A vagrant file for building a VM for running isoseq v4.0 workflow.

Vagrantfile

# -*- mode: ruby -*-
# vi: set ft=ruby :
# for issue at https://github.com/PacificBiosciences/Bioinformatics-Training/issues/15
VAGRANTFILE_API_VERSION = "2"

Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
  config.vm.box = "ubuntu/xenial64"
  config.vm.network "forwarded_port", guest:8080, host:8080
config.vm.synced_folder "/Volumes/Promise_Pegasus/fearjm/pacbio_prelim", "/home/ubuntu/pacbio_prelim", :mount_options => ["dmode=755", "fmode=644"]  config.vm.provider "virtualbox" do |vb|
    vb.customize ["modifyvm", :id, "--memory", "20048"]
    vb.customize ["modifyvm", :id, "--cpus", "8"]
  end

$script = <<BOOTSTRAP
apt-get update
apt-get -y upgrade
apt-get -y install rsync
apt-get -y install git
apt-get -y install python-minimal
apt-get -y install libpython2.7-dev
apt-get -y install gfortran
apt-get -y install g++
apt-get -y install graphviz
apt-get -y install make
apt-get -y install cmake
apt-get -y install zlib1g*
apt-get -y install python*-pkgconfig
apt-get -y install libopenblas-*
apt-get -y install libfreetype*
apt-get -y install libboost-{dev,dbg}
apt-get -y install libboost-{iostreams,system,program-options}*

mkdir /opt/pacbio
chown ubuntu:ubuntu /opt/pacbio

su ubuntu - -c "git clone git://github.com/PacificBiosciences/pitchfork"
su ubuntu - -c "cd pitchfork && git checkout isoseq_sa4.0.0"
su ubuntu - -c "cd pitchfork && echo 'PREFIX = /opt/pacbio/pitchfork' > settings.mk"
su ubuntu - -c "cd pitchfork && echo 'HAVE_PYTHON = /usr/local/bin/python2.7' >> settings.mk"
su ubuntu - -c "cd pitchfork && echo 'HAVE_CMAKE  = /usr/local/bin/cmake' >> settings.mk"
su ubuntu - -c "cd pitchfork && echo 'HAVE_BOOST  = /usr' >> settings.mk"
su ubuntu - -c "cd pitchfork && make init && make bax2bam && make isoseq-core"

BOOTSTRAP

  config.vm.provision :shell, :inline => $script
end