Overview

Teaching: 35 min
Exercises: 0 min

Questions

• Building Containers

Objectives

• Build a Container

FIXME

Building and Modifying Containers

The following is an example of a singularity recipe file. I will install the base OS and then configure the tools it needs to install applications.

There are sections in the recipe file to control the build process.

The first lines define the OS its version and packages. In the code here its docker layers for ubuntu

There are no files included with this recipe.

The post section is where applications are configured and loaded.

The application we will start with here will be Samtools.

Bootstrap:docker
From:ubuntu
%labels
       MAINTAINER Richard Yanicky
%files
       # Files for Build Go Here
%post
       # DEBCONF Configuration
    export DEBIAN_FRONTEND=noninteractive DEBCONF_NONINTERACTIVE_SEEN=true
    echo "tzdata tzdata/Areas select US" >> /opt/preseed.txt
    echo "tzdata tzdata/Zones/US select Chicago" >> /opt/preseed.txt
    debconf-set-selections /opt/preseed.txt
    rm /opt/preseed.txt
    # Update System
       apt update && apt upgrade -y
    apt install -y wget make locales build-essential bzip2 libncurses5-dev libbz2-dev liblzma-dev zlib1g-dev
    locale-gen en_US.UTF-8
   cd /opt
    wget https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2
    bzip2 -d samtools-1.12.tar.bz2
    tar -xf samtools-1.12.tar
    cd samtools-1.12
    ./configure --prefix=/opt/samtools
    make
    make install
    cd /opt
    rm samtools-1.12.tar
    rm -rf samtools-1.12
%runscript
    /opt/samtools/bin/samtools
    echo "/opt/samtools/bin/samtools/"

This will install the OS and samtools By default it will run samtools.

To modify the recipe just add the application install instructions.

In this case we are adding bcftools.

It should be added at the end of %post before the runscript section.

wget https://github.com/samtools/bcftools/releases/download/1.12/bcftools-1.12.tar.bz2
    bzip2 -d bcftools-1.12.tar.bz2
    tar -xf bcftools-1.12.tar
    cd bcftools-1.12
    ./configure --prefix=/opt/bcftools
    make
    make install
    cd /opt
    rm bcftools-1.12.tar
    rm -rf bcftools-1.12

The %runscript section will need to be modified. We now can run either samtools or bcftools and the container will need to allow us to pass the application name.

the following changes need to be made to the PATH and runscript.

The $@ allows us to pass the command to run into the container.

%environment
        export PATH=$PATH:/opt/samtools/bin:/opt/bcftools/bin

%runscript
    echo $PATH
    exec "$@"

singularity run samtoolsbcf.sif samtools

singularity shell samtoolsbcf.sif

Key Points

• First key point. Brief Answer to questions. (FIXME)