How to set up Singularity on Ubuntu 18.04

How to set up Singularity on Ubuntu 18.04

Sources used:
	https://sylabs.io/guides/3.5/admin-guide/installation.html#installation-on-linux
	https://singularity-tutorial.github.io/
	https://stackoverflow.com/questions/42186003/how-to-uninstall-golang
	https://golang.org/doc/install

install dependencies:

sudo apt-get update && sudo apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev wget pkg-config git cryptsetup

download go: https://golang.org/dl/
sudo tar -C /opt/ -xzf go1.14.linux-amd64.tar.gz
export PATH=$PATH:/opt/go/bin
go version (should be the version from above, if not you might have to: sudo apt-get remove golang-go && sudo apt-get remove --auto-remove golang-go)
Test go compiler:
	nano hello.go
		package main
		import "fmt"
		func main() { fmt.Printf("hello, world\n") }
	go build hello.go
	./hello	

Singularity version 3.5.3-1.1.el7 is currently on the cluster:

export VERSION=3.5.3 && \
    wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
    tar -xzf singularity-${VERSION}.tar.gz && \
    cd singularity

./mconfig && \
    make -C ./builddir && \
    sudo make -C ./builddir install


Make a Singularity container
----------------------------
Run a docker container with Singularity
  singularity run docker://godlovedc/lolcow

for the next steps work on a local drive, network drives do not work! (use: df -h to find out if necessary):

make a file:
  nano Singularity

with the following content:
	BootStrap: debootstrap
	OSVersion: trusty
	MirrorURL: http://us.archive.ubuntu.com/ubuntu/

	%runscript
	    echo "This is what happens when you execute the container..."

	%post
	    echo "Hello from inside the container"
	    sed -i 's/$/ universe/' /etc/apt/sources.list
      apt-get update
      apt-get -y install vim fortune cowsay lolcat
      apt-get clean

  %environment
      export PATH=/usr/games:$PATH
      export LC_ALL=C


Create a sandbox container:
	sudo /usr/local/bin/singularity build --sandbox lolcow Singularity

Edit the sandbox container, install stuff, try out etc.
	sudo singularity shell --writable lolcow

Create a full container:
	sudo /usr/local/bin/singularity build lolcow.simg Singularity

See the recipe file used to create the container:
	singularity inspect --deffile lolcow.simg

Run the container with arguments: 
	singularity exec lolcow.simg cowsay 'How did you get out of the container?'

Pass i/o around (1):
	echo "The grass is always greener over the septic tank" > input
	cat input | singularity exec lolcow.simg cowsay > output
	cat output

Pass i/o around (2):
	./lolcow.simg #leads to the output 'This is what happens when you run the container...'
	Change the %runscript section to e.g.:
	    #!/bin/bash
	    if [ $# -ne 2 ]; then
		echo "Please provide an input and an output file."
		exit 1
	    fi
	    cat $1 | cowsay > $2
	./lolcow.simg input output.txt
  
If you want to copy files to the container add a $files section in the container description, which copies the designed file or directory into a specified location in the container
  %files
    /groups/scicompsoft/home/preibischs/software/jdk1.8.0_112 jdk