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|
# 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](http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz) 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](../common.mk) if this feature is not required or the required libraries are not available)
- libboost-iostreams-dev
- zlib1g-dev
- for [comparative AUGUSTUS](README-cgp.md) (multi-species, CGP):
(set COMPGENEPRED = false in [common.mk](../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](../common.mk) if this feature is not required or the required library is not available)
- libmysql++-dev (add MYSQL = false to [common.mk](../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](../auxprogs/bam2wig/README.md). Note that it shouldn't be a problem to compile AUGUSTUS without bam2wig. In practice, you can simply use [`bamToWig.py`](../scripts/bamToWig.py) to accomplish the same task.
- For compiling homgenemapping
(set BOOST = FALSE in [auxprogs/homgenemapping/src/Makefile](../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](../scripts/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](https://github.com/samtools/samtools) - 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](#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](../common.mk) (see here: [Troubleshooting](#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](https://zlib.net) - 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](../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](https://www.boost.org/) - 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](../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](https://tangentsoft.com/mysqlpp)
- 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](../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](https://www.sqlite.org)
- 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](../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](https://www.gnu.org/software/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](../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](http://lpsolve.sourceforge.net/) - 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](../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](https://people.engr.tamu.edu/davis/suitesparse.html) - 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](../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](https://github.com/pezmaster31/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](https://github.com/samtools/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](https://github.com/samtools/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](https://github.com/ComparativeGenomicsToolkit/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](https://github.com/walaj/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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