Announcing File Upload with BaseMount

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 – and now upload – 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 v0.12) includes:

  • Write-mode: project and appresult creation, file upload
  • Properties can be viewed and edited
  • Improved documentation
  • Relaxed timeout for low bandwidth
  • Unmount assistance, listing blocking processes and offering lazy-unmount

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:

File upload

Uploading FASTQ files was already possible using bs upload sample (see BaseSpaceCLI below), and this remains the preferred method to upload samples with pre-validation.

BaseMount’s new file upload allows you to upload any kind of file to BaseSpace: BAM, VCF, etc.
In BaseSpace these files are shown inside app results as if they had been generated by an app. They may then be used as inputs for downstream apps.

For example, if you have a set of VCFs locally, which you want to compare with VCAT, you can now easily upload them from the command line before launching the VCAT app.

Run upload is not supported yet.

Demo

Here is a quick example of how easy it is to upload a file to a new AppResult:

# Mount your BaseSpace account
mkdir BaseSpace
basemount BaseSpace

# Create new project
cd BaseSpace/Projects
mkdir myNewProject

# Create new AppResult (the only entity able to store files other than fastq)
cd myNewProject/AppResults
mkdir myNewAppResult
cd myNewAppResult

# Create a file there (or copy one with `cp`)
echo "Hello BaseSpace" > Files/hello.txt

# Mark the container as "Complete"
basemount-cmd mark-as-complete
# (You can now navigate to your BaseSpace account in a browser
#  and check that the file is present in the myNewProject project)

BaseSpaceCLI Support for OS X

As well as BaseMount, we are also releasing an update to BaseSpaceCLI (our other set of tools under the “BaseSpace CLI Tools” umbrella).

This BaseSpaceCLI update includes:

  • OS X support
  • More app input types supported by the import app command (including AmpliconDS and Tumor/Normal app)
  • Selection in “list” command (eg. --sample-name, --project-name etc.) uses globs instead of substring matching, to improve precision.

Installation instructions and more details can be found on the BaseSpaceCLI help page.

Feedback

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

About Eric Smith

Eric Smith is a product owner for BaseSpace.

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