We are pleased to announce a new release of BaseMount, our FUSE driver to mount your BaseSpace account as a Linux filesystem. BaseMount allows you to navigate on the command line through projects, samples, runs and app results, and interact directly with the associated files exactly as you would with any other local file system.

BaseMount allows you to download, upload – and now delete – files, but maybe more importantly, it allows you to work interactively with your files stored on BaseSpace without having to download them. You may, for example, run samtools directly on a large BAM file, and it will only fetch the blocks needed for your query.

This update (BaseMount v0.14) includes:

  • Move-to-trash and restore-from-trash
  • Refresh command
  • New bm-cmd tool, a shorter alias for basemount-cmd
  • Moved passphrase encryption to –passphrase

As always, you can install or update BaseMount using the command line

sudo bash -c "$(curl -L https://basemount.basespace.illumina.com/install)"

More details can be found on the following pages:

Moving BaseSpace Sequence Hub Entities to the Trash

A series of basemount-cmd operations now allow you to control the trash:

  • move-to-trash: Delete current entity
    Available in: project, run, sample, appresult and appsession entities
  • move-to-trash-preserve-metadata: Delete only the Data directory from the run, preserving the entity and the other files
    Available in: run entities
  • restore-from-trash: Restore entity to main account
    Available in: .Trash/{entity-name} directories

Important note: If you previously authenticated with an older version of BaseMount, your stored access token may not contain the scope needed for trash operations.
To fix this, you need to delete your current configuration (by using basemount --remove-config [--config=<config>]) and run BaseMount again to re-authenticate.


Here is a quick example to create a project, move it to the trash and restore it from the trash:

# Force reauthentication to get TRASH capabilities
# Only needed the first time you use this new version
basemount --remove-config

# Mount your BaseSpace account
mkdir BaseSpace
basemount BaseSpace

# Create new project
cd BaseSpace/Projects
mkdir myNewProject

# Move project to the trash
basemount-cmd --path myNewProject move-to-trash # or simply: rmdir myNewProject

# View project in the trash
ls -ld ../.Trash/myNewProject

# Restore project from the trash
basemount-cmd --path ../.Trash/myNewProject restore-from-trash

Refresh is Here!

Yes, finally! You can now run basemount-cmd refresh (or its shorter alias bm-cmd r<tab><tab>) to force-reload the information shown in your current directory from the BaseSpace Sequence Hub server.

This is useful if you create entities outside BaseMount (for example if you create a project using the website) and want to use them in an already-mounted BaseMount directory.

This command is available in the Projects, Runs and .Trash directories and their sub-directories.


Please visit our BaseSpace Google group for inquiries and to submit feedback.