BaseSpace™ CLI v1.0.0 is here!

By Swathi A. Ramani, Staff Product Manager – BaseSpace Sequence Hub

 If you’ve been using BaseSpace Sequence Hub for some time now, then you probably know that there is a lot more to the platform than the browser console. The Command Line Interface (CLI) is an easy-to-use command line tool that enables users to do more with BaseSpace via managing common (and not so common) tasks associated with their genomic data and analysis.

The CLI has been in development for over 4 years, and was created by our talented UK team. They needed automation tools to help sequence more than 20 petabases of data for the 100k Genomes Project. Over the past few months, we’ve been hard at work on the next generation of the CLI. We are thrilled to announce that our CLI is no longer in Beta! In our latest release, we have launched the officially supported BaseSpace (BS) Sequence Hub (BSSH) CLI v1.0.0, and all the exciting features that come with it. In the years since the initial release, we saw incredible product uptake and a lot of positive feedback from the BaseSpace community. With this launch announcement, we are delivering on some of your biggest requests for a robust feature set that simplifies data and analysis wrangling and process automation. This is a great foundation on which we can continue expanding our toolset.

Rich Built-in Features

BS CLI v1.0.0 is a completely different beast from its previous version. With just one file to download and configure, you can control multiple BaseSpace services and automate them through scripts, including uploading samples, downloading runs, launching or stopping apps and workflows, setting custom quality filters for your runs, launching analysis workflows, generate pre-signed URLs, and much more ! 

These include: 

  • Flexible install process: The CLI is installed by downloading a single binary with no additional dependencies, which enables you to install the CLI in an environment where you do not have administrator privileges.
  • Support for Linux, Mac and Windows (32 and 64 bit) operating systems
  • Rich options for listing details and filtering with customized output for seamless multi-command pipelines and scripts
  • Powerful data management features including creation, renaming and deletion of BSSH entities
  • Efficient upload of FASTQ datasets or any other file types, coupled with fast download of runs, projects, biosamples and datasets
  • Parameterize, launch, monitor and kill analyses running remotely in BSSH

Importantly, we’ve made sure the above features work nicely together so you don’t have to do the plumbing yourself. For a full list of worked examples visit our help site.

Try It Out Today! 

Our new BS CLI v1.0.0 is ready to serve as your standard toolchain to programmatically read, create and manipulate data in your BSSH account, automate routine tasks, as well as to efficiently manage your applications. You can try it out right now by following the instructions on our help site

If you are using existing tools like BaseMount or BaseSpace Copy, these will continue to work. However, as we continue to improve the developer experience, we hope to consolidate our existing tools and add new features to the BS CLI v1.0.0 toolchain. 

The more you use BS CLI v1.0.0, the more you will see how powerful it is. We can’t wait to see what you build with it! As always, let us know how we are doing. We want to incorporate best practices in the toolchain as much as possible, so it becomes customary, so please submit any requests in via this blog, twitter or techsupport@illumina.com. Happy hacking! 

  • The BaseSpace Sequence Hub Team

For Research Use only.

QB#8581

 

 

 

BaseMount: A Linux command line interface for BaseSpace

BaseSpace was designed with a graphical, web-based interface to enable push-button analytics, and sharing of NGS data. We also realize that there are some use cases, especially while working with bulk data, where a Linux-based command line interface (CLI) is more convenient.  We are therefore happy to announce the early access release of BaseMount, a tool that can be used to mount your BaseSpace data as a Linux file system. With BaseMount you can navigate 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 is a FUSE driver, which operates in user-space and uses the BaseSpace API to generate the file system structure for both the metadata and actual file-based data.

To install, please go to the BaseMount page: basemount.basespace.illumina.com and run the installation script. We have several tutorial videos as well as a Help Page to get you started. The Help page also has information on hardware and operation system requirements.

Continue reading BaseMount: A Linux command line interface for BaseSpace