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

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

This currently installs only a single-genome version without comparative gene prediction capability:

sudo apt install augustus augustus-data augustus-doc

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

After retrieving Augustus change into the main directory containing the Dockerfile and issue

docker build -t augustus .

The following dependencies may be required for AUGUSTUS:

• Optional libraries for gzip compressed input (uncomment ZIPINPUT = TRUE in common.mk):
  • libboost-iostreams-dev
  • zlib1g-dev
• Optional for comparative (multi-species, CGP) AUGUSTUS with SQLite (uncomment COMPGENEPRED = true and SQLITE = true in common.mk):
  • 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 common.mk):
  • libgsl-dev
  • libboost-graph-dev
  • libboost-all-dev
  • libsuitesparse-dev
  • liblpsolve55-dev
  • libmysql++-dev
• 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.

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.

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

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

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.

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/

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/index.gsp.

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)

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

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.