b2b-utils

This package contains a set of programs and utilities for working with genomic data. Software in the 'alpha' folder is awaiting updating, testing, or documentation and should be handled with care. Please see the documentation page or in-program --help for usage and details.

Installation

Using Conda

These tools are now available through the Bioconda package b2b-utils. You can install with e.g.:

conda install -c bioconda b2b-utils
# or probably faster:
mamba install -c bioconda b2b-utils

Note that not all tool dependencies are automatically installed along with the base package, in order to keep the installation footprint down. Each tool checks for any underlying dependencies at run-time and should give an informative error if they are not found. All dependencies are available within Conda and can be installed individually as needed. Alternatively, you can install a complete environment, including all tool dependencies, using the environment.yml file included in this repository. The following command will install b2b-utils and all dependencies into the b2b-utils environment:

conda env create -f <path-to-downloaded-environment.yml>
# or probably faster:
mamba env create -f <path-to-downloaded-environment.yml>

NOTE: This is not necessary for most of the tools in this suite, which should run from the base Conda package without any additional installs.

From source

For non-Conda users, the tools can be installed from source in Linux (and possibly other platforms) as follows:

git clone https://github.com/jvolkening/b2b-utils.git
cd b2b-utils
perl Build.PL
./Build
./Build test
./Build install