I tried binding my $HOME directory (with the license file saved there) and it tells me $HOME is already bound… It goes on to tell me that it can’t find the license. When I echo $FS_LICENSE, it spits out the file path.
Just to be precise - ls inside the container (as oppose to the host)? In other words did you try singularity exec ~/my_images/fmriprep-1.2.5.simg ls -al /home/jsmith/license.txt?
Alterantively singularity exec ~/my_images/fmriprep-1.2.5.simg cat /home/jsmith/license.txt?
If so, did you try running via
singularity run --cleanenv ~/my_images/fmriprep-1.2.5.simg /data2/users/jsmith/BIDS/bidsTest/ /data2/users/jsmith/fmriPrep/ participant --skip_bids_validation --fs-license-file /home/jsmith/license.txt
(passing the absolute path to the license, muting host env variables)
If anyone is running into this problem and can’t figure it out… My typo was continuing the command line on to a new line using " \ "… Apparently it doesn’t work in CentOS 7. I got it to work by typing it all on one really long line