Updated Command Line Tools – Wait for App Dependencies

We are pleased to announce a minor release of BaseSpaceCLI (0.8.10) with some improvements to existing tools and a new tool – bs wait.

‘bs wait’

The new wait command for BaseSpaceCLI is analogous to the shell command wait and was designed to help connect together separate app launches. The wait command accepts as arguments one or more appsessions and will then wait for these appsessions to finish, polling based on a specified interval (default 60 seconds). Once they have all finished, bs wait returns the appresults that have been generated by the provided appsessions. The intention is that these appresults can then be passed into another app launch, providing some limited app-chaining capabilities.
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New BaseSpaceCLI Tools

We are pleased to announce the third release (version 0.8) of BaseSpaceCLI, which includes a major new tool and a number of minor features. To install the new release, run this script:

$ sudo bash -c "$(curl -L https://bintray.com/artifact/download/basespace/helper/install.sh)"

BaseSpace Copy

With this release of BaseSpaceCLI we are introducing a new high-performance copy tool called BaseSpace Copy or bscp, which provides the following features:

  • Rich and flexible URI mechanism to specify source and target for copies
  • Multi-threaded for performance and to cope with high-latency connections
  • Excellent data integrity, all part data is hashed and verified. Ability to export md5sum compatible sum file for future data verification.
  • Resumable downloading

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Announcing BaseMount with Trash control

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.

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Enhancements to Run Monitoring

We’ve recently added some improvements to the Sequencing Runs list. These updates should help to quickly get basic quality information about each run, without needing to click into Run details pages.

For example, % reads passed filter (%PF), average %Q30, yield, and cycles (for Read1 and Read2) are now columns on the Runs list.

Run Quality Metrics

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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

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Introducing BaseSpaceCLI

In July, we released an early-access version of BaseMount, a command-line tool to allow you to navigate your BaseSpace account and work with your files on-demand.

To complement this browsing capability, we are adding to the suite of BaseSpace Command Line Tools by releasing the BaseSpaceCLI (Command Line Interface). BaseSpaceCLI provides two new areas of functionality, uploading samples and launching apps, but also comes with a host of other commands to help you work with your BaseSpace data and apps.

BaseSpace Command Line Tools

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Introducing App Versioning

We’re excited to announce support for versions of BaseSpace apps. The App Store has been very successful, and with this success comes the need to publish improved versions of apps.

Every app will now have a single entry in the App Store, and you may choose the version on each App Description page.

app-launch-menu

Each app version will have two new sections on the App Description page. The “Release Notes” section will list the changes since the last version. And the optional “What’s New” section can contain the latest updates about a version, such as bugs discovered since publication or changes to the version’s price.

isaac-enrichment

It’s important that once app versions are published, they can no longer be changed. This way apps can be used to analyze many samples in exactly the same way.

We’ve added some features to ensure that samples can be analyzed consistently during experiments. If you navigate to the App Description page of an app you’ve launched before, your default view will be the version that you launched the last time. Also, once an app version is published, it can no longer be changed by developers. Bug fixes and improvements can be added in new versions.

We’ll let you know if a new version is available. If you are on the App Description page of an older version, you will be notified that a new version is available.

app-launch-notification

App developers will notice some nice improvements to our developer portal, which include a new page to create and view app versions.

devportal

We hope you find these changes useful, and we all look forward to improved versions of apps!