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@@ -11,9 +11,7 @@ Enhancements
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.. feature
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* Allow selecting subset of collection by group tag
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
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`Pull Request 5457`_
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* Copy data from a cloud-based storage to a Galaxy history
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(thanks to `@VJalili <https://github.com/VJalili>`__).
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`Pull Request 5835`_
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@@ -225,12 +223,6 @@ Enhancements
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* small improvement to the too xsd docs regarding discovered_datasets
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(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
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`Pull Request 6490`_
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* Implement ``group:`` tags (toward multi-factor analysis with group tagging)
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`Pull Request 6491`_
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* Allow setting tags on targets & contents in data fetch API.
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`Pull Request 6499`_
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* Integrate tagging into the rule builder.
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`Pull Request 6500`_
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* Cache chrom_info generation when mapping over collections.
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`Pull Request 6515`_
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* More optimized HID generation - in one commit instead of two.
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@@ -254,8 +246,6 @@ Enhancements
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`Pull Request 6539`_
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* Test case for nested collection input to flatten in a workflow.
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`Pull Request 6541`_
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* Allow Consuming Tags in the Apply Rules Tool
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`Pull Request 6545`_
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* Integration test for the interaction of nested object stores and jobs.
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`Pull Request 6546`_
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* Configure object store for datasets in job handler instead of web thread.
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@@ -264,10 +254,6 @@ Enhancements
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`Pull Request 6552`_
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* Unified dataset permission API.
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`Pull Request 6568`_
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* Add tagging rule to history level rule builder, copy HDAs when building
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collection
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
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`Pull Request 6572`_
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* Add API endpoint to fetch a history's workflow invocations.
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`Pull Request 6580`_
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* Improve robustness of tour Selenium test.
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@@ -314,9 +300,6 @@ Enhancements
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* Add Seurat datatype: rdata.seurat
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(thanks to `@mblue9 <https://github.com/mblue9>`__).
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`Pull Request 6648`_
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* Allow group tag selection also for multiple="true" inputs
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
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`Pull Request 6661`_
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* Various link and documentation fixes
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(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
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`Pull Request 6662`_
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@@ -330,8 +313,6 @@ Enhancements
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`Pull Request 6681`_
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* Add self help to error reporting interface
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`Pull Request 6711`_
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* Undo auto-propagation of group tags.
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`Pull Request 6750`_
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* Client build startup changes
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`Pull Request 6753`_
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* Add graph dot datatype and enable it in visualisations
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@@ -8,14 +8,6 @@ September 2018 Galaxy Release (v 18.09)
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Highlights
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===========================================================
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**OpenID Connect Support**
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Galaxy now supports using OpenID Connect for user login, relying on trusted
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identity providers to manage authentication. This is intended to replace the
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old (and mostly deprecated, on the web) OpenID 2.0 logins. Read more at
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https://galaxyproject.org/admin/authentication/
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`https://github.com/galaxyproject/galaxy/pull/4474`
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**Extensive Workflow Enhancements**
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Workflows got a lot of love this time around, with new runtime parameters for
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subworkflows, exposed workflow versions, and zoom capability in the editor, to
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@@ -24,6 +16,19 @@ Highlights
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(link up PRs)
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**Group Tags**
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Galaxy now contains powerful new features for multiple factor analysis of collections
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of datasets. The concept of group tags has been added to Galaxy. These are a special
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class of tags that describe key-value pairs that can be attached to the contents of a
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collection during upload or using collection operation tools. These tags can describe
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multiple sets of variables for the contents of a collection. Once set, these tags can
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be consumed intelligently by tools that need to divide collections into multiple
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overlapping factors or sets of datasets. A special thanks to `@mvdbeek <https://github.com/mvdbeek>`__ for devising and implementing this approach.
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`Pull Request 5457`_, `Pull Request 6491`_, `Pull Request 6661`_,
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`Pull Request 6750`_, `Pull Request 6499`_, `Pull Request 6500`_,
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`Pull Request 6572`_, `Pull Request 6545`_
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**Python 3 Beta Support**
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After almost 3 years of work and more than 100 pull requests, we are proud
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to announce the Beta-stage support for running Galaxy under Python 3.
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@@ -51,7 +56,13 @@ See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for a
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Security
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========
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(TODO: Add notes)
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Unauthorized File System Operations via New Upload API
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------------------------------------------------------
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Tracked as GX-2018-0006. Servers running Galaxy 18.05 should be updated as soon as possible.
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See `the public announcement for full details
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<http://announce.list.galaxyproject.org/GX-2018-0006-Unauthorized-File-System-Operations-via-New-Upload-API-td4639432.html>`__.
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Breaking Changes
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================
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