Installation

For releases 2015.11 and later

BioBuilds releases starting with 2015.11 use Continuum Analytics’ conda installer for installation and package management. Users who have not already installed a previous conda-based release and are not already using conda should first download the appropriate Miniconda release:

and run "bash Miniconda-latest-<os>-<arch>.sh" to install conda.

Once you have installed conda, you can then install a BioBuilds release by running the following commands from your shell:

conda update conda
conda create -c biobuilds -p /path/to/biobuilds-YYYY.MM biobuilds==YYYY.MM

where “YYYY.MM” is the release identifier (e.g., 2015.11 or 2016.04).

For releases up to 2015.04

BioBuilds releases up to and including 2015.04 were distributed as a tarball for Mac OS X (Intel) and Debian and Red Hat Linux distributions. The tarball includes all binaries, their dependencies, and source code.The top-level directory in the tarball contains the following:

install directory/bin                
                 /include
                 /lib
                 /src
                 /share                
                 /env.sh
                 /MD5SUMS.txt

The executables are located in the ‘bin‘ directory, while the headers are in ‘include‘ and libraries in ‘lib‘.  The original bioinformatics packages used to build BioBuilds are included for reference in the ‘src‘ directory.   The ‘env.sh‘ file can be ‘sourced’ to include BioBuilds paths into your runtime environment using the following command:

$ source <install_directory>/env.sh

Sourcing the ‘env.sh‘ will add the following environment variables to your environment:

BIOBUILDS_HOME:  Path to the toplevel BioBuild directory.
BIOBUILDS_BIN: Path to the BioBuilds binary executable directory.
BIOBUILDS_LIB: Path to the BioBuilds library directory.
BIOBUILDS_JAVA: Path to the BioBuilds java files.

And most importantly, the BIOBUILDS_BIN, BIOBUILDS_LIB, and BIOBUILDS_JAVA are prepended to your PATH, LD_LIBRARY_PATH, and CLASSPATH, respectively, so that the tools are all callable directly from the shell.

Important: By prepending the paths, BioBuilds versions of tools and supporting libraries will be picked up first when executing any application. If you have other tools built outside of BioBuilds, you may need to adjust the paths accordingly.

MD5SUMS.txt includes MD5 checksums for all binaries. This can be used to validate your installation over time to ensure that the binaries are the same ones that shipped with BioBuilds.

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