Basic Singularity usage

The singularity documentation can be found here: https://sylabs.io/guides/3.2/user-guide/index.html

Running software in existing containers

To run software in an existing container, simply

module load Singularity

Then add singularity exec to the front of the normal command. For Example:

# normal megahit command
megahit -1 $r1 -2 $r2 -t 40 --presets meta-sensitive -o Megahit_meta-sensitive_out/
# singularity megahit command
singularity path/to/container/megahit.sif megahit -1 $r1 -2 $r2 -t 40 --presets meta-sensitive -o Megahit_meta-sensitive_out/

To build a Container with singularity on Greatlakes

  1. Set up remote building with singularity

    • create account at cloud.sylabs.io

    • click on your profile in the top right corner

    • click on access token

    • add a name to the create new access token section (something that tells you where you are going to run from i name mine greatlakes)

    • click create

    • copy the resulting token

    • login to greatlakes

    • module load singularity

    • then run the following and follow the prompt:

    you must update this key every 30 days

  2. Building a container from a conda install

Building a singularity container requires a def file. The def file contains the instructions to make this file and the following template will work for any software that can be installed using conda

Bootstrap: shub
From: scleveland/centos7-base-singularity

%environment
export PATH=/opt/conda/bin:$PATH

%post
yum update -y
yum  install -y @"Development Tools"
yum install -y git curl which python3 python3-devel vim htop wget tar bzip2 gzip lz4 lzma mesa-libGL mesa-libGLU

# install anaconda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
export PATH=/opt/conda/bin:$PATH
conda update -y conda
conda init

# install Bioinformatics tools through conda
conda install -y -c bioconda -c conda-forge megahit

All you have to do is replace the conda install line with your conda install command. Makes sure to include the -y flag though. THis makes the install not require user input.