diekhans/Augustus

Genome annotation with AUGUSTUS

Gene Prediction with AUGUSTUS

INTRODUCTION
INSTALLATION
RUNNING AUGUSTUS
WEB-SERVER
COMPARATIVE GENE PREDICTION
AUTHORS AND CONTACT
REFERENCES
LICENSES

INTRODUCTION

AUGUSTUS is a program to find genes and their structures in one or more genomes. More ...

INSTALLATION

Windows

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 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 https://github.com/Gaius-Augustus/Augustus.git

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 and issue

docker build -t augustus .

Install dependencies

The following dependencies are required for AUGUSTUS:

• For gzip compressed input: (set ZIPINPUT = false in common.mk if this feature is not required or the required libraries are not available)
  • libboost-iostreams-dev
  • zlib1g-dev
• For comparative AUGUSTUS (multi-species, CGP): (set COMPGENEPRED = false in common.mk if the libraries required by the CGP version are not available. Augustus can then only be run in single-genome mode, which is what most users need.)
  • libgsl-dev
  • libboost-all-dev
  • libsuitesparse-dev
  • liblpsolve55-dev
  • libsqlite3-dev (add SQLITE = false to common.mk if this feature is not required or the required library is not available)
  • libmysql++-dev (add MYSQL = false to common.mk if this feature is not required or the required library is not available)
• For compiling bam2hints and filterBam:
  • libbamtools-dev
• For compiling utrrnaseq:
  • libboost-all-dev (version must be >Boost_1_49_0)
• For compiling bam2wig:
  • Follow these instructions. Note that it shouldn't be a problem to compile AUGUSTUS without bam2wig. In practice, you can simply use bamToWig.py to accomplish the same task.
• For compiling homgenemapping (set BOOST = FALSE in ./auxprogs/homgenemapping/src/Makefile if the option --printHomologs is not required or the required libraries are not available)
  • libboost-all-dev

Compile from sources

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

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_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/

WEB-SERVER

AUGUSTUS can also be run through a web-interface at http://bioinf.uni-greifswald.de/augustus/ and a web service at http://bioinf.uni-greifswald.de/webaugustus/.

Scripts

Many scripts require Perl.

Running the python3 script bamToWig.py has the following software dependencies:

• Python3
• twoBitInfo and faToTwoBit from http://hgdownload.soe.ucsc.edu/admin/exe . bamToWig.py will automatically download these tools to the working directory during execution if they are not in your $PATH.
• samtools (available e.g. at https://github.com/samtools/samtools or via package managers)

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

3 book chapters with command line walkthroughs

LICENSES

All source code, i.e.

• the AUGUSTUS source code (src/.cc, include/.hh)
• the scripts (scripts/*)
• the auxiliary programs (auxprogs/)
• the tree-parser (src/scanner, src/parser)
• the unit tests (src/unittests)

is under the Artistic License.