For alpha fold workflow zaiyan was trying to mimic this setup
https://pegasus.isi.edu/documentation/user-guide/data-transfers.html#hybrid-shared-filesystem-with-non-shared-filesystem-semantics

however, the compute jobs that are launched by the container fail because of failure in data transfer inside the container

LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/.singularity.d/libs
2022-12-14 11:07:20,089 INFO: --------------------------------------------------------------------------------
2022-12-14 11:07:20,089 INFO: Starting transfers - attempt 1
2022-12-14 11:07:22,111 ERROR: Expected local file does not exist: /scitech/shared/scratch-90-days/mzalam/alpha2/mzalam/pegasus/Alphafold-workflow/run0034/00/00/GA98.fasta
2022-12-14 11:07:22,111 ERROR: Expe

The planner created this in pegasus lite
printf "\n###################### Staging in input data and executables ######################\n" 1>&2

1. stage in data and executables
   pegasus-transfer --threads 1 1>&2 << 'eof'
   [
   Unknown macro: { "type"}

   ,
   ...

however, the singularity exec does not have the directory mounted
singularity exec --no-home --bind $PWD:/srv singularity-container.sif /srv/jackhmmer_uniref90_ID0000001-cont.sh