Installation - bpp/bpp-tutorial-geneflow GitHub Wiki

Detailed instructions on installing BPP are available on the GitHub site.

For this tutorial we will use BPP v4.8.4. You can either compile BPP from source, or download a pre-compiled binary distribution:

Compiling BPP from source

You can download and compile the source distribution (smaller download size) or clone the whole repository:

Source distribution To download the source distribution from a release and build the executable and documentation, use the following commands:

wget https://github.com/bpp/bpp/archive/v4.8.4.tar.gz
tar zxvf v4.8.4.tar.gz
cd bpp-4.8.4/src
make

Cloning the repo Instead of downloading the source distribution as a compressed archive, you could clone the repo and build it as shown below.

git clone https://github.com/bpp/bpp
cd bpp/src
make

Pre-compiled BPP binaries

Binary distributions are provided for x86-64, aarch64 and ppc64le systems running GNU/Linux, macOS and Windows.

For a GNU/Linux x86_64 system:

wget https://github.com/bpp/bpp/releases/download/v4.8.4/bpp-4.8.4-linux-x86_64.tar.gz
tar zxvf bpp-4.8.4-linux-x86_64.tar.gz

For a GNU/Linux aarch64 (ARM64) system:

wget https://github.com/bpp/bpp/releases/download/v4.8.4/bpp-4.8.4-linux-aarch64.tar.gz
tar zxvf bpp-4.8.4-linux-aarch64.tar.gz

For a GNU/Linux ppc64le system:

wget https://github.com/bpp/bpp/releases/download/v4.8.4/bpp-4.8.4-linux-ppc64le.tar.gz
tar zxvf bpp-4.8.4-linux-ppc64le.tar.gz

For a Mac with an Apple Silicon CPU:

wget https://github.com/bpp/bpp/releases/download/v4.8.4/bpp-4.8.4-macos-aarch64.tar.gz
tar zxvf bpp-4.8.4-macos-aarch64.tar.gz

For a Mac with an Intel CPU:

wget https://github.com/bpp/bpp/releases/download/v4.8.4/bpp-4.8.4-macos-x86_64.tar.gz
tar zxvf bpp-4.8.4-macos-x86_64.tar.gz

If you are using Windows, download and extract (unzip) the contents of this file:

https://github.com/bpp/bpp/releases/download/v4.8.4/bpp-4.8.4-win-x86_64.zip

Linux and Mac: You will now have the binary distribution in a folder called bpp-4.8.4-linux-x86_64 or bpp-4.8.4-macos-x86_64. The binary file is located in the bin subfolder, i.e. bin/bpp. We recommend making a copy or a symbolic link to the binary in a folder included in your $PATH.

Windows: You will now have the binary distribution in a folder called bpp-4.8.4-win-x86_64. The bpp executable is called bpp.exe.

Older versions are available in releases

Setting up the PATH variable - Linux example

mkdir -p $HOME/bin
cp bpp-4.8.4-linux-x86_64/bin/bpp $HOME/bin
export PATH=$PATH:$HOME/bin

If using BASH, you can include the $HOME/bin folder in the path permanently by adding an entry to your .bashrc file:

echo 'PATH=$PATH:$HOME/bin' >> $HOME/.bashrc

Using the Amazon Cloud

A BPP binary is already available on the Amazon Cloud system used by Physalia, and is accessible by all users. It resides in the /user/local/bin folder which is in $PATH, and can be executed by running

bpp

from inside any folder.

Using a generic HPC

The following instructions serve as guidelines on how to install BPP on a server or a desktop Linux system. Connect to the computer via ssh, and install the BPP program by creating a $HOME/bin folder, copying the bpp binary there, and adding the folder to $PATH. Note: the command modifying the .bashrc file has to be ran only once. Do not execute that line if you are re-doing the steps.

# connect to the computer
ssh username@IPADDRESS

# download and install BPP
wget https://github.com/bpp/bpp/releases/download/4.8.4/bpp-4.8.4-linux-x86_64.tar.gz
tar zxvf bpp-4.8.4-linux-x86_64.tar.gz
mkdir bin
cp bpp-4.8.4-linux-x86_64/bin/bpp bin

# include '$HOME/bin' in your PATH
export PATH=$PATH:$HOME/bin
echo 'PATH=$PATH:$HOME/bin' >> $HOME/.bashrc      # only run this once

# delete the temporary files
rm -Rf bpp-4.8.4-linux-x86_64
rm bpp-4.8.4-linux-x86_64.tar.gz

Obtaining the tutorial files

cd
wget https://github.com/bpp/bpp-tutorial-geneflow/raw/main/data/baobab.tar.gz
tar zxvf baobab.tar.gz
rm baobab.tar.gz