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README.md

Build Status

Gene Prediction with AUGUSTUS

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

INTRODUCTION

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

INSTALLATION

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/index.gsp.

Scripts

Many scripts require Perl.

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

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/*.pl)
  • the auxiliary programs (auxprogs/)
  • the tree-parser (src/scanner,src/parser)

is under the Artistic License.

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