Move Vagrant provisioning to script

Vagrantfile

@@ -65,46 +65,5 @@ Vagrant.configure("2") do |config|
   # Enable provisioning with a shell script. Additional provisioners such as
   # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
   # documentation for more information about their specific syntax and use.
-  config.vm.provision "shell", inline: <<-SHELL
-    sudo apt-get update
-    sudo apt-get install -y g++ libncurses5-dev python-dev python3-dev emacs cmake
-    cd
-    # Stampy
-    curl -O http://www.well.ox.ac.uk/~gerton/software/Stampy/stampy-latest.tgz
-    tar xfz stampy-latest.tgz
-    cd stampy
-    make
-    cd ..
-    # VCFTools
-    wget https://downloads.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz
-    tar xfz vcftools_0.1.13.tar.gz
-    cd vcftools_0.1.13
-    make
-    cd ..
-    # Cortex
-    git clone --recursive https://github.com/iqbal-lab/cortex.git
-    cd cortex
-    bash install.sh
-    for k in 31 63 95 127; do
-      for ncol in 1 2 3 9 10 11; do
-        make cortex_var MAXK=$k NCOLS=$ncol
-      done
-    done
-    echo 'export PERL5LIB="${HOME}/cortex/scripts/analyse_variants/bioinf-perl/lib/:${HOME}/cortex/scripts/calling/:${PERL5LIB}"' >> .profile
-    echo 'export PATH="${HOME}/cortex/scripts/analyse_variants/needleman_wunsch/:${PATH}"' >> .profile
-    cd ..
-    # McCortex
-    git clone --recursive -b develop https://github.com/mcveanlab/mccortex.git
-    cd mccortex
-    cd libs && make all && cd ..
-    for k in 31 63 95 127; do
-      make all test MAXK=31
-    done
-    cd ..
-    # Freebayes
-    git clone --recursive https://github.com/ekg/freebayes.git
-    cd freebayes
-    make
-    cd ..
-  SHELL
+  config.vm.provision "shell", path: "travis/provision-vm.sh"
 end

travis/provision-vm.sh

@@ -0,0 +1,44 @@
+sudo apt-get update
+sudo apt-get install -y g++ libncurses5-dev python-dev python3-dev emacs cmake autoconf
+
+# Stampy
+cd
+curl -O http://www.well.ox.ac.uk/~gerton/software/Stampy/stampy-latest.tgz
+tar xfz stampy-latest.tgz
+cd stampy
+make
+
+# VCFTools
+cd
+wget https://downloads.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz
+tar xfz vcftools_0.1.13.tar.gz
+cd vcftools_0.1.13
+make
+
+# Cortex
+cd
+git clone --recursive https://github.com/iqbal-lab/cortex.git
+cd cortex
+bash install.sh
+for k in 31 63 95 127; do
+  for ncol in 1 2 3 9 10 11; do
+    make cortex_var MAXK=$k NCOLS=$ncol
+  done
+done
+echo 'export PERL5LIB="${HOME}/cortex/scripts/analyse_variants/bioinf-perl/lib/:${HOME}/cortex/scripts/calling/:${PERL5LIB}"' >> .profile
+echo 'export PATH="${HOME}/cortex/scripts/analyse_variants/needleman_wunsch/:${PATH}"' >> .profile
+
+# McCortex
+cd
+git clone --recursive -b develop https://github.com/mcveanlab/mccortex.git
+cd mccortex
+cd libs && make all && cd ..
+for k in 31 63 95 127; do
+  make all test MAXK=31
+done
+
+# Freebayes
+cd
+git clone --recursive https://github.com/ekg/freebayes.git
+cd freebayes
+make