Typical workflow

Given a tool, the general workflow will be:

1. Generate a Singularity definition file.
2. Generation of a Singularity image from the definition file (generally sudo singularity build <image> <definition_file>.)
3. Generation of the wrapper and symlinks to make the tools seamlessly available to the user

Example: spades

Definition files

Spades is readily available from BioConda, so we can generate a definition file using the templating scripts:

fill_template.pl package=spades version=3.14.1 > spades_3.14.1.def

This will look like:

Bootstrap: docker
From: centos:centos7.6.1810


%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env


%post
    yum -y install epel-release wget which nano curl zlib-devel
    yum -y groupinstall "Development Tools"

    mkdir -p /opt/software

    cd /opt/software
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b

    /opt/software/conda/bin/conda config --add channels defaults
    /opt/software/conda/bin/conda config --add channels conda-forge
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda create -p /opt/software/conda_env -y spades=3.14.1    
    source /opt/software/conda/bin/activate /opt/software/conda_env

    cd /opt/software

%runscript
    exec spades.py "$@"

Build the image

This step is very standard:

sudo singularity build spades~3.14.1 spades_3.14.1.def

Run the image

With entrypoint

We defined that spades.py is the entry point so the image itself can be executed as:

spades~3.14.1 -1 file_R1.fq -2 file_R2.fq -o assembly

that is equivalent to

singularity run spades~3.14.1 -1 file_R1.fq -2 file_R2.fq -o assembly

Without entrypoint

If the package has more binaries we want to use beyond the entrypoint (in our case spades.py) each binary can be executed with singularity exec IMAGE binary:

singularity exec spades~3.14.1 spades-bwa

Wrappers

To make the execution of a program seamless one can make a wrapper script like the following (calling it, for example, spades~3.14.1.sh):

#!/bin/bash
IMAGE=/path/to/spades~3.14.1
singularity exec $IMAGE $(basename "$0") "$@"

and then generate a set of symlinks to it:

for BIN in spades.py spades-bwa;
do
  ln -s spades~3.14.1.sh $BIN
done

this way the execution of spades.py or spades-bwa will resemble the native installation of the tool.