Python 3.5
conda env create -f environment.yaml: Create a new environment with specifications in environment.yaml (See Start-up)
conda activate py35: Activate the new environment to use it
conda env list: Get a list of all my environments, active environment is shown with *
conda list: List all packages and versions installed in active environment
conda env remove --name bio-env: Delete an environment and everything in it
conda deactivate: Deactivate the current environment

Installing Packages¶

Anaconda includes both the Python and R programming languages, most of the common Python libraries used in science and engineering (including NumPy, SciPy, Matplotlib, and pandas), and many commonly used R packages (https://anaconda.org/).

conda install -c anaconda pandas: Install Pandas into your activate environment