How to mount my local dir

[rl4940]

Hi Nanocdisco team:

Thank you for developing this great tool.
I have a question may be on the side of singularity, that how to mount my dir into the container, in order to use my fast5 files from local computer.

[duceppemo]

sample=my_sample

# Create writable container
singularity build --sandbox nd_analysis nanodisco.sif

# Create new folders inside writable container to add own data
[ -d /home/bioinfo/nd_analysis/home/nanodisco/dataset/"${sample}"/natif ] || mkdir -p /home/bioinfo/nd_analysis/home/nanodisco/dataset/"${sample}"/natif
[ -d /home/bioinfo/nd_analysis/home/nanodisco/dataset/"${sample}"/wga ] || mkdir -p /home/bioinfo/nd_analysis/home/nanodisco/dataset/"${sample}"/wga

# Start interactive shell and bind own data
singularity run \
    --no-home \
    -B /media/36tb/data/nanopore/native_nano-0007/fast5_basecalled_single_demultiplexed/"${sample}":/home/nanodisco/dataset/"${sample}"/natif:ro \
    -B /media/36tb/data/nanopore/wga_nano-0008/fast5_basecalled_single_demultiplexed/"${sample}":/home/nanodisco/dataset/"${sample}"/wga:ro \
    -B /home/bioinfo/ref:/home/nanodisco/reference \
    -w nd_analysis

# Re-define variable inside container
sample=my_sample

# From within the container
nanodisco preprocess \
    -p 64 \
    -f dataset/"${sample}"/natif  \
    -s "${sample}"_natif \
    -o analysis/"${sample}"/preprocessed_subset \
    -r reference/my_ref.fna

nanodisco preprocess \
    -p 64 \
    -f dataset/"${sample}"/wga \
    -s "${sample}"_wga \
    -o analysis/"${sample}"/preprocessed_subset \
    -r reference/my_ref.fna
# etc.

[touala]

Hello,

Thank you for sharing your solution. This also helped putting back this issue on my radar. I would recommend trying #64 (comment) which do not require to bind volumes to singularity container.

[duceppemo]

I found that post after. It’s is indeed much easier to use `exec` rather than `run` with binding. I was not familiar with singularity before trying nanodisco, so I had to spend some time trying out a bunch of stuff to understand what would work and what would not. The only drawback from using `exec` is that, if I recall correctly, it requires relative paths and won’t work with absolute paths (so I had to move my fast5 folders and my ref folder in a common location. I’m not sure if is this a singularity requirement of if it’s specific to nanodisco.

[touala]

Ok perfect. The relative path requirement is coming from singularity. There might be ways around it but I always used relative path...