#!/bin/bash # Installation script for common software on machines in pauper cluster. Assumes Ubuntu 22.04 # Some of these installations will fail under 18.04 # Version: 1.2 # Editor: ngranger, sysjosh # Changes: Added some 22.04 equivalent packages to update from 20.04 script # 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 bedops apt install -y bedtools apt install -y bioperl apt install -y bioperl-run apt install -y bowtie apt install -y bowtie2 apt install -y build-essential apt install -y bzip2 apt install -y canu apt install -y cd-hit 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 imagemagick apt install -y jellyfish apt install -y kallisto apt install -y lftp apt install -y libcurl4-openssl-dev apt install -y libssl-dev apt install -y libtool-bin 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 ncbi-tools-bin apt install -y ncftp 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 plocate apt install -y primer3 apt install -y pymol apt install -y python3 apt install -y python3-pip apt install -y r-base apt install -y rasmol apt install -y raxml apt install -y samtools apt install -y screen apt install -y ssh apt install -y stringtie apt install -y sudo apt install -y tabix 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