install_dependencies.sh

#!/bin/bash

## Ubuntu based updates

sudo apt-get -y update

sudo apt -y install gcc

sudo apt-get install -y zlib1g-dev

sudo apt-get install -y libbz2-dev

sudo apt-get install -y liblzma-dev

sudo apt install -y make

###### JRE, bgzip  ############################

sudo apt install -y openjdk-11-jre-headless

sudo apt install -y tabix

######## bcftools (v 1.7), vcftools (v 0.1.15), Python2, pip, numpy, pandas and pyVCF ############

sudo apt install -y bcftools
sudo apt install -y vcftools

sudo add-apt-repository -y universe
sudo apt install -y python2
#sudo apt install python-numpy
#sudo apt install python-pandas

sudo apt install -y curl
curl https://bootstrap.pypa.io/pip/2.7/get-pip.py --output get-pip.py
sudo python2 get-pip.py

pip2 install numpy
pip2 install pandas
pip2 install PyVCF


########### SIMdrom ###############

mkdir jars
cd jars

wget https://github.com/visze/simdrom/releases/download/v0.0.2/simdrom-cli-0.0.2.jar

cd ..


########### Download files ###############

mkdir data_files

cd data_files

wget https://vccri-denovo.s3.us-west-2.amazonaws.com/TrioSim/data_files/chromosome_name.txt
wget https://vccri-denovo.s3.us-west-2.amazonaws.com/TrioSim/data_files/denovo-db.non-ssc-samples.variants_hg38LiftedOver_decoy_hla_UCSC_SNP_INDEL.vcf
wget https://vccri-denovo.s3.us-west-2.amazonaws.com/TrioSim/data_files/denovo-db.non-ssc-samples.chr22.UCSC_SNP_INDEL.vcf
wget https://vccri-denovo.s3.us-west-2.amazonaws.com/TrioSim/data_files/chr22_hg38_sites.vcf
wget https://vccri-denovo.s3.us-west-2.amazonaws.com/TrioSim/data_files/ALL.WGS_GRCh38_sites.20170504.vcf.gz
wget https://vccri-denovo.s3.us-west-2.amazonaws.com/TrioSim/data_files/ALL.WGS_GRCh38_sites.20170504.vcf.gz.tbi


##### Executables ####

cd ..

chmod +x *.sh *.py