#This software should be installed

#java (e.g., openjdk)
apt-get install -y openjdk-11-jdk #Debian/Ubuntu

#velvet
https://github.com/dzerbino/velvet/archive/refs/tags/v1.2.10.tar.gz
tar xfz v1.2.10.tar.gz
cd velvet-1.2.10
make 'MAXKMERLENGTH=149'
cp velvetg velveth /usr/local/bin
cd ..

#fastuniq
wget https://sourceforge.net/projects/fastuniq/files/FastUniq-1.1.tar.gz
tar xfz FastUniq-1.1.tar.gz
cd FastUniq/source
make
cp fastuniq /usr/local/bin
cd ../..

#BWA
git clone https://github.com/lh3/bwa.git
cd bwa
make
cp bwa /usr/local/bin
cd ..

#samtools
wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2
tar xjvf samtools-1.8.tar.bz2
cd samtools-1.8
autoheader
autoconf -Wno-syntax
./configure --without-curses
make all all-htslib
make install all-htslib
cd ..

#bedtools
wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz
tar -zxvf bedtools-2.29.1.tar.gz
cd bedtools2
make
make install
cd ..

#vcftools
git clone https://github.com/vcftools/vcftools
cd vcftools
./autogen.sh
./configure
make
make install
cd ..