Installing FSL with EasyBuild was and is still an issue.
An alternative is to use a Docker/Singularity FSL generator named neurodocker.
TL;DR: use the FSL Singularity image
We already did the steps below and you can use the version we already built.
(baobab)-[sagon@login2 ~]$ ml GCC/9.3.0 Singularity/3.7.3-Go-1.14
(baobab)-[sagon@login2 ~]$ srun singularity run /opt/ebsofts/FSL/6.0.3-singularity/fsl603.sif
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Singularity>
do not forget to submit this as a proper Slurm job (srun or sbatch) as usual.
How to build yourself the Singularity image
Here we explained how we built the image. This can be useful for other neuro softs of if you want another version.
First download neurodocker container using… Singularity itself:
ml GCC/9.3.0 Singularity/3.7.3-Go-1.14
singularity build neurodocker-0.7.0.sif docker://repronim/neurodocker:0.7.0
You can then generate a Singularity spec file for FSL using neurodocker.
singularity run neurodocker-0.7.0.sif generate singularity
--pkg-manager apt \
--base debian:buster-slim \
--fsl version=6.0.3 > fsl603.Singularity
Then you need to build the FSL container. This takes a looott of time, be patient.
singularity build --fakeroot fsl603.sif fsl603.Singularity
Once done, you can run FSL!
(baobab)-[sagon@login2 ~]$ singularity run fsl603.sif
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Singularity>