PEMA investigating metabarcoding


To run PEMA you need either Docker or Singularity on your computer environment.

Singularity is the best choice especially when you are running on a HPC or a cloud environment.

For more details on how to set Docker or/and Singularity, please check on the Running on HPC and Running on a personal computer according to your machine.

Once you have a virtualization environment set, you need to build the input directory for PEMA. Once this is ready, you will need to mount this directory from you local, physical machine into the container environment to allow PEMA to run.

Here are the steps to do so!

Get PEMA on your computer environment

Being containerized, PEMA is extremely easy to be ready-to-go on your machine.

You just need a single command according to the virtualization platform you are using:


Singularity has exactly the same notion on how to pull a container.

So, in this case, the command you will have to run is

singularity pull shub://hariszaf/pema:<tag>

You should always specify the PEMA version you are about to download by replacing <tag> with that

For example, to download the v.2.0.3 PEMA version, you would run:

singularity pull shub://hariszaf/pema:v.2.0.3


You just need to pull the PEMA image of the version (this will be the <tag> on the following commands) you want.

docker pull hariszaf/pema:<tag>

If you leave <tag> blank, then you will automatically download the latest PEMA version.

In case, you would like to get a specific PEMA version, let’s say v.1.3.2 for example, you just replace <tag> with the version

docker pull hariszaf/pema:v.1.3.1

As PEMA is a rather large image, this will take some minutes, depending on your internet connection.

Once the download is complete, you are ready to go!