Installation

Requirements

  • A UNIX-based operating system (like Linux or MacOS) with bash is recommended. This software has not been tested with the Windows shell.
  • seabreeze requires conda >= 23.3.1 to install python packages and manage environments. We recommend Miniforge, a minimal conda installer that is similar to Miniconda.
  • ISEScan, one of the dependencies, is not compatible with some ARM-based systems, and users may face issues.

We recommend creating a dedicated conda environment for seabreeze, to avoid package conflicts. 

conda env create --name seabreeze

Once built, activate the environment:

conda activate seabreeze

Finally, install the package from bioconda.

conda install seabreeze-genomics -c bioconda

In case this does not work, try specifying:

conda install seabreeze-genomics -c conda-forge -c bioconda

Install from GitHub

Download the latest release of seabreeze from the [Github Repository](https://github.com/barr>

seabreeze only requires an intial conda environment to be set up. Navigate to the seabreeze diectory and run the following command:

 conda env create --name seabreeze --file environment.yml

Activate the conda environment before running the commands.

conda activate seabreeze

Finally,

pip install .

You're all set! See Usage to get started.

Optional

By default, seabreeze creates conda environments and installs packages in the seabreeze directory. However, if you plan to use seabreeze multiple times, or with different directories for different samples, then it can be helpful to have a common location on your system to store environments. This can save disk space and time by avoiding repeated installation of environments.

Create a folder for Snakemake to store conda environments. We recommend a directory in $HOME, but it could be anywhere.

mkdir $HOME/snakemake_conda_envs

Append this line to your ~/.bashrc, ~/.zshrc or as applicable to the shell you are using, using the path to the directory created in the previous step.

export SNAKEMAKE_CONDA_PREFIX=$HOME/snakemake_conda_envs