May 2018 Galaxy Release (v 18.05)¶
- New Interface Style Library
- Unlimited Browser Upload Size
Support for chunked and resumable file uploads out-of-the-box. This should effectively eliminate browser-based limitations on the size of files that can be uploaded to Galaxy.
- New Powerful Rule-Based Data Uploader
Galaxy now features a powerful new interface for manipulating lists of rules for processing metadata that can be used to describe the upload of arbitrarily complex collections as well as individual datasets. These rules can be used to build collections from lists of URLs, FTP directory contents, data library folders, and tabular sample sheets or exports from external data sources. The same technique can be applied to the metadata of an existing collection, enabling very flexible filtering, sorting, relabelling, grouping, flattening, and general re-organization of collections. This client widget is backed by a powerful new hierarchical upload API and a new collection operation tool.
Check out this tutorial describing new techniques for loading large numbers of datasets and complex collections into Galaxy.
- GDPR Beta Mode
We introduce beta GDPR privacy mode. Admins can enable it to help them comply with the European Union law known as General Data Protection Regulation, which goes into effect on May 25, 2018. Thanks to @hexylena.
- New HIV-TRACE Plugin
Integration of a new visualization plugin - HIV-TRACE. Thanks to @veg!
- Visualization Frameworks Unified
The charts and generic visualization frameworks have been merged together into a single coherent one. You can use a new menu option to list and search all available visualizations.
- To get a new Galaxy repository run:
$ git clone -b release_18.05 https://github.com/galaxyproject/galaxy.git
- To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_18.05 && git pull --ff-only origin release_18.05
See the community hub for additional details regarding the source code locations.
vcffilter by devteam allowed RCE¶
Older versions of the VCF filter tool in the vcffilter repository by devteam allowed remote code execution due to missing character escaping.
If you have this repository installed in your Galaxy, please update to the revision
4:6b935ab36d7b or newer and disable/uninstall all older versions.
chartsrepository that powers Galaxy built-in visualizations that need backend computation has been moved to the IUC account. In order for these visualization options to keep working, admins need to install the following repository: iuc/charts.
Removed support for the Graphite statistics middleware. We continue to further support the
We reworked how compressed archives (zip, gz, bz etc.) are being defined and handled in Galaxy. As a result, if you have a custom
datatypes_conf.xmlconfiguration file, you should remove the compressed sniffers that used to be in the sample file but now are not. Otherwise you will encounter non-breaking errors in the logs.
We have removed the deprecated symlink static/scripts/packed -> . If you used it please change your (proxy) configuration. An example can be seen here.
Sniffing framework with constrained memory and I/O. Pull Request 5793
Infrastructure for dynamic compressed datatypes. Pull Request 5794
Capture more HDA state transitions in the history panel. Pull Request 5749
Add fasta.gz datatype. Pull Request 5553
Avoid silent tool upgrades during workflow imports. Pull Request 5821
Many awesome Python 3 related fixes (thanks to @nsoranzo and @mvdbeek). Pull Request 5359, Pull Request 5422, Pull Request 5453, Pull Request 5461, Pull Request 5492, Pull Request 5494, Pull Request 5458, Pull Request 5636,`Pull Request 5642`_, Pull Request 5427, Pull Request 5451
Remove unused mapping code. Pull Request 5450
Add middleware and instrumentation to allow per-request SQL debugging. Pull Request 5539
More and more robust Selenium tests. Pull Request 5559, Pull Request 5882, Pull Request 5886, Pull Request 5876, Pull Request 5836, Pull Request 5701, Pull Request 5771, Pull Request 5754, Pull Request 5714, Pull Request 5705, Pull Request 5708, Pull Request 5710, Pull Request 5706, Pull Request 5707
Implement basic cache on toolbox
to_dictobjects. Pull Request 5570
Performance optimization to avoid producing deep-copies of tool input dictionaries. Pull Request 5646
Disable tool input datatype validation for dropped history items. Pull Request 5657
Add a script for dumping library file paths for backup. Pull Request 5436
Populate column selector for datasets which are not ready yet. Pull Request 5680
Fix role handling library manager. Pull Request 5681
GFF updates to handle
##FASTAdirective. Pull Request 5686
Memory and performance fixes for upload tool. Pull Request 5689
Fixes for testing
Dockerfilerecipe. Pull Request 5693
Improve galaxy update commands, update some bootstrap checkpoints. Pull Request 5731
extract_genomic_dnatool from tool sample. Pull Request 5741
More backend speed ups for user’s workflow index query. Pull Request 5755
Fix all bundled scripts for the switch to YAML configuration. Pull Request 5769
Lock pysam to 0.14.1 in Pipfile. Pull Request 5798
Client related readme and
Makefileclarifications. Pull Request 5800
Add link that explains quota management to quota indicator. Pull Request 5811
Improve startup interoperability with Conda. Pull Request 5854
Implement the API version of the Docker containers interface. Pull Request 5861
Add Mocha/Chai client test framework. Pull Request 5888
Remove unused client route. Pull Request 5907
static/scripts/*from the dev branch, add to .gitignore. Pull Request 5434
History contents client code refactoring. Pull Request 5448
make client-productionwarning from build scripts. Pull Request 5508
Update tool conf samples for recent changes. Pull Request 5637
Extend grid framework with formal support for delayed columns. Pull Request 5789
Fixes for plugin directory staging. Pull Request 5810
Remove defunct CasperJS tests. Pull Request 5567
Eliminate unused pre-created datasets concept in upload API. Pull Request 5604
Fix tool state performance for large collections. Pull Request 5997
Fix initial binding for slow query logging. Pull Request 5401
Default slow request tracking to disabled. Pull Request 5513
Hack to fix bug in uploader where it sometimes posts with empty “file_type”. Pull Request 5692
Relax validation condition for dynamic parameters. Pull Request 5702
Fix issue where some elements of collections wouldn’t render in the UI. Pull Request 5703
Fix mulled Docker caching. Pull Request 5735
Drop old charts building from makefile/package scripts Pull Request 5737
Add additional validation to numeric input element. Pull Request 5750
Various scatterplot fixes. Pull Request 5752
Fix copying tags for collections when copying histories. Pull Request 5766
/api/whoamiAPI endpoint for master key. Pull Request 5773
Fix SQL query for “workflows shared with me” as part of workflow index. Pull Request 5782
Fix model operation tools that produce standalone datasets. Pull Request 5784
upload_common.pyensure hda is added to a session. Pull Request 5816
Fix conditional parameter handling. Pull Request 5864
Remove deprecated controller endpoint and link to preferred implementation. Pull Request 5887
Fix admin data library dataset permissions. Pull Request 5899
Fix display of the tour index names. Pull Request 5900
Fix Trackster links. Pull Request 5916
Fix bug with removing workflow outputs from a node. Pull Request 5935
Fix for running in containers when
job_tmpis set in
job_conf.xml. Pull Request 5937
Fix for running jobs in containers. Pull Request 5938
Fix dropdown click and highlighting behavior. Pull Request 5945
Fix shared history list bug. Pull Request 5962
Thanks for using Galaxy!