Building AUGUSTUS

Download sources

To obtain the most recent complete version, clone the GitHub 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

Install dependencies

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 utilities bam2hints and filterBam:
  - libbamtools-dev zlib1g-dev
- for compiling utility utrrnaseq:
  - libboost-all-dev (version must be >Boost_1_49_0)
- for compiling utility 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
- for scripts:
  - Perl
  - Python3
- for the python3 script bamToWig.py:
  - 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. via package managers or here - see notes below)

Install dependencies

as root use your package manager to install the desired dependencies

apt-get update
apt-get install build-essential wget git autoconf

# Install dependencies for AUGUSTUS comparative gene prediction mode (CGP)
apt-get install libgsl-dev libboost-all-dev libsuitesparse-dev liblpsolve55-dev
apt-get install libsqlite3-dev libmysql++-dev

# Install dependencies for the optional support of gzip compressed input files
apt-get install libboost-iostreams-dev zlib1g-dev

# Install dependencies for bam2hints and filterBam
apt-get install libbamtools-dev zlib1g-dev

# Install additional dependencies for bam2wig
apt-get install samtools libhts-dev

# Install additional dependencies for homGeneMapping and utrrnaseq
apt-get install libboost-all-dev

# Install additional dependencies for scripts
apt-get install cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl libyaml-perl libdbd-mysql-perl
apt-get install --no-install-recommends python3-biopython

as a non-root user you can either
- download package archives for the dependencies and install them into a specified directory (for an example see here: Troubleshooting/MySQL )
- or install the dependencies from source
  
  in both cases, you need to set the appropriate include and library paths, e.g. in common.mk (see here: Troubleshooting ).

Compile from sources

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

make augustus

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

For AUGUSTUS and utilities use

make

Troubleshooting

The proposed solutions have been tested with Ubuntu 20.04. For other systems/architectures, the paths and commands given may have to be adapted.
With root rights, you can install the libraries in the default folders. To do this, please remove the prefix argument in the configure, cmake and bootstrap commands and INSTALL from the make call.

zlib - library for compression methods

possible error messages

  /usr/bin/ld: cannot find -lz
  /usr/bin/ld: genbank.o: in function boost::detail::sp_counted_impl_p<boost::iostreams::symmetric_filter ...
  genbank.cc: ... undefined reference to boost::iostreams::detail::zlib_base::reset(bool, bool)'

solutions

switch off zlib usage by setting ZIPINPUT = false in common.mk and do not make utility programs bam2wig, bam2hints and filterBam
or install package apt-get install zlib1g-dev

or install from source

execute

  mkdir -p /your/path/to/zlib/zlib_build
  cd /your/path/to/zlib/zlib_build
  wget -O zlib-1.2.11.tar.gz https://sourceforge.net/projects/libpng/files/zlib/1.2.11/zlib-1.2.11.tar.gz/download
  tar xzf zlib-1.2.11.tar.gz
  cd /your/path/to/zlib/zlib_build/zlib-1.2.11
  ./configure --prefix=/your/path/to/zlib/zlib_install
  make
  make install

add to common.mk

  INCLUDE_PATH_ZLIB := -I/your/path/to/zlib/zlib_install/include
  LIBRARY_PATH_ZLIB := -L/your/path/to/zlib/zlib_install/lib -Wl,-rpath,/your/path/to/zlib/zlib_install/lib

check: the missing file should be here

 /your/path/to/zlib/zlib_install/lib/libz.so

Boost - C++ libraries

possible error messages

  ../include/types.hh:16:10: fatal error: boost/archive/text_oarchive.hpp: No such file or directory
  ../include/genome.hh:24:10: fatal error: boost/graph/adjacency_list.hpp: No such file or directory
  /usr/bin/ld: cannot find -lboost_iostreams
  /usr/bin/ld: cannot find -lboost_serialization

solutions

switch off boost usage by setting BOOST = false, COMPGENEPRED = false and ZIPINPUT = false in common.mk do not make utility program utrrnaseq
or install package apt-get install libboost-all-dev

or install from source

execute (don't set ZLIB variables if zlib is installed on standard locations)

  mkdir -p /your/path/to/boost/boost_build
  cd /your/path/to/boost/boost_build
  wget -O boost_1_76_0.tar.gz https://sourceforge.net/projects/boost/files/boost/1.76.0/boost_1_76_0.tar.gz/download
  tar xzf boost_1_76_0.tar.gz
  cd /your/path/to/boost/boost_build/boost_1_76_0
  export ZLIB_INCLUDE=/your/path/to/zlib/zlib_install/include
  export ZLIB_LIBRARY_PATH=/your/path/to/zlib/zlib_install/lib
  ./bootstrap.sh --prefix=/your/path/to/boost/boost_install --with-libraries=all
  ./b2 install --prefix=/your/path/to/boost/boost_install

add to common.mk

  INCLUDE_PATH_BOOST := -I/your/path/to/boost/boost_install/include
  LIBRARY_PATH_BOOST := -L/your/path/to/boost/boost_install/lib -Wl,-rpath,/your/path/to/boost/boost_install/lib

check: the missing files should be here

 /your/path/to/boost/boost_install/include/boost/archive/text_oarchive.hpp
 /your/path/to/boost/boost_install/lib/libboost_iostreams.so

MySQL

possible error messages

  ../include/randseqaccess.hh:21:10: fatal error: mysql++/mysql++.h: No such file or directory
  /usr/bin/ld: cannot find -lmysqlclient
  /usr/bin/ld: cannot find -lmysqlpp

solutions

switch off MySQL usage by setting MYSQL = false in common.mk
or install package apt-get install libmysql++-dev

or as non-root user install package archives into a specified directory (beware of further recursive dependencies at link and runtime)

execute (replace the archives mentioned here with the ones necessary for your system/architecture)

  mkdir /your/path/to/mysql
  cd /your/path/to/mysql
  # libmysql++3v5:
  wget        libmysql++3v5_3.2.5-1build1_amd64.deb http://de.archive.ubuntu.com/ubuntu/pool/universe/m/mysql++/libmysql++3v5_3.2.5-1build1_amd64.deb
  dpkg-deb -x libmysql++3v5_3.2.5-1build1_amd64.deb /your/path/to/mysql/mysql_install
  # libmysql++-dev:
  wget        libmysql++-dev_3.2.5-1build1_amd64.deb http://de.archive.ubuntu.com/ubuntu/pool/universe/m/mysql++/libmysql++-dev_3.2.5-1build1_amd64.deb
  dpkg-deb -x libmysql++-dev_3.2.5-1build1_amd64.deb /your/path/to/mysql/mysql_install
  # libmysqlclient21:
  wget        libmysqlclient21_8.0.23-0ubuntu0.20.04.1_amd64.deb http://security.ubuntu.com/ubuntu/pool/main/m/mysql-8.0/libmysqlclient21_8.0.23-0ubuntu0.20.04.1_amd64.deb
  dpkg-deb -x libmysqlclient21_8.0.23-0ubuntu0.20.04.1_amd64.deb /your/path/to/mysql/mysql_install
  # libmysqlclient-dev:
  wget        libmysqlclient-dev_8.0.23-0ubuntu0.20.04.1_amd64.deb http://security.ubuntu.com/ubuntu/pool/main/m/mysql-8.0/libmysqlclient-dev_8.0.23-0ubuntu0.20.04.1_amd64.deb
  dpkg-deb -x libmysqlclient-dev_8.0.23-0ubuntu0.20.04.1_amd64.deb /your/path/to/mysql/mysql_install

add to common.mk

  INCLUDE_PATH_MYSQL := -I/your/path/to/mysql/mysql_install/usr/include -I/your/path/to/mysql/mysql_install/usr/include/mysql
  LIBRARY_PATH_MYSQL := -L/your/path/to/mysql/mysql_install/usr/lib/x86_64-linux-gnu -Wl,-rpath,/your/path/to/mysql/mysql_install/usr/lib/x86_64-linux-gnu

check: the missing files should be here

 /your/path/to/mysql/mysql_install/usr/include/mysql++/mysql++.h
 /your/path/to/mysql/mysql_install/usr/lib/x86_64-linux-gnu/libmysqlclient.so

installation from source code is quite time-consuming and requires many architecture-specific dependencies and is therefore not listed here

SQLite

possible error messages

  ../include/sqliteDB.hh:13:10: fatal error: sqlite3.h: No such file or directory
  /usr/bin/ld: cannot find -lsqlite3

solutions

switch off SQLite usage by setting SQLITE = false in common.mk
or install package apt-get install libsqlite3-dev

or install from source

execute

  mkdir -p /your/path/to/sqlite3
  cd /your/path/to/sqlite3
  wget sqlite-autoconf-3350500.tar.gz https://www.sqlite.org/2021/sqlite-autoconf-3350500.tar.gz
  tar zxf sqlite-autoconf-3350500.tar.gz
  cd /your/path/to/sqlite3/sqlite-autoconf-3350500
  ./configure --prefix=/your/path/to/sqlite3/sqlite3_install
  make
  make install

add to common.mk

  INCLUDE_PATH_SQLITE := -I/your/path/to/sqlite3/sqlite3_install/include
  LIBRARY_PATH_SQLITE := -L/your/path/to/sqlite3/sqlite3_install/lib -Wl,-rpath,/your/path/to/sqlite3/sqlite3_install/lib

check: the missing files should be here

 /your/path/to/qlite3/sqlite3_install/include/sqlite3.h
 /your/path/to/sqlite3/sqlite3_install/lib/libsqlite3.so

GSL - GNU Scientific Library

possible error messages

  parser/../../include/contTimeMC.hh:18:10: fatal error: gsl/gsl_matrix.h: No such file or directory
  /usr/bin/ld: cannot find -lgsl

solutions

switch off gsl usage by setting COMPGENEPRED = false in common.mk
or install package apt-get install libgsl-dev

or install from source

execute

  mkdir /your/path/to/gsl
  cd /your/path/to/gsl
  wget gsl-latest.tar.gz https://mirror.ibcp.fr/pub/gnu/gsl/gsl-latest.tar.gz
  tar zxf gsl-latest.tar.gz
  cd /your/path/to/gsl/gsl-2.6/
  ./configure --prefix=/your/path/to/gsl/gsl_install
  make
  make install

add to common.mk

  INCLUDE_PATH_GSL := -I/your/path/to/gsl/gsl_install/include
  LIBRARY_PATH_GSL := -L/your/path/to/gsl/gsl_install/lib -Wl,-rpath,/your/path/to/gsl/gsl_install/lib

check: the missing files should be here

 /your/path/to/gsl/gsl_install/include/gsl/gsl_matrix.h
 /your/path/to/gsl/gsl_install/lib/libgsl.so

lp_solve - Mixed Integer Linear Programming (MILP) solver

possible error messages

  alignment.cc:16:10: fatal error: lp_lib.h: No such file or directory
  /usr/bin/ld: cannot find -llpsolve55

solutions

switch off lp_solve usage by setting COMPGENEPRED = false in common.mk
or install package apt-get install liblpsolve55-dev

or install from source

execute

  mkdir /your/path/to/lpsolve
  cd /your/path/to/lpsolve
  wget -O lp_solve_5.5.2.11_source.tar.gz https://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.11/lp_solve_5.5.2.11_source.tar.gz/download
  tar zxf lp_solve_5.5.2.11_source.tar.gz
  cd /your/path/to/lpsolve/lp_solve_5.5
  chmod +x ./lpsolve55/ccc ./lp_solve/ccc
  cd /your/path/to/lpsolve/lp_solve_5.5/lpsolve55
  ./ccc
  cd /your/path/to/lpsolve/lp_solve_5.5/lp_solve
  ./ccc
  mkdir -p /your/path/to/lpsolve/lpsolve_install/include
  cp /your/path/to/lpsolve/lp_solve_5.5/*.h /your/path/to/lpsolve/lpsolve_install/include/
  mkdir -p /your/path/to/lpsolve/lpsolve_install/lib
  cp /your/path/to/lpsolve/lp_solve_5.5/lpsolve55/bin/ux64/liblpsolve55.* /your/path/to/lpsolve/lpsolve_install/lib/

add to common.mk

  INCLUDE_PATH_LPSOLVE := -I/your/path/to/lpsolve/lpsolve_install/include
  LIBRARY_PATH_LPSOLVE := -L/your/path/to/lpsolve/lpsolve_install/lib -Wl,-rpath,/your/path/to/lpsolve/lpsolve_install/lib

check: the missing files should be here

 /your/path/to/lpsolve/lpsolve_install/include/lp_lib.h
 /your/path/to/lpsolve/lpsolve_install/lib/liblpsolve55.so

SuiteSparse - A Suite of Sparse matrix software

possible error messages
```
  /usr/bin/ld: cannot find -lcolamd
```

solutions

switch off SuiteSparse usage by setting COMPGENEPRED = false in common.mk
or install package apt-get install libsuitesparse-dev

or install from source

execute

  git clone https://github.com/DrTimothyAldenDavis/SuiteSparse.git /your/path/to/suitesparse/suitesparse
  cd /your/path/to/suitesparse/suitesparse/SuiteSparse_config
  make install INSTALL=/your/path/to/suitesparse/suitesparse_install
  cd /your/path/to/suitesparse/suitesparse/COLAMD
  make install INSTALL=/your/path/to/suitesparse/suitesparse_install

add to common.mk

  INCLUDE_PATH_SUITESPARSE := -I/your/path/to/suitesparse/suitesparse_install/include
  LIBRARY_PATH_SUITESPARSE := -L/your/path/to/suitesparse/suitesparse_install/lib -Wl,-rpath,/your/path/to/suitesparse/suitesparse_install/lib

check: the missing file should be here

 /your/path/to/suitesparse/suitesparse_install/lib/libcolamd.so

Bamtools - handling BAM files

possible error messages

  bam2hints.cc:16:10: fatal error: api/BamReader.h: No such file or directory
  /usr/bin/ld: cannot find -lbamtools

solutions

do not make utility programs bam2hints and filterBam
or install package apt-get install libbamtools-dev

or install from source

cmake or cmake3 must be installed (use the installed one in next steps)
```
     apt-get install cmake
```
(or see https://cmake.org)

download sources

  git clone https://github.com/pezmaster31/bamtools.git /your/path/to/bamtools/bamtools

or alternatively download the zipped version from https://github.com/pezmaster31/bamtools/zipball/master and unpack:

  mkdir -p /your/path/to/bamtools/bamtools
  unzip pezmaster31-bamtools-v2.5.1-23-g2391b1a.zip -d /your/path/to/bamtools/bamtools
  mv /your/path/to/bamtools/bamtools/pezmaster31-bamtools-2391b1a/* /your/path/to/bamtools/bamtools/

execute (don't set ZLIB variables if zlib is installed on standard locations)

  mkdir -p /your/path/to/bamtools/bamtools_build
  cd /your/path/to/bamtools/bamtools_build
  cmake \
    -DCMAKE_INSTALL_PREFIX=/your/path/to/bamtools/bamtools_install \
    -DZLIB_LIBRARY=/your/path/to/zlib/zlib_install/lib/libz.so \
    -DZLIB_INCLUDE_DIR=/your/path/to/zlib/zlib_install/include \
    /your/path/to/bamtools/bamtools
  make
  make install

add to common.mk

  INCLUDE_PATH_BAMTOOLS := -I/your/path/to/bamtools/bamtools_install/include/bamtools
  LIBRARY_PATH_BAMTOOLS := -L/your/path/to/bamtools/bamtools_install/lib -Wl,-rpath,/your/path/to/bamtools/bamtools_install_dir/lib

check: the missing files should be here

 /your/path/to/bamtools/bamtools_install/include/bamtools/api/BamReader.h
 /your/path/to/bamtools/bamtools_install/lib/libbamtools.a

HTSlib - accessing common file formats, such as SAM, CRAM and VCF

possible error messages

  bam2wig.c:12:10: fatal error: bgzf.h: No such file or directory
  /usr/bin/ld: cannot find -lhts

solutions

do not make utility program bam2wig
or install packages apt-get install samtools libhts-dev

or install from source

execute (don't set ZLIB variables if zlib is installed on standard locations, set variables for bz2 and lzma if available and used or don't set the disable options if bz2 and lzma are installed on standard locations)

  git clone https://github.com/samtools/htslib.git /your/path/to/htslib/htslib_build
  cd /your/path/to/htslib/htslib_build
  git submodule update --init --recursive
  autoreconf -i
  ./configure --prefix=/your/path/to/htslib/htslib_install \
    CPPFLAGS=-I/your/path/to/zlib/zlib_install/include \
    LDFLAGS=-L/your/path/to/zlib/zlib_install/lib \
    --disable-bz2 \
    --disable-lzma
  make
  make install

add to common.mk

  INCLUDE_PATH_HTSLIB   := -I/your/path/to/htslib/htslib_install/include/htslib
  LIBRARY_PATH_HTSLIB   := -L/your/path/to/htslib/htslib_install/lib -Wl,-rpath,/your/path/to/htslib/htslib_install/lib

check: the missing files should be here

 /your/path/to/htslib/htslib_install/include/htslib/bgzf.h
 /your/path/to/htslib/htslib_install/lib/libhts.a

Test failures

SAMtools

possible error messages
```
  samtools: not found
```

solutions

install package apt-get install samtools

or install from source

execute (don't set ZLIB and htslib variables and flags if both are installed on standard locations, remove the --without-curses if this library is installed on standard locations)

  git clone https://github.com/samtools/samtools.git /your/path/to/samtools/samtools_build
  cd /your/path/to/samtools/samtools_build
  autoheader
  autoconf -Wno-syntax
  ./configure \
    --prefix=/your/path/to/samtools/samtools_install \
    --with-htslib=/your/path/to/htslib/htslib_install \
    --without-curses \
    CPPFLAGS=-I/your/path/to/zlib/zlib_install/include \
    LDFLAGS="-L/your/path/to/zlib/zlib_install/lib -Wl,-rpath,/your/path/to/zlib/zlib_install/lib -L/your/path/to/htslib/htslib_install/lib -Wl,-rpath,/your/path/to/htslib/htslib_install/lib"
  make
  make install

change PATH in your shell

  export PATH="$PATH:/your/path/to/samtools/samtools_install/bin/"

HAL - Hierarchical Alignment (HAL) Format API

possible error messages
```
  halLiftover is not executable
```

solution

install from source

install package apt-get install libhdf5-dev

execute (don't set ZLIB variables if zlib is installed on standard locations)

  # install hdf5 from source if libhdf5-dev is not installed:
  mkdir -p /your/path/to/hdf5/hdf5_build
  cd /your/path/to/hdf5/hdf5_build
  wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz
  tar xzf hdf5-1.10.1.tar.gz
  cd /your/path/to/hdf5/hdf5_build/hdf5-1.10.1
  ./configure --enable-cxx --prefix=/your/path/to/hdf5/hdf5_install \
     --with-zlib="/your/path/to/zlib/zlib_install/include,/your/path/to/zlib/zlib_install/lib"
  make
  make install
  export PATH="$PATH:/your/path/to/hdf5/hdf5_install/bin"
  
  # install sonLib
  git clone https://github.com/benedictpaten/sonLib.git /your/path/to/sonLib
  cd /your/path/to/sonLib
  export CPPFLAGS="-I/your/path/to/zlib/zlib_install/include -L/your/path/to/zlib/zlib_install/lib"
  make
  unset CPPFLAGS
  
  # install hal
  git clone https://github.com/ComparativeGenomicsToolkit/hal.git /your/path/to/hal
  cd /your/path/to/hal
  export RANLIB=ranlib
  make

change PATH in your shell

  export PATH="$PATH:/your/path/to/hdf5/hdf5_install/bin"
  export PATH="$PATH:/your/path/to/hal/bin/"

SeqLib - handling BAM files

possible error messages

  ./headers/bamseqlibaccess.hh:8:10: fatal error: SeqLib/BamRecord.h: No such file or directory
  /usr/bin/ld: cannot find -lseqlib

solutions
- do not make utility program filterBam
- use Bamtools instead of SeqLib for processing BAM files in filterBam
- or install package apt-get install libseqlib-dev (and maybe also necessary apt-get install libssw-dev libjsoncpp-dev)
- or install from source
  - install dependencies to zlib, bz2 and lzma
    
    apt-get install zlib1g-dev liblzma-dev libbz2-dev
  - download sources
```
  git clone --recursive https://github.com/walaj/SeqLib.git /your/path/to/SeqLib
```
  - execute
```
  cd /your/path/to/SeqLib
  ./configure
  make
  make install
```
  - add to common.mk
```
  INCLUDE_PATH_SEQLIB := -I/your/path/to/SeqLib -I/your/path/to/SeqLib/htslib
  LIBRARY_PATH_SEQLIB := -L/your/path/to/SeqLib/lib  -Wl,-rpath,/your/path/to/SeqLib/lib
```
  - check: the missing files should be here
```
 /your/path/to/SeqLib/SeqLib/BamRecord.h
 /your/path/to/SeqLib/lib/libseqlib.a
```

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INSTALL.md

INSTALL.md

Building AUGUSTUS

Download sources

Install dependencies

Compile from sources

Troubleshooting

zlib - library for compression methods

Boost - C++ libraries

MySQL

SQLite

GSL - GNU Scientific Library

lp_solve - Mixed Integer Linear Programming (MILP) solver

SuiteSparse - A Suite of Sparse matrix software

Bamtools - handling BAM files

HTSlib - accessing common file formats, such as SAM, CRAM and VCF

Test failures

SAMtools

HAL - Hierarchical Alignment (HAL) Format API

SeqLib - handling BAM files

Files

INSTALL.md

Latest commit

History

INSTALL.md

File metadata and controls

Building AUGUSTUS

Download sources

Install dependencies

Compile from sources

Troubleshooting

zlib - library for compression methods

Boost - C++ libraries

MySQL

SQLite

GSL - GNU Scientific Library

lp_solve - Mixed Integer Linear Programming (MILP) solver

SuiteSparse - A Suite of Sparse matrix software

Bamtools - handling BAM files

HTSlib - accessing common file formats, such as SAM, CRAM and VCF

Test failures

SAMtools

HAL - Hierarchical Alignment (HAL) Format API

SeqLib - handling BAM files