choose mount point for singularity containers?

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Issue #1286 new
Former user created an issue

Hi,

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?

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