Scientific Filesystem in CharlieCloud

by vs 8 years ago

GNU/Linux • xterm-256color • bash 1981 views

A new user to CharlieCloud (<–me) and running a workflow that is implemented with the Scientific Filesystem, and tested with Docker and Singularity. Can I figure out, during this recording, how to map it to CharlieCloud? Let’s find out!

TLDR, it comes down to:

Charliecloud

  ch-run -b data:/scif/data /var/tmp/snakemake.ch -- /bin/bash
  cd $HOME/Documents/Dropbox/Code/scif/examples/snakemake.scif  
  export PATH=/opt/conda/bin:$PATH  
  snakemake all

Singularity

  singularity shell --bind data/:/scif/data snakemake.simg
  snakemake all

Docker

   docker run -v $PWD/data:/scif/data:z -v $PWD:/working_dir -it -w /working_dir --entrypoint /bin/bash vanessa/snakemake.scif
   snakemake all

And the CharlieCloud (that looks complex) is likely not needing all of those lines (this is due to my inexperience of just an hour or two using it). This could probably be run externally (without shelling in) given that I can export the path properly. Super cool!! I promise to write this up more robustly, this is just a “quick and dirty” for now :)

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