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# Gene Prediction with AUGUSTUS



AUGUSTUS is a program to find genes and their structures in one or more genomes. [More ...](docs/


## Ubuntu 18.04 or later
This currently installs only a single-genome version without comparative gene prediction capability:
sudo apt install augustus augustus-data augustus-doc

## Clone from GitHUB

To obtain the most recent complete version, first, clone the repository

git clone
or, alternatively, [download]( and unpack the AUGUSTUS source package with
tar -xzf augustus.current.tar.gz

## Docker

After retrieving Augustus change into the main directory containing the 
[Dockerfile](Dockerfile) and issue

docker build -t augustus .

## Install dependencies

The following dependencies may be required for AUGUSTUS:
- Optional libraries for gzip compressed input (uncomment ZIPINPUT = TRUE in
  - libboost-iostreams-dev
  - zlib1g-dev
- Optional for comparative (multi-species, CGP) AUGUSTUS with SQLite (uncomment COMPGENEPRED = true and SQLITE = true in
  - libgsl-dev
  - libboost-graph-dev
  - libboost-all-dev
  - libsuitesparse-dev
  - liblpsolve55-dev
  - libsqlite3-dev
- Optional for comparative (mutli-species, CGP) AUGUSTUS with MySQL (uncomment COMPGENEPRED = true and MYSQL = true in
  - libgsl-dev
  - libboost-graph-dev
  - libboost-all-dev
  - libsuitesparse-dev
  - liblpsolve55-dev
  - libmysql++-dev
- For compiling bam2hints and filterBam:
  - libbamtools-dev
- For compiling bam2wig:
  - Follow [these instructions](./auxprogs/bam2wig/README.txt)
- For compiling utrrnaseq:
  - libboost-all-dev (version must be >Boost_1_49_0)

## Compile from sources

Once all dependencies are available, you can compile AUGUSTUS using make.


After compilation has finished, the command bin/augustus should be executable and print a usage message.

## Install locally

As a normal user, add the directory of the executables to the PATH environment variable, for example:

export PATH=$PATH:~/augustus/bin:~/augustus/scripts

## Install globally

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).

export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/

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 can also be run through a web-interface at and a web service at


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/](docs/

[3 book chapters with command line walkthroughs](


All source code, i.e.
  - the AUGUSTUS source code (src/*.cc, include/*.hh)
  - the scripts (scripts/*.pl)
  - the auxiliary programs (auxprogs/)
  - the tree-parser (src/scanner,src/parser)
is under the [Artistic License](src/LICENSE.TXT).