CS-FileSystem

This is a user-space filesystem for exposing Cybershuttle data sources.

This version loads ATLAS metadata from a TSV file and exposes each protein entry as a directory containing a metadata.json file.

/tmp/atlas_mount/
  atlas/
    1r6w_A/
      metadata.json
    2y44_A/
      metadata.json

Requirements

Linux

sudo apt install cargo
sudo apt install -y libfuse3-dev libfuse-dev pkg-config

macOS

brew install pkgconf
brew install --cask macfuse

macFUSE may require approval in System Settings -> Privacy & Security.

ATLAS TSV

Place the ATLAS metadata TSV somewhere local. The examples below assume the TSV is at:

data/2024_11_18_ATLAS_info.tsv

The TSV is not committed to the repository. Create the data directory and copy or download the file there:

mkdir -p data
cp /path/to/2024_11_18_ATLAS_info.tsv data/

Run

Build and mount the filesystem:

mkdir -p /tmp/atlas_mount
cargo run --release -- data/2024_11_18_ATLAS_info.tsv /tmp/atlas_mount

Leave that command running while the filesystem is mounted.

In another terminal:

ls /tmp/atlas_mount
ls /tmp/atlas_mount/atlas | head
ls /tmp/atlas_mount/atlas/1r6w_A
cat /tmp/atlas_mount/atlas/1r6w_A/metadata.json

Unmount

Linux:

fusermount -u /tmp/atlas_mount

macOS:

diskutil unmount /tmp/atlas_mount