Galaxy Upgrade Highlights

New features in Galaxy 2018 update

Interactive Tours

The interactive tours framework allows developers and deployers to build interactive tutorials for users superimposed on the actual Galaxy web front end. Unlike video tutorials, these will not become stale and are truly interactive (allowing users to actually navigate and interact with Galaxy).

Nested Workflows

Workflows may now run other workflows as a single abstract step in the parent workflow. This allows for reusing or sub workflows in your analyses.

New chemical datatypes

Galaxy now detects and supports many molecular datatypes.

Galaxy chat

Admins can now plug in the included communication server to enable users of their instance to use real-time chat within the Galaxy interface. Please see the documentation to learn how to activate and use this feature.

Galaxy UI plugins - Webhooks

We introduce Galaxy Webhooks - optional plugins for the web UI that allow for better customization of your instance.

Workflow run form replaced

The workflow run form has been replaced by one backed by the new tool form and the API. Nicer, faster, standardized.

New interface for user preferences

User preferences menu has been reworked for clarity and consistency.

Support for compressed FASTQ formats

You can now upload compressed (with gzip or bzip2) FASTQ files without them being unpacked automatically (as it was until now). For this, to work you have to select the proper type when uploading (e.g. instead of fastqsanger you select fastqsanger.gz or fastqsanger.bz2 for compressed files). Existing tools will work as before and future tools will be able to consume archives and save space in your quota.

Tag your data with propagating hashtags

Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships.

Drag & Drop datasets into tool inputs

The interface now allows dragging datasets from history panel into the content selectors of the tool form.

Upload directly to a collection

You can now bypass the history manipulation and upload your data straight into a collection for convenience.

Singularity

Tool execution using the HPC-friendly container technology Singularity is now supported. Custom containers can be specified by the Galaxy admin on a per job destination basis or standardized containers corresponding to Conda requirements can be built or downloaded automatically using the mulled toolkit built into Galaxy (just like is possible for Docker).

Download entire collection

Downloading whole collections is now possible from the history interface.

Switch tool versions in workflows

You can now select exactly what version of the tool you want to use when building workflows.

Performance and User Experience Improvements

We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time. We achieved this by optimizing database queries, implementing the cache, rethinking presentation, and adding progress bars and loading indicators where needed.

Dataset Collection Usability

This release has significantly improved the usability of Galaxy dataset collections.

New BAM datatypes

Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype).

Security and stability

There are also numerous security and stability improvements in this release.