#!/bin/bash # get dm3 and reformat into single fasta file echo "getting dm3 and reformatting into single fasta file" wget -q http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/chromFa.tar.gz tar -xvzf chromFa.tar.gz cat chr*.fa > dm3.fa rm chromFa.tar.gz chr*.fa #install PacBio smrtanalysis suite (including blasr PacBio long-read mapping engine) echo "installing PacBio smrtanalysis suite" wget http://programs.pacificbiosciences.com/l/1652/2013-11-05/2tqk4f bash smrtanalysis-2.1.1-centos-6.3.run --extract-only --rootdir ./ rm smrtanalysis-2.1.1-centos-6.3.run