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###Installation on Linux (Ubuntu)

You will need working knowledge of terminal and command line utilities in order to install/run funannotate. By far the most challenging aspect is installing all of the dependencies correctly. You will also need to have sudo privileges to get all of these tools installed. I'm going to use LinuxBrew to install a few of these packages, note there are other ways (notably sudo-apt), however Linux Brew provides up to date binaries for many science based programs and for a non-computer scientist (me) I find it easier to use. Note, you may have most if not all of these dependencies installed on a server, thus you can skip ahead to install funannotate if you know what you are doing. The setup script will help you determine what is not installed.

####Step-by-step instructions:

  1. install dependencies (instructions for brand new Ubuntu box, i.e. Virutal box)
#now install libraries and necessary files
sudo apt-get update
sudo apt-get install -y build-essential
sudo apt-get upgrade -y
sudo apt-get dist-upgrade -y
sudo apt-get install -y git cmake
sudo apt-get install python-dev python-setuptools python-pip
sudo apt-get install libatlas-base-dev libfreetype6-dev libz-dev libboost-iostreams-dev libpng-dev pkg-config curl
sudo apt-get install python-numpy python-scipy python-pandas python-matplotlib python-biopython python-psutil python-sklearn
sudo apt-get install bioperl cpanminus
  1. Install perl modules via cpanm or cpan or manually
cpanm Getopt::Long Pod::Usage File::Basename threads threads::shared \
        Thread::Queue Carp Data::Dumper YAML Hash::Merge Logger::Simple Parallel::ForkManager \
        DBI Text::Soundex Scalar::Util::Numeric
  1. Install LinuxBrew
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/linuxbrew/go/install)"

#add to ~/.bash_aliases
sudo gedit ~/.bash_aliases

#add the following and save, reload terminal
export PATH="$HOME/.linuxbrew/bin:$PATH"
export MANPATH="$HOME/.linuxbrew/share/man:$MANPATH"
export INFOPATH="$HOME/.linuxbrew/share/info:$INFOPATH"

#setup linuxbrew
brew doctor
brew tap homebrew/dupes
brew tap homebrew/science
brew tap nextgenusfs/tap
brew update
  1. Install funannotate and dependencies using LinuxBrew
brew install freetype
brew install funannotate
  1. Install python modules via PIP - some of the packages in apt-get are too old, so upgrade with -U
pip install -U biopython numpy pandas scipy matplotlib seaborn natsort goatools fisher scikit-learn
  1. Download RepeatMasker libraries from RepBase you will need to register
wget --user name --password pass http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/repeatmaskerlibraries-20150807.tar.gz
tar zxvf repeatmaskerlibraries-20150807.tar.gz -C $HOME/.linuxbrew/opt/repeatmasker/libexec

#now setup RepeatMasker
cd $HOME/.linuxbrew/opt/repeatmasker/libexec
./configure <config.txt

#softlink GFF script to bin
ln -s $HOME/.linuxbrew/opt/repeatmasker/libexec/util/rmOutToGFF3.pl $HOME/.linuxbrew/bin
  1. Download and install GeneMark-ES/ET here
#uncompress and then move gmes_petap subdirectory to /usr/local
tar zxvf $HOME/Downloads/gm_et_linux_64.tar.gz
sudo mv gm_et_linux_64/gmes_petap/ /usr/local

#download key, then move to home directory
gunzip gm_key_64.gz
cp $HOME/Downloads/gm_key_64 ~/.gm_key
  1. Add several components and ENV variables to ~/.bash_aliases which will get sourced by bashrc
#example using gedit
sudo gedit ~/.bash_aliases

#add folder for GeneMark to PATH, HomeBrew will take care of other tools
export PATH="/usr/local/gmes_petap:$PATH"

#add environmental variables
export AUGUSTUS_CONFIG_PATH=$HOME/.linuxbrew/opt/augustus/libexec/config
export EVM_HOME=$HOME/.linuxbrew/opt/evidencemodeler
export GENEMARK_PATH=/usr/local/gmes_petap
export BAMTOOLS_PATH=$HOME/.linuxbrew/opt/bamtools/bin
  1. Re-launch a terminal window (or type source ~/.bash_aliases). Finally run funannotate setup script to download databases and identify any problems.
#navigate into funannotate install directory
cd $HOME/.linuxbrew/opt/funannotate/libexec

#run setup script
./setup.sh

The script will download and format necessary databases and then check all of the dependencies of funannotate - any tool not properly installed will be flagged by the script.

####Python Dependencies:

  • Python 2
  • Biopython
  • psutil
  • natsort
  • goatools
  • numpy
  • pandas
  • matplotlib
  • seaborn
  • sklearn library

####Software Dependencies:

  • HomeBrew
  • Perl
  • BioPerl
  • Blast+
  • Hmmer3
  • EVidenceModeler
  • RepeatModeler
  • RepeatMasker
  • GMAP
  • Blat - if using PASA results to train Augustus
  • pslCDnaFilter (kent tools) - if using PASA results to train Augustus
  • BedTools
  • Augustus
  • GeneMark-ES/ET (gmes_petap.pl)
  • BamTools
  • Genome Annotation Generator (gag.py)
  • tbl2asn
  • BRAKER1 (optional if training Augustus with RNA-seq data BAM file)
  • Mummer
  • RAxML
  • mafft
  • trimal

####Environmental variables: EVM_HOME, GENEMARK_PATH, BAMTOOLS_PATH, AUGUSTUS_CONFIG_PATH