Requirements
Git [optional]
Git
Git is a highly recommended optional requirement, it will allow cloing the github repository, which contains helper scripts which make running the container much easier.
Git can be installed via the following commands in different linux systems
#CentOS or RHEL
sudo yum install epel-release
sudo yum -y install git
#Debian/Ubuntu
sudo apt install git
Singularity
As the name suggests GOMAP-Singularity is a Singularity container (http://singularity.lbl.gov). The container itself has all the requirements for GOMAP installed and can be used with a simple commands as long as the singularity container system is installed in the system used.
Note
It is highly recommended to use the GOMAP-Singularity container in the linux system. GOMAP-Singularity has been tested Ubuntu as standalone and RHEL & CentOS in an HPC environment
Installing Singularity on Debian/Ubuntu
Singularity can be installed in standalone linux systems via the instructions provided here.
Steps to install singularity on Debian/Ubuntu based systems are given below. Check here for instructions to install for other systems.
sudo wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | \
sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
sudo apt-get update
sudo apt-get install -y singularity-container
Using Singularity in HPC
Most HPC systems have singularity installed and ready to use. You can check if singularity is available by checking in Spack based environment modules by using the command in line 1. If singularity is installed then it can be loaded by runisssng the line 2.
#Check if singularity is installed
module avail singularity
module spider singularity
#Load singularity
module load singularity