Conda recipes for the sanger-pathogens channel: https://anaconda.org/sanger-pathogens

• Introduction
• Usage
• License
• Feedback/Issues

Conda is an open source package and environment management system. This repository hosts recipes for packages on the sanger-pathogens Anaconda channel.

Conda recipes that are to be made available as packages on the sanger-pathogens Anaconda channel are stored in the recipes directory. This follows the same subdirectory structure as Bioconda and conda-forge.

Conda environments are collections of their packages and dependencies and are found in the environments directory. The environments that are in production are in the production directory. The package lists which can be used to generate these environments are found in the package-lists directory.

The environments in the production directory are built on linux machines. For MacOS specific environments there is a separate local-osx directory.

Before building the environments, make sure that you have the following Conda channels set up.

conda config --add channels 'defaults'   # lowest priority
conda config --add channels 'bioconda'
conda config --add channels 'conda-forge'
conda config --add channels 'sanger-pathogens'   # highest priority

To build the sanger-pathogens environment from the sanger-pathogens package list:

conda create -n sanger-pathogens
conda install --yes --file package-lists/sanger-pathogens.txt

To export the environment:

conda env export -n sanger-pathogens | cut -f -2 -d "=" | grep -v "prefix" > sanger-pathogens.yml

For the sanger-pathogens-deployment environment, the package perl-yaml-xs comes from a different channel at the moment so there is an extra step in the build even though the package is in the requirements file.

conda create -n sanger-pathogens-deployment
conda install --yes --file package-lists/sanger-pathogens-deployment.txt
conda install -n sanger-pathogens-deployment -c eumetsat perl-yaml-xs

Alternatively, you can add the eumetsat channel before running the first conda install but you will need to make sure it has the lowest priority.

To use the recipes and/or their corresponding packages you will need to install Conda.

The Conda recipes in this repository are freely available, licensed under GPL v3.

Please report any issues to the issues page or email [email protected].