Installation

0. Pre-requisites

fGAP requires several softwares installed before running the command. We provide simple installation guide for each software. The guide was intensely tested in Ubuntu 14.04 LTS (Unfortunately, we do not provide the supports for other platforms including Windows, OS X, or other Linux distributions in this version).

Download fGAP

Download fGAP using GitHub clone. Suppose we are installing fGAP in your $HOME directory, but you are free to change the location.

cd $HOME
git clone https://github.com/mbnmbn00/fGAP.git

BLAST+ installatioon

BLAST+ is used in Maker and BUSCO running.

sudo apt-get install ncbi-blast+

Trinity installation

Trinity performs efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. https://github.com/trinityrnaseq/trinityrnaseq/wiki

Download and Install Trinity v2.2.0 using github.

cd $HOME/fGAP/external
git clone https://github.com/trinityrnaseq/trinityrnaseq.git
cd trinityrnaseq
make

Maker2 installation

Maker2 is an eay-to-use annotation pipeline designed for emerging model organism genomes. http://www.gmod.org/wiki/MAKER

Please note that you need a proper license to use Maker2.

# Move to install directory
cd $HOME/fGAP/tools/

# Download and unzip maker2 named maker-2.31.8.tgz
tar -zxvf maker-2.31.8.tgz

# Install Maker2 pre-requisites
cd maker/src
sudo apt-get install libpq-dev
sudo apt-get install exonerate # version 2.2.0
perl Build.PL
sudo ./Build installdeps
./Build installexes
./Build install

# Configure RepeatMasker
# First download repbase manually at http://www.girinst.org/server/RepBase/index.php
# Then move it to $HOME/fGAP/maker/exe/RepeatMasker/
tar -zxvf repeatmaskerlibraries-20150807.tar.gz # Or whatever you downloaded
cd $HOME/fGAP/tools/maker_2.31.8/exe/RepeatMasker/
./configure

# **TRF PROGRAM**
# This is the full path to the TRF program.
# This is now used by RepeatMasker to mask simple repeats.
# Enter path [  ]:
$HOME/fGAP/maker/exe/RepeatMasker/trf

# Add a Search Engine:
# 1. CrossMatch: [ Un-configured ]
# 2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]
# 3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
# 4. HMMER3.1 & DFAM: [ Un-configured ]

# 5. Done
# Enter Selection:
2

# **RMBlast (rmblastn) INSTALLATION PATH**
# This is the path to the location where
# the rmblastn and makeblastdb programs can be found.
# Enter path [  ]:
$HOME/fGAP/maker_2.31.8/exe/RepeatMasker/rmblast/bin

RepeatModeler installation

RepeatModeler is a de-novo repeat family identification and modeling package.

http://www.repeatmasker.org/RepeatModeler.html

Install RepeatModeler and its dependencies.

# Check perl version (ensure version > 5.8.8)
perl -v

# Now install RepeatModeler
cd $HOME/fGAP/tools/
wget http://www.repeatmasker.org/RepeatModeler-open-1-0-8.tar.gz
tar -zxvf RepeatModeler-open-1-0-8.tar.gz
cd RepeatModeler/
perl ./configure

# **REPEATMASKER INSTALLATION PATH**
# This is the path to the location where
# the RepeatMasker program suite can be found.
# Enter path [  ]:
$HOME/fGAP/maker/exe/RepeatMasker/

# **RECON INSTALLATION PATH**
# This is the path to the location where
# the RECON program suite can be found.
# Enter path [  ]:
$HOME/fGAP/tools/RECON-1.08/bin

# **RepeatScout INSTALLATION PATH**
# This is the path to the location where
# the RepeatScout program suite can be found.
# Enter path [  ]:
$HOME/fGAP/tools/RepeatScout-1/

# **TRF INSTALLATION PATH**
# This is the path to the location where
# the TRF program can be found.
# Enter path [  ]:
$HOME/fGAP/maker/exe/RepeatMasker

# Add a Search Engine:
# 1. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]
# 2. WUBlast/ABBlast: [ Un-configured ]

# 3. Done
# Enter Selection:
1

# **RMBlast (rmblastn) INSTALLATION PATH**
# This is the path to the location where
# the rmblastn and makeblastdb programs can be found.
# Enter path [  ]:
$HOME/fGAP/maker/exe/RepeatMasker/rmblast/bin

Braker1 installation

Braker1 is an unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS.

http://exon.gatech.edu/genemark/braker1.html

Install Braker1 and its dependencies.

# Copy gm_key
cp $HOME/fGAP/tools/gm_et_linux_64/gm_key ~/.gm_key

# Perl modules
sudo cpan YAML
sudo cpan App::cpanminus
sudo cpanm File::Spec::Functions
sudo cpanm Hash::Merge
sudo cpanm List::Util
sudo cpanm Logger::Simple
sudo cpanm Module::Load::Conditional
sudo cpanm Parallel::ForkManager
sudo cpanm POSIX
sudo cpanm Scalar::Util::Numeric
sudo cpanm YAML

# For bamtools
sudo apt-get install zlib1g-dev

InterProScan installation

InterProScan scans a sequence for matches against the InterPro protein signature databases.

https://github.com/ebi-pf-team/interproscan/wiki

Install InterProScan.

cd $HOME/fGAP/tools/
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.18-57.0/interproscan-5.18-57.0-64-bit.tar.gz
tar -zxvf interproscan-5.18-57.0-64-bit.tar.gz

Install Python modules

fGAP requires several python modules and they can be installed by pip.

# Install pip
sudo apt-get install python-pip

# Install needed modules
sudo pip install biopython
sudo pip install numpy
sudo pip install intervaltree

You can check if fGAP is correctly installed.

python $HOME/fGAP/check_dependencies.py -o tmp