cluster/software/cluster-singularities.md

+**Table of content**
+
+[[_TOC_]]
+
+Singularity containers are isolated systems, containing their own operating system which means that the user do not need to worry about dependencies and other requirements, that they might not be able to satisfy on their systems. As they are isolated, they are highly stable and highly transportable.
+
+They are created for three reasons:
+
+- a program is too difficult to install as a module
+- to install a program we need root permission
+- publisher can ask for one, in order to reproduce the analysis 
+
+   
+
+# Container available
+
+All singularity containers available can be found in /home/mass/opt/griddata/Singularity_containers/containers.
+
+# Use a singularity container
+
+First, the singularity module must be loaded: 
+```bash
+$ module load singularity/3.2.1
+```
+
+Then the container must be bind to the path of all file you will need to access:
+```bash
+$ export SINGULARITY_BIND=path/to/any/location/it/will/need/to/write/or/read/data/from
+```
+
+Finally, to use it, the following command must be used:
+```bash
+$ singularity exec <path/to/container/container_name> <usual_command>
+```
+
+# Interesting link and contact
+
+More information about Singularity Containers can be found on this webpage: https://sylabs.io/singularity/.
+
+For any questions on their utilisation, don't hesitate to contact the bioinformatic team: bioinfo.giga@uliege.be
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