wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
mv bedtools.static.binary bedtools
chmod +x bedtools

wget https://newcontinuum.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar -jxvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
make

wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
unzip fastqc_v0.12.1.zip

wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
tar -jxvf samtools-1.17.tar.bz2
cd samtools-1.17
make
sudo make install

wget https://github.com/broadinstitute/picard/releases/download/3.1.0/picard.jar

pip install deeptools

pip install MACS2

wget http://homer.ucsd.edu/homer/configureHomer.pl
perl ./configureHomer.pl -install
perl ./configureHomer.pl -install hg19
perl ./configureHomer.pl -install hg38

rsync -aP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ ./

wget https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz
tar -zxf v0.24.2.tar.gz