build_walk_through.txt

## These instructions can be used to test build a container locally
## For use with snakemake, the container must be on singularity hub.
##   To upload to singularity hub, you simply need to change the Singularity build definition and 
     push to the github repository associated with the singularity image.
     See shub_upload_instructions.txt

#For setting up vagrant on mac, see singularity instructions
https://www.sylabs.io/guides/3.2/user-guide/installation.html#install-on-windows-or-mac

##TO BUILD VAGRANT VM## ----------------------------------------------

brew cask install virtualbox && \
    brew cask install vagrant && \
    brew cask install vagrant-manager
    
mkdir vm-singularity && \
    cd vm-singularity

vagrant destroy && \
    rm Vagrantfile
    
export VM=sylabs/singularity-3.2-ubuntu-bionic64 && \
    vagrant init $VM && \
    vagrant up && \
    vagrant ssh

#This created this directory to contain the vm
~/Documents/vm-singularity

# I Added this to the vagrant file within the config section 
# so that I can access the build_spec document

Vagrant.configure("2") do |config|
  # ... other configuration
  
  config.vm.provision "file", source: "~/Documents/projects/monogenic/singularity", destination: "$HOME/remote/singularity"
end

##RUN THE FOLLOWING FOR RUNNING THE VAGRANT VM ## ----------------------------
#This is the only command that needs to be done to start the vagrant session
#the provision flag makes sure that file provisioning is done, i.e. the desired files will be copied onto the vm for use

cd vm-singularity
vagrant up --provision && vagrant ssh 

##To end
exit

## To stop VM
vagrant halt

##RUN THE FOLLOWING TO CREATE THE CONTAINER ## ----------------------------
sudo singularity build monogenic.sif singularity_build.def