Is it possible to "mount" filesystem with Cloud Workstation

Nick Hirschmüller

Hi all,

I'm currently processing WES plink files on the UKB RAP, and the longest step by far is downloading the data to the worker when using a Cloud Workstation.

With the Swiss Army Knife, I know I can "mount" the filesystem to avoid this time-consuming download. However, I prefer to prototype workflows in a Cloud Workstation. I’m wondering if it's possible to use a similar mounting option there, or if I need to install "dxfuse" first.

If it is possible, it would be fantastic to have a small tutorial how to do it, because I think it would benefit a lot of people.

Cheers!

 

Comments

2 comments

Date Votes
  • Comment author
    Nick Hirschmüller
    • Edited

    I actually found what I was looking for in the README of dxfuse..

     

    For reference, here are the steps:

    # request workstation
dx run cloud_workstation -imax_session_length=10h --allow-ssh --instance-type "mem3_ssd3_x8" --priority "low"
# download dx fuse
wget https://github.com/dnanexus/dxfuse/releases/download/v1.4.0/dxfuse-linux
sudo mv dxfuse-linux /usr/bin/dxfuse
sudo chmod 777 /usr/bin/dxfuse

mkdir remote_dir
dxfuse remote_dir "<PROJECT NAME>"
# then run your command, for example
# install plink2 first
plink2 --bfile ukb23158_c9_b0_v1 --freq --out ~/allele_frequencies --no-categorical

    Afterwards you can just go into remote_dir and run your commands..

    4
  • Comment author
    Rui Li

    dxfuse will ‘work’ but it's unstable for larger files, e.g. CRAM files

    0

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