Downloading and installing BEAST on UNIX/Linux
BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.
Downloading BEASTTip: If you want to install BEAST on the Mac OS X command-line, we strongly recommend using the Homebrew package manager. .
BEAST can be downloaded from the following link:
This will download a compressed tar archive (a ‘.tgz’ file).
The latest version of BEAST can always be found here: https://github.com/beast-dev/beast-mcmc/releases/latest
Installing using CondaThe simplest option for installing BEAST is to use the anaconda package and environment manager. We recommend installing the minimal version, miniconda.
https://docs.anaconda.com/miniconda/
Once installed you can create an environment for running BEAST:
conda create -n beast
activate it:
conda activate beast
and then install BEAST from the bioconda channel:
conda install beast -c bioconda
finally test the installation:
beast -beagle_info
This will also work in the Mac OS X command line
Installing directly Installing OpenJDK 8Ubuntu-based linux operating systems have Open JDK installed as their default Java installation. To install Open JDK 8 (both JRE and JDK), you can run the following commands:
sudo apt-get install openjdk-8-jre sudo apt-get install openjdk-8-jdk
Installing Oracle Java 8If you’d like to use Oracle Java instead of Open JDK, you will require the PPA maintained by Webupd8 Team before proceeding with the installation:
sudo apt-add-repository ppa:webupd8team/java sudo apt-get update sudo apt-get install oracle-java8-installer
Note: if the apt-add-repository command is not found, first install the following:
sudo apt-get install software-properties-common
The PPA also contains a package to automatically set Java environment variables, by simply running the following command:
sudo apt-get install oracle-java8-set-default
You can now edit the /etc/environment configuration file and add the following entries to set JAVA_HOME and JRE_HOME environment variables:
JAVA_HOME=/usr/lib/jvm/java-8-oracle JRE_HOME=/usr/lib/jvm/java-8-oracle/jre
Installing BEAST Downloading and running BEAST on LinuxStart by downloading and unpacking the compressed .tar.gz file:
tar -zxvf BEASTv10.5.0.tgz
You can now go to the /bin directory and run BEAUti and BEAST from this directory:
cd BEASTv10.5.0/bin ./beauti ./beast
Adding the executables to the system pathTo add the BEAUti and BEAST executables to the system’s path (to run from outside the /bin directory), you need to edit your system’s profile:
nano ~/.bash_profile
and add the path to the /bin directory:
export PATH=$PATH:$HOME/BEASTv10.5.0/bin/
To reload the changes to the profile immediately without logging out or restarting your computer, run the following:
source ~/.bash_profile
Verify your current system’s path settings by typing:
echo $PATH
Creating symbolic links in a directory of choiceln -s Downloads/BEASTv10.5.0/bin/beauti beauti ln -s Downloads/BEASTv10.5.0/bin/beast beast
Running BEAST from a jar file (with GUI)Go to the /lib directory where you extracted the linux .tar.gz file:
cd BEASTv10.5.0/lib java -jar beauti.jar java -jar beast.jar
Running BEAUti and BEAST from a jar file (without GUI)In that same /lib directory, provide command-line options for BEAST to run with:
java -jar beast.jar -seed 1234 example.xml
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