Create Home directory for RepBox

mkdir $HOME/RepBox/bin
REPBOX=$HOME/RepBox/bin
cd $REPBOX

Included Dependencies

HelitronScanner

# Version included, download is not needed.

SINE_Scan

# Modified version is included and downloading is not necessary; simple run the setup bash script located in the SINE_Scan directory.

Installing Dependencies

Tandem Repeat Finder (source)

wget https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz
tar xzvf v4.*
cd TRF-4*
mkdir build
cd build
../configure
make
sudo make install
cd $REPBOX

RepeatScout (source)

wget http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz
tar xzvf RepeatScout-1.0.6.tar.gz
cd RepeatScout-1.0.6
make
cd $REPBOX

RMBLAST (pre-compiled)

wget http://www.repeatmasker.org/rmblast/rmblast-2.14.0+-x64-macosx.tar.gz
tar xzvf rmblast-2.14.0+-x64-macosx.tar.gz
cd $REPBOX

LTR_retriever (pre-compiled)

wget -qO- https://github.com/oushujun/LTR_retriever/archive/refs/tags/v2.9.0.tar.gz > ltr_retriever_v2.9.0.tar.gz
tar xzvf ltr_retriever_v2.9.0.tar.gz
cd $REPBOX

MAFFT (source)

wget --no-check-certificate https://mafft.cbrc.jp/alignment/software/mafft-7.490-with-extensions-src.tgz
tar xvf mafft-7.490-with-extensions-src.tgz
cd mafft-7.490-with-extensions/core
sed '1s@^PREFIX = /usr/local$@PREFIX = ~/RepBox/mafft-7.490-with-extensions@' Makefile > temp && mv temp Makefile
make clean
make
make install
cd ..
cd extensions
sed '1s@^PREFIX = /usr/local$@PREFIX = ~/RepBox/mafft-7.490-with-extensions@' Makefile > temp && mv temp Makefile
make clean
make
make install
cd $REPBOX

CD-HIT (source)

wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
tar xvf cd-hit-v4.8.1-2019-0228.tar.gz
cd cd-hit-v4.8.1-2019-0228
sudo make openmp=no
sudo make install
cd $REPBOX

NINJA (Homebrew & source)

wget https://wheelerlab.org/software/ninja/files/ninja.tgz
tar xvf ninja.tgz

MITEFinderII

git clone https://github.com/jhu99/miteFinder.git
cd miteFinder
make
cd $REPBOX

VSEARCH

Development environment for RepBox was Intel macOS and install instructions for VSEARCH are consistent with this architecture. Please refer to the VSEARCH GitHub for instructions specific to your system.

wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-macos-x86_64.tar.gz
tar xzf vsearch-2.22.1-macos-x86_64.tar.gz
cd vsearch-2.22.1-macos-x86_64

Local Homebrew Formulas - https://github.com/Ensembl/homebrew-external/tree/master

# MUSCLE 
brew install local_homebrew_formulas/muscle.rb

# EMBOSS
brew install local_homebrew_formulas/emboss.rb

# Bedtools
brew install local_homebrew_formulas/bedtools.rb

# BLAST
brew install local_homebrew_formulas/blast.rb

#GenomeTools (LTRHarvest)
brew install local_homebrew_formulas/genometools.rb

#RECON
brew install local_homebrew_formulas/recon.rb

#dos2unix
brew install local_homebrew_formulas/dos2unix.rb

RepeatModeler 2.0.1

cd $HOME/RepBox/bin
wget https://github.com/Dfam-consortium/RepeatModeler/archive/refs/tags/2.0.1.tar.gz
tar -zxvf 2.0.1.tar.gz
cd RepeatModeler-2.0.1/

RepeatMasker 4.1.3.p1

cd $HOME/RepBox/bin
wget https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.3-p1.tar.gz
tar xvf RepeatMasker-4.1.3-p1.tar.gz
head -25 RepeatMasker/Libraries/Dfam.h5 # Check for release 3.6

Repbase

Updated versions are behind a paywall. Most-recent open-access version included is RepBaseRepeatMaskerEdition-20181026.tar.gz

cd $HOME/RepBox/bin
cp RepBaseRepeatMaskerEdition-20181026.tar.gz RepeatMasker
cd RepeatMasker
tar xvf RepBaseRepeatMaskerEdition-20181026.tar.gz

RepeatModeler & RepeatMasker Configuration

### RepeatModeler
cd $HOME/RepBox/bin
perl ./RepeatModeler-2.0.1/configure

cd $HOME/RepBox/bin
### RepeatMasker
perl ./RepeatMasker/configure

shelvasha/RepBox