Difference between revisions of "Galaxy Upgrade Highlights"
| (10 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
[[Category:Software]][[Category:Galaxy]] | [[Category:Software]][[Category:Galaxy]] | ||
| − | + | __NOTOC__ | |
| − | + | ==List of new features in Galaxy 2018 upgrade== | |
| − | =Galaxy 2018 | + | ===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. | |
| − | === | + | ====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). | 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. | ||
| − | + | ====Security and stability==== | |
| − | + | There are numerous security and stability improvements in this release. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | ====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The workflow run form has been replaced by one backed by the new tool form and the API.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. | The workflow run form has been replaced by one backed by the new tool form and the API.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. | User preferences menu has been reworked for clarity and consistency. | ||
| − | + | ====Tag your data with propagating hashtags==== | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships. | 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. | The interface now allows dragging datasets from history panel into the content selectors of the tool form. | ||
| + | ====Switch tool versions in workflows==== | ||
| + | You can now select exactly what version of the tool you want to use when building workflows. | ||
| − | + | ===Collections=== | |
| + | ====Dataset Collection Usability==== | ||
| + | This release has significantly improved the usability of Galaxy dataset collections. | ||
| + | ====Upload directly to a collection==== | ||
You can now bypass the history manipulation and upload your data straight into a collection for convenience. | You can now bypass the history manipulation and upload your data straight into a collection for convenience. | ||
| − | + | ====Download entire collection==== | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Downloading whole collections is now possible from the history interface. | Downloading whole collections is now possible from the history interface. | ||
| − | + | ===Data types=== | |
| − | + | ====Support for compressed FASTQ formats==== | |
| − | You can now select | + | 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. |
| − | + | ====New BAM datatypes==== | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype). | Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype). | ||
| − | + | ====New chemical datatypes==== | |
| − | + | Galaxy now detects and supports many molecular datatypes. | |
| − | |||
| − | |||
Latest revision as of 20:34, 18 April 2018
List of new features in Galaxy 2018 upgrade
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.
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.
Security and stability
There are numerous security and stability improvements in this release.
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.
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.
Switch tool versions in workflows
You can now select exactly what version of the tool you want to use when building workflows.
Collections
Dataset Collection Usability
This release has significantly improved the usability of Galaxy dataset collections.
Upload directly to a collection
You can now bypass the history manipulation and upload your data straight into a collection for convenience.
Download entire collection
Downloading whole collections is now possible from the history interface.
Data types
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.
New BAM datatypes
Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype).
New chemical datatypes
Galaxy now detects and supports many molecular datatypes.