Anduril is developed and tested on Linux. This User Guide includes example commands for Ubuntu, but other Linux distributions (e.g., Red Hat Enterprise Linux) work equally well.
The easiest way to get started is using Docker.
docker run -ti --rm anduril/core anduril -h
The above command prints the help message of the Anduril command line tool.
To make the Docker environment more useful, you can import a host folder (
./shared) into the container (
/opt/shared) using the following:
docker run -ti --rm -v $(pwd)/shared:/opt/shared anduril/core bash
Native installation may be preferred for production environments, such as for cluster deployment.
External dependencies of Anduril core and important components are:
|Name||Ubuntu 16.04 package|
|Java 7 or 8||openjdk-8-jdk|
Installation on Ubuntu
Paste the following script into a Bash shell. To install into a different folder than
~/anduril, modify lines two and three.
sudo apt-get install ant mercurial git default-jdk python r-base-dev git clone https://bitbucket.org/anduril-dev/anduril --branch stable ~/anduril export ANDURIL_HOME=~/anduril export PATH="$ANDURIL_HOME/bin:$PATH" anduril build anduril install tools
To get started, see the help message of the Anduril command line tool:
git: command not found
You do not have Git installed. Install it prior to invoking
anduril: command not found
You must add $ANDURIL_HOME/bin to your PATH, where $ANDURIL_HOME is the installation folder. Alternatively, you can call $ANDURIL_HOME/bin/anduril using the full path.
Error: Unable to access jarfile anduril.jar
(1) Your Anduril installation folder is not found correctly. Set the $ANDURIL_HOME environment variable to point to the folder that contains files such as anduril.jar. Ensure the environment variable is setup when you log in (e.g., by placing it into
(2) Your Anduril engine is not built. Build with
Installing additional component bundles
In addition to the core system that provides workflow facilities, Anduril includes component bundles (“modules”) for various analysis tasks. You can start with a basic system and add features if you need them.
Anduril developers distribute the following component bundles. In addition, Anduril is fully extensible by third parties, so you can write your own component bundles or find third-party distributed bundles.
|flowand||Flow cytometry (FACS) analysis|
|microarray||DNA/RNA microarray analysis|
|sequencing||DNA/RNA sequencing analysis (NGS)|
|tools||Commonly used tools. Already installed above.|
Bundles are installed using
anduril install BUNDLE-NAME(S). For example, to install the microarray and sequencing bundles, type:
anduril install microarray sequencing
This installs the Anduril-specific code, but many components depend on external libraries and command-line tools as well. External dependencies are installed using
anduril install-dep. External dependencies can be large, so you can narrow the selection using bundle (
-b flag) and component (
-c flag) names. For example, to install all external depedencies of the tools bundle, run:
anduril install-dep -b tools
Anduril recognizes the following environment variables:
$ANDURIL_HOME: Points to the Anduril installation folder. This folder contains files such as anduril.jar and build.sbt.
$ANDURIL_BUNDLES(usually not needed): List of folders (separated by
:) that are searched for Anduril components.
$ANDURIL_HOME/bundlesis always searched, so it is not needed on
$ANDURIL_BUNDLES. This variable is needed if you have multiple bundle locations, or want to override a bundle with your own version (such as when developing a bundle).
anduril tool uses
$ANDURIL_HOME to locate the installation folder, but
$ANDURIL_HOME is not mandatory in the following cases:
andurilis invoked using an absolute or relative path, and not obtained from
andurilis obtained from
PATH, but it is a symbolic link to the installation folder (
bin/anduril). In this case,
andurilcan determine the installation folder by following the symbolic link