I'm experiencing issues using a singularity container for a rule in my workflow run on a HPC cluster. The singularity container itself is functioning just fine and is able to bind properly when called directly from the command line, but when i invoke it with snakemake in the following Snakefile:
rule all: output: "test.html", singularity: "shub://deanpettinga/rnaseq:edger" shell: "touch test.html"
with this command
$ snakemake --use-singularity --singularity-args '-B /my_dir'
i get this error:
ERROR : Failed to mount home directory /my_dir/path/to/my/snakemake/project/ -> /path/to/singularity/var/singularity/mnt/session/my_dir/path/to/my/snakemake/project: Permission denied ABORT : Retval = 255
it seems as though the admins are reluctant to change permissions, so i'm wondering:
would it be possible to set the mount point in a location of the user's choice to avoid such an issue?