update Singularity file, add singularity Makefile methods

.gitignore

@@ -8,3 +8,8 @@ nextflow
 .now.projectlog.tsv
 .conda.old.*
 trace.txt*
+*.simg
+singularity-vm/image/multiqc.txt
+singularity-vm/image/Singularity
+singularity-vm/.vagrant/
+.DS_Store

Makefile

@@ -40,6 +40,50 @@ docker-test: docker
 	docker run --rm -ti stevekm/nf-bio-basic bash
 
 
+# ~~~~~ CREATE SINGULARITY IMAGE ON MAC USING VAGRANT ~~~~~ #
+# # Requires Vagrant install:
+# brew cask install virtualbox
+# brew cask install vagrant # https://releases.hashicorp.com/vagrant/2.0.1/vagrant_2.0.1_x86_64.dmg
+# brew cask install vagrant-manager
+# #
+# set up directories and files for Vagrant
+vagrant-installed:
+	type vagrant >/dev/null 2>&1 || { echo >&2 "Vagrant required but not found. Aborting."; exit 1; }
+
+# singularity-vm:
+# 	mkdir -p singularity-vm
+#
+# singularity-vm/Vagrantfile: singularity-vm
+# 	if [ ! -f singularity-vm/Vagrantfile ]; then \
+# 	cd singularity-vm && \
+# 	vagrant init singularityware/singularity-2.4 && \
+# 	sed -i '' 's|  # config.vm.synced_folder "../data", "/vagrant_data"|  config.vm.synced_folder "image", "/image"|' Vagrantfile ; \
+# 	fi
+#
+# singularity-vm/image: singularity-vm
+# 	mkdir -p singularity-vm/image
+
+singularity-vm/image/Singularity:
+	/bin/cp -v Singularity singularity-vm/image/Singularity
+
+# Create the Singularity container file
+singularity-vm/image/nf-bio-basic.simg: singularity-vm/image/Singularity
+	cd singularity-vm && \
+	vagrant up && \
+	vagrant ssh -c 'cd /image && sudo singularity build nf-bio-basic.simg Singularity'
+
+singularity-container: singularity-vm/image/nf-bio-basic.simg
+
+singularity-vm/image/multiqc.txt: singularity-vm/image/nf-bio-basic.simg
+	cd singularity-vm && \
+	vagrant up && \
+	vagrant ssh -c 'cd /image && singularity exec nf-bio-basic.simg multiqc --version > multiqc.txt'
+
+singularity-test: singularity-vm/image/multiqc.txt
+	cat singularity-vm/image/multiqc.txt
+
+
+
 # ~~~~~ RUN PIPELINE ~~~~~ #
 # $ make run EP='-profile sge -resume'
 run: install

Singularity

@@ -1,6 +1,7 @@
-BootStrap: debootstrap
+BootStrap: docker
 OSVersion: xenial
 MirrorURL: http://us.archive.ubuntu.com/ubuntu/
+From: ubuntu:16.04
 
 %post
     # ~~~~~ BASIC SETUP ~~~~~ #

singularity-vm/Vagrantfile

@@ -0,0 +1,70 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# All Vagrant configuration is done below. The "2" in Vagrant.configure
+# configures the configuration version (we support older styles for
+# backwards compatibility). Please don't change it unless you know what
+# you're doing.
+Vagrant.configure("2") do |config|
+  # The most common configuration options are documented and commented below.
+  # For a complete reference, please see the online documentation at
+  # https://docs.vagrantup.com.
+
+  # Every Vagrant development environment requires a box. You can search for
+  # boxes at https://vagrantcloud.com/search.
+  config.vm.box = "singularityware/singularity-2.4"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # NOTE: This will enable public access to the opened port
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine and only allow access
+  # via 127.0.0.1 to disable public access
+  # config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  config.vm.synced_folder "image", "/image"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Display the VirtualBox GUI when booting the machine
+  #   vb.gui = true
+  #
+  #   # Customize the amount of memory on the VM:
+  #   vb.memory = "1024"
+  # end
+  #
+  # View the documentation for the provider you are using for more
+  # information on available options.
+
+  # 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
+  #   apt-get update
+  #   apt-get install -y apache2
+  # SHELL
+end