Gene Prediction with AUGUSTUS
AUGUSTUS is a program to find genes and their structures in one or more genomes. More ...
Windows users can use the Windows Subsystem for Linux (WSL) to install AUGUSTUS exactly as described below for Linux. How to set up the WSL for AUGUSTUS is described here.
Ubuntu 18.04, Debian 9 or later
Until Ubuntu 21.04 and Debian 11 only as single-genome version, since then with capability for comparative gene prediction.
sudo apt install augustus augustus-data augustus-doc
Create a docker image from Dockerfile using:
git clone https://github.com/Gaius-Augustus/Augustus.git cd Augustus docker build -t augustus .
Create a Singularity Image File from the Singularity Definition File using
git clone https://github.com/Gaius-Augustus/Augustus.git cd Augustus singularity build augustus.sif Singularity.def
Building AUGUSTUS from source
See INSTALL.md for details.
Download source code from github and compile:
git clone https://github.com/Gaius-Augustus/Augustus.git cd Augustus make augustus
After compilation has finished, the command bin/augustus should be executable and print a usage message.
For utilities use
As a normal user, add the directory of the executables to the PATH environment variable, for example:
You can install AUGUSTUS globally, if you have root privileges, for example:
sudo make install
Alternatively, you can exectue similar commands to those in the "install" section of the top-level Makefile to customize the global installation.
Optional: set environment variable AUGUSTUS_CONFIG_PATH
If the environment variable AUGUSTUS_CONFIG_PATH is set, augustus and etraining will look there for the config directory that contains the configuration and parameter files, e.g. '~/augustus/config'. You may want to add this line to a startup script (like ~/.bashrc).
If this environment variable is not set, then the programs will look in the path ../config relative to the directory in which the executable lies. As a third alternative, you can specify this directory on the command line when you run augustus: --AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
REFERENCES AND DOCUMENTATION
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), pages 637–644, doi: 10.1093/bioinformatics/btn013
For further references see docs/REFERENCES.md
All source code, i.e.
- the AUGUSTUS source code (
- the scripts (
- the auxiliary programs (
- the tree-parser (
- the unit tests (
is under the Artistic License.