How to create an Ubuntu singularity container with cufflinks installed

Requirements: Your computer is running either Ubuntu 16.04 or Ubuntu 17.04.

Install Singularity

First install the required packages debootstrap and git .

ubuntu@laptop:~$ sudo apt-get install debootstrap git

Install Singularity on Ubuntu 16.04

ubuntu@laptop:~$ cat /etc/issue
Ubuntu 16.04.3 LTS \n \l

ubuntu@laptop:~$ 

Follow the install instructions under the section Option 1: Download latest stable release

Install Singularity on Ubuntu 17.04

ubuntu@laptop:~$ cat /etc/issue
Ubuntu 17.04 \n \l

ubuntu@laptop:~$ sudo apt-get install singularity-container

Create a Singularity container

Clone this git repository

ubuntu@laptop:~$ cd /tmp
ubuntu@laptop:/tmp$ git clone git@github.com:eriksjolund/cufflinks-ubuntu-singularity-container.git

Create an empty Singularity container

ubuntu@laptop:~$ singularity create /tmp/container.img

Use the file cufflinks_ubuntu_singularity to install Ubuntu 17.04 and cufflinks in the container

ubuntu@laptop:~$ sudo singularity bootstrap /tmp/container.img /tmp/cufflinks-ubuntu-singularity-container/cufflinks_ubuntu_singularity

The bootstrap command took about 3 minutes on my computer.

To run cufflinks execute

ubuntu@laptop:~$ singularity exec /tmp/container.img cufflinks --help 2>&1 | head -1
cufflinks: unrecognized option '--help'
ubuntu@laptop:~$   

I just realized cufflinks has not yet implemented the "--help" flag, but anyway the cufflinks software is at least running.