![]() Please see the conda environment file documentation for more information. Specific package versions can be specified using the and = operators.įor example, samtools<=1.11 will install the latest version of samtools less than or equal to 1.11. In the example, the citipy package is installed using pip. Pip: the pip package manager is used to install additional packages. Channels can be thought of as additional repositories that contain packages.ĭependencies: the packages that will be installed in the conda environment. This name will be used to reference the environment in the conda activate command.Ĭhannels: the channels to be used when creating the conda environment. The environment.yml file provides the following instructions for creating the conda environment: This is the ideal order of dependencies and should be followed to reduce possible installation issues. The pip dependencies are added to the end of the environment file to reduce conda/pip installation issues from being used in the same environment. The pip dependency is required to install the citipy package using the pip package manager. Make sure the folders exist and are writable. In the example below, the CONDA_ENVS_DIRS and CONDA_PKGS_DIRS are set to a folder in the RIS Data Storage Platform. See the conda documentation for more information. CONDA_PKGS_DIRS: the path to the directory where conda packages.CONDA_ENVS_DIRS: the path to the directory where conda environments.condarc file to avoid having to enter them for each job. ![]() The environment variables can be defined in your. Interactive Job Submission Defining Environment Variablesīegin by defining the environment variables that will be used during creation of the conda environment. The conda environment will be located in the RIS Data Storage Platform so that any changes will persist between jobs.Īs an example, a sequence analysis conda environment will be created containing the following tools: The purpose of this tutorial is to demonstrate the steps required to build and use a custom conda-based environment in RIS using an existing Docker image. If you need to review that information, please see the links below.ĭocker Basics: Building, Tagging, & Pushing A Custom Docker Image The information on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. ![]()
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