#!/bin/bash
# Installation script for common software on machines in pauper cluster.   Assumes Ubuntu 20.04
# Some of these installations will fail under 18.04
# Version: 1.2
# Editor: sysalex
# Changes: Added minimap

# exit when any command fails
set -e

# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
# echo an error message before exiting
trap 'echo "\"${last_command}\" command filed with exit code $?."' EXIT

apt install -y augustus
apt install -y automake
apt install -y bcftools
apt install -y bedtools
apt install -y bioperl
apt install -y bioperl-run
apt install -y blast2
apt install -y bowtie
apt install -y bowtie2
apt install -y build-essential
apt install -y bzip2
apt install -y canu
apt install -y cmake
apt install -y cowsay
apt install -y cpp
apt install -y curl
apt install -y dialign
apt install -y dos2unix
apt install -y emacs
apt install -y fastdnaml
apt install -y fastp
apt install -y fastqc
apt install -y fasttree
apt install -y file
apt install -y firefox
apt install -y flexbar
apt install -y g++
apt install -y gcc
apt install -y gdebi
apt install -y gdebi-core
apt install -y git
apt install -y gzip
apt install -y hisat2
apt install -y htop
apt install -y imagej
apt install -y jellyfish
apt install -y kallisto
apt install -y libboost-iostreams-dev
apt install -y libcurl4-openssl-dev
apt install -y libssl-dev
apt install -y libvcflib-tools
apt install -y libxml2-dev
apt install -y mafft
apt install -y make
apt install -y memtest86+
apt install -y minimap
apt install -y minimap2
apt install -y mpich
apt install -y mrbayes
apt install -y mysql-server
apt install -y net-tools
apt install -y nfs-common
apt install -y nginx
apt install -y njplot
apt install -y openjdk-8-jdk
apt install -y openssh-client
apt install -y openssh-server
apt install -y openssl
apt install -y parallel
apt install -y perl
apt install -y python3-pip
apt install -y primer3
apt install -y pymol
apt install -y python
apt install -y r-base
apt install -y rasmol
apt install -y raxml
apt install -y samtools
apt install -y screen
apt install -y snp-sites
apt install -y ssh
apt install -y stringtie
apt install -y sudo
apt install -y tmux
apt install -y trimmomatic
apt install -y vcftools
apt install -y vim

pip3 install numpy
pip3 install HTSeq
pip3 install matplotlib
pip3 install scipy
pip3 install tabulate