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INSTALL.md

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Installation of FunGAP

FunGAP requires several dependencies installed before running. The installation procedure described here was intensely tested on Ubuntu 14.04 LTS. Note that Maker2 and Repbase require registration for download and installation.

  1. Download FunGAP
  2. BLAST+ installation
  3. Trinity installation
  4. Maker2 installation
  5. RepeatModeler installation
  6. Braker1 installation
  7. BUSCO Installation
  8. InterProScan installation
  9. Install Python modules

Download FunGAP

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

cd $HOME
git clone https://github.com/CompSynBioLab-KoreaUniv/FunGAP.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 sequencing data. https://github.com/trinityrnaseq/trinityrnaseq/wiki

Download and install Trinity v2.2.0 using github.

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

Maker2 installation

Maker2 is an easy-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. ###

Download and move maker-2.31.8.tgz to your FunGAP directory

mv maker-2.31.8.tgz $HOME/FunGAP/external/

Unzip maker2

cd $HOME/FunGAP/external/
tar -zxvf maker-2.31.8.tgz

Install Maker2 pre-requisites

cd $HOME/FunGAP/external/maker/src
sudo apt-get install libpq-dev
perl Build.PL
sudo ./Build installdeps
./Build installexes
./Build install

Configure RepeatMasker. First, download repbase manually from http://www.girinst.org/server/RepBase/index.php
Then move it to $HOME/FunGAP/external/maker/exe/RepeatMasker/

cd $HOME/FunGAP/external/maker/exe/RepeatMasker/
tar -zxvf repeatmaskerlibraries-20150807.tar.gz
./configure

# **TRF PROGRAM**
# This is the full path to the TRF program.
# This is now used by RepeatMasker to mask simple repeats.
# Enter path [  ]:
path/to/FunGAP/external/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 [  ]:
path/to/FunGAP/external/maker/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

Install RepeatModeler

cd $HOME/FunGAP/external/
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 [  ]:
path/to/FunGAP/external/maker/exe/RepeatMasker/

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

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

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

cp $HOME/FunGAP/external/gm_et_linux_64/gm_key ~/.gm_key

Install 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

BUSCO Installation

Busco: Benchmarking Universal Single-Copy Orthologs http://busco.ezlab.org/

Download BUSCO dataset.

cd $HOME/FunGAP/data/
wget http://busco.ezlab.org/v1/files/fungi_buscos.tar.gz
tar -zxvf fungi_buscos.tar.gz

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/FunGAP/external/
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

FunGAP 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  # version 1.65 tested
sudo pip install numpy  # version 1.6.1 tested
sudo pip install networkx  # version 1.1 tested
sudo pip install matplotlib  # version 1.5.x tested
sudo pip install markdown2  # version 2.3.3 tested

You can check if FunGAP is correctly installed.

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