Apptainer def file for FSL

fsl.def

Bootstrap: debootstrap
OSversion: focal
MirrorURL: https://us.archive.ubuntu.com/ubuntu/

%environment
    export FSLDIR="/usr/local/fsl"
    export DEBIAN_FRONTEND="noninteractive"
    export LANG="en_US.UTF-8"

%post
    apt update  -y && \
    apt upgrade -y && \
    apt install -y    \
      python3         \
      wget            \
      file            \
      dc              \
      pulseaudio      \
      libquadmath0    \
      libgtk2.0-0     \
      firefox         \
      libgl1          \
      libgomp1 &&     \
      wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py && \
      python3 ./fslinstaller.py -d /usr/local/fsl/

%startscript
      sh -c . /usr/local/fsl/etc/fslconf/fsl.sh && /bin/bash

%runscript
      sh -c . /usr/local/fsl/etc/fslconf/fsl.sh && exec echo "$@"

Notes on using the container

To run an application:

apptainer exec --nv fsl.sif /usr/local/fsl/bin/fsleyes