Installation Instructions

Check to see if Conda is already installed

If you have ever installed the Anaconda Python distribution on your local machine, then you already have Conda installed! Mac and Linux users can check whether Conda is installed by running the following command in a terminal.

$ which conda
/Users/$USERNAME/miniconda3/bin/conda

If Conda has already been installed on your machine, then this command should return the absolute path to the conda executable.

Windows users should search for “Anaconda” to see if the “Anaconda Command Prompt” shows up as an option, if it does then you already have Conda installed.

Old version of Anaconda?

If you previously installed the Anaconda Python distribution you may have an old version of Conda. You can check your version of Conda with the following command.
$ conda --version
If you have a version of Conda that is 4.5 (or older), then it is probably best to uninstall your Anaconda Python distribution and then reinstall the most recent version.

Install Python 3 version of Miniconda

If Conda has not been installed on your machine, then install the Python 3 version of Miniconda for your OS. As the name suggests, Miniconda is a “mini” version of the Anaconda Python distribution that includes only Conda, a Python 3 distribution, and any necessary OS-specific dependencies.

For convenience here are links to the 64-bit Miniconda installers.

Prefer Miniconda to Anaconda

I suggest installing Miniconda which combines Conda with Python 3 (and a small number of core systems packages) instead of the full Anaconda distribution. Installing only Miniconda will encourage you to create separate environments for each project (and to install only those packages that you actually need for each project!). Project specific environments enhance portability and reproducibility of your research and workflows.

Besides, if you really want the full Anaconda distribution you can always create an new conda environment and install it using the following command.
$ conda create --name my-anaconda-env anaconda=5.3
We will discuss the above command in great depth in the workshop.

Windows installation

After you downloaded the Windows GUI installer, double click on it and follow the instructions (accept license, etc.). You can use the defaults except for the “Advanced Installation Options” where you would tick on “Add Miniconda3 to my PATH environment variable”.

Mac OSX installation

After you downloaded the Mac OSX GUI installer, double click on it and follow the instructions (accept license, etc.). When you are asked where to install Miniconda, you should leave the default option to “install for me only”. If you get the error message “You cannot install Miniconda in this location,” reselect “Install for me only”. Then you should be able to continue to the next. The default option will modify your PATH in ~/.bash_profile. If you open the terminal after installation is over, you would see “(base)” on the left side of prompt.

Linux installation

I will walk through the steps for installing on Linux systems below as installing on Linux systems is slightly more involved. First, download the 64-bit Python 3 install script for Miniconda (clicking the link above will download the same script!).

wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Run the Miniconda install script. Follow the prompts on the installer screens. If you are unsure about any setting, accept the defaults (you can change them later if necessary).

bash Miniconda3-latest-Linux-x86_64.sh

Once the install script completes, you can remove it.

rm Miniconda3-latest-Linux-x86_64.sh

Verifying your Conda installation

In order to verify that you have installed Conda correctly run the conda help command. Output of the command should look similar to the following.

$ conda help
usage: conda [-h] [-V] command ...

conda is a tool for managing and deploying applications, environments and packages.

Options:

positional arguments:
  command
    clean        Remove unused packages and caches.
    config       Modify configuration values in .condarc. This is modeled
                 after the git config command. Writes to the user .condarc
                 file (/Users/drpugh/.condarc) by default.
    create       Create a new conda environment from a list of specified
                 packages.
    help         Displays a list of available conda commands and their help
                 strings.
    info         Display information about current conda install.
    init         Initialize conda for shell interaction. [Experimental]
    install      Installs a list of packages into a specified conda
                 environment.
    list         List linked packages in a conda environment.
    package      Low-level conda package utility. (EXPERIMENTAL)
    remove       Remove a list of packages from a specified conda environment.
    uninstall    Alias for conda remove.
    run          Run an executable in a conda environment. [Experimental]
    search       Search for packages and display associated information. The
                 input is a MatchSpec, a query language for conda packages.
                 See examples below.
    update       Updates conda packages to the latest compatible version.
    upgrade      Alias for conda update.

optional arguments:
  -h, --help     Show this help message and exit.
  -V, --version  Show the conda version number and exit.

conda commands available from other packages:
  env

At the bottom of the help menu you will see a section with some optional arguments for the conda command. In particular you can pass the --version flag which will return the version number. Again output should look similar to the following.

$ conda --version
conda 4.8.2

Make sure you have the most recent version

Once Conda exists on your machine, then run the following command to make sure that you have the most recent version and patches.

$ conda update --name base --channel defaults --yes conda

You can re-run this command at any time to update to the most recent version of Conda.

Initializing your shell for Conda

Key parts of Conda’s functionality require that it interact directly with the shell within which Conda commands are being invoked as such each shell must be configured to make use of them. The conda init command initializes a shell for use with Conda by making changes to your system that are specific and customized for each shell. Conda supports a number of different shells and you can run conda init --help to see the complete list.

Mac OSX and Linux users will want to initialize Conda for Bash as follows. If you are installing on Linux, then you may be prompted to initialize Conda for your shell when running the installation script. If so, then you can safely skip this step.

$ conda init bash

Windows users can either use the Anaconda Command Prompt or the Anaconda Powershell Prompt which are already initialized for Conda or they can initialize Conda for Powershell as follows.

> conda init powershell

After running conda init you will need to close and restart your shell for changes to take effect. Alternatively, Mac OS and Linux users can reload your ~/.bashrc profile (which was changed by running the conda init command). To reload your ~/.bashrc profile, use the following command.

$ source ~/.bashrc

If you want to reverse or “undo” the changes made by conda init, then you can re-run the conda init command and pass the --reverse option. Again, in order for the reversal to take effect you will likely need to close and restart your shell session.

Add bioconda as a channel

This version of introduction to conda will use bioinformatics examples and therefore it is important to configure conda to look in the bioconda repository for the packages required.

> conda config --add channels bioconda

To confirm this has added the biconda channel to your .condarc file run the command below.

conda config --show channels

This should show bioconda in the list of channels:

channels:
  - bioconda
  - defaults

Use of Binder instead of installing Conda (Optional)

If you wish to get started with this course without installing Conda, then you can use a pre-configured instance running on Binder by clicking on the link below.

Workspace for Conda environments

In order to maintain a consistent workspace for all your conda environment, we will create a new introduction-to-conda-for-data-scientists directory on your Desktop and store our conda environment in this directory. On Mac OSX and Linux running following commands in the Terminal will create the required directory on the Desktop.

$ cd ~/Desktop
$ mkdir introduction-to-conda-for-data-scientists
$ cd introduction-to-conda-for-data-scientists

For Windows users you may need to reverse the direction of the slash and run the commands from the command prompt.

> cd ~\Desktop
> mkdir introduction-to-conda-for-data-scientists
> cd introduction-to-conda-for-data-scientists

Alternatively, you can always “right-click” and “create new folder” on your Desktop. All the commands that are run during the workshop should be run in a terminal within the introduction-to-conda-for-data-scientists directory.