mirror of
https://github.com/galaxyproject/galaxy.git
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initial curated release notes for 16.07
This commit is contained in:
Martin Cech
@@ -0,0 +1,843 @@
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.. to_doc
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-------------------------------
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16.07
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-------------------------------
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Conda
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-------------------------------
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* Install via conda
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||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__
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and `@bwlang <https://github.com/bwlang>`__.)
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`Pull Request 2554`_
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* install Conda at startup; enable conda_auto_init in sample conf
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`Pull Request 2759`_
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API
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-------------------------------
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* TS API: add endpoint to check current user
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`Pull Request 2243`_
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* Users API: add the update endpoint
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`Pull Request 2595`_
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Collections
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-------------------------------
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* Collection Operations (Limited)
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`Pull Request 2434`_
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* Implement UI to display list of lists dataset collections
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`Pull Request 2613`_
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Datatypes
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-------------------------------
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* Add support to PDBQT molecule datatype
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(thanks to `@leobiscassi <https://github.com/leobiscassi>`__.)
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`Pull Request 2452`_
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* Add the trackhub composite datatype
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||||
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
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`Pull Request 2348`_
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* Import mothur datatypes
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||||
(thanks to `@shiltemann <https://github.com/shiltemann>`__.)
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||||
`Pull Request 2038`_
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||||
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||||
Highlighted Enhancements
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||||
-------------------------------
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||||
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||||
* Galactic Radio Telescope
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(thanks to `@erasche <https://github.com/erasche>`__.)
|
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`Pull Request 2455`_
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* Galaxy Communication Server
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||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__
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and `@bgruening <https://github.com/bgruening>`__.)
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||||
`Pull Request 2515`_
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* Add DTD to Galaxy
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||||
(thanks to `@ericenns <https://github.com/ericenns>`__.)
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`Pull Request 2579`_
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* Azure blob objectstore
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||||
(thanks to `@zfrenchee <https://github.com/zfrenchee>`__.)
|
||||
`Pull Request 2621`_
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* HTCondor Docker Integration
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||||
(thanks to `@bgruening <https://github.com/bgruening>`__.)
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||||
`Pull Request 2278`_
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* Kubernetes job runner
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||||
(thanks to `@pcm32 <https://github.com/pcm32>`__.)
|
||||
`Pull Request 2314`_
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||||
* improvements to toolbox search
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||||
`Pull Request 2273`_
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||||
* Generate metadata in separate conda environment
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||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
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`Pull Request 2253`_
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* Reports: new pages and improvements
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||||
(thanks to `@BalthazarPavot <https://github.com/BalthazarPavot>`__.)
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||||
`Pull Request 2664`_
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* Nicer bug report emails
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||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2143`_
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||||
* Tools with auto_format='true' connectable in workflow editor
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||||
(thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
|
||||
`Pull Request 2144`_
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* Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip
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>= 8.1)
|
||||
`Pull Request 2383`_
|
||||
* Allow tool form to listen to history
|
||||
(thanks to `@nturaga <https://github.com/nturaga>`__.)
|
||||
`Pull Request 2476`_
|
||||
* Add EDAM operations to tools and expose in API
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
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||||
`Pull Request 2379`_
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Enhancements
|
||||
-------------------------------
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||||
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* Add filter_failed_datasets_from_collection.py script
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(thanks to `@chambm <https://github.com/chambm>`__.)
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`Pull Request 2358`_
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||||
* Run workflow form revision
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||||
`Pull Request 2077`_
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||||
* galaxy-lib tweaks
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||||
`Pull Request 2110`_
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* Automate and clarify more of the release process.
|
||||
`Pull Request 2117`_
|
||||
* API: add server_starttime to api/configuration
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||||
`Pull Request 2124`_
|
||||
* This should fix bug `#1892
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||||
<https://github.com/galaxyproject/galaxy/issues/1892>`__ in toolshed
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||||
(thanks to `@nturaga <https://github.com/nturaga>`__.)
|
||||
`Pull Request 2142`_
|
||||
* Use "$NCPUS" if defined to set GALAXY_SLOTS
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
|
||||
`Pull Request 2145`_
|
||||
* Replacing the _getIndex method by UnderscoreJS method _.findIndex()
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__.)
|
||||
`Pull Request 2157`_
|
||||
* activation config touch
|
||||
`Pull Request 2158`_
|
||||
* Implement ``single_user = <email>`` config option.
|
||||
`Pull Request 2165`_
|
||||
* More documentation and flexibility for FTP imports.
|
||||
`Pull Request 2168`_
|
||||
* Stats prefix configurability and conditional wheel req.
|
||||
`Pull Request 2171`_
|
||||
* Fix running tool tests if remote user middleware is enabled.
|
||||
`Pull Request 2173`_
|
||||
* Improve handling of a missing R environment.
|
||||
`Pull Request 2215`_
|
||||
* Quote some parameters in Trim tool command
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2248`_
|
||||
* Tool execution dependency resolution already contains the relevant
|
||||
`Pull Request 2254`_
|
||||
* add Saskia to contributors
|
||||
`Pull Request 2256`_
|
||||
* A pass adding new contributors from 15.10->16.04(ish).
|
||||
`Pull Request 2257`_
|
||||
* Sort contributors by surname ASC.
|
||||
`Pull Request 2258`_
|
||||
* Add grunt watcher on the .less files
|
||||
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
|
||||
`Pull Request 2274`_
|
||||
* requirements updates (end of custom Whoosh)
|
||||
`Pull Request 2276`_
|
||||
* Enhance library functions for tools.
|
||||
`Pull Request 2279`_
|
||||
* Shift asbool handling in datatypes api so that an appropriate error m…
|
||||
`Pull Request 2286`_
|
||||
* More small fixes from downstream projects.
|
||||
`Pull Request 2292`_
|
||||
* For published workflow display, Provide a better error when the workf…
|
||||
`Pull Request 2302`_
|
||||
* Bump sqlite3 version
|
||||
(thanks to `@matthdsm <https://github.com/matthdsm>`__.)
|
||||
`Pull Request 2307`_
|
||||
* Show DCE count in collection and HDCA views
|
||||
`Pull Request 2326`_
|
||||
* Client library updates
|
||||
`Pull Request 2328`_
|
||||
* Revise form data visitor
|
||||
`Pull Request 2330`_
|
||||
* UI, history: update using xhr date header
|
||||
`Pull Request 2335`_
|
||||
* History/Sharable model user sharing API
|
||||
`Pull Request 2340`_
|
||||
* Update to latest galaxy-lib.
|
||||
`Pull Request 2354`_
|
||||
* Revise portlet view, integrate collapsible option
|
||||
`Pull Request 2360`_
|
||||
* Fix issue with lowercasing in datatypes/registry.py
|
||||
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
|
||||
`Pull Request 2361`_
|
||||
* Improve composite output tool test.
|
||||
`Pull Request 2363`_
|
||||
* Fix release notes generator
|
||||
`Pull Request 2366`_
|
||||
* Upgrade shared ui libraries, add test cases
|
||||
`Pull Request 2368`_
|
||||
* Python3: use open() instead of file()
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2370`_
|
||||
* More clarification of release process.
|
||||
`Pull Request 2372`_
|
||||
* Update template to include the release of the Docker container
|
||||
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__.)
|
||||
`Pull Request 2378`_
|
||||
* Remove backported importlib and ordereddict
|
||||
`Pull Request 2380`_
|
||||
* Note on updating tool testing
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2381`_
|
||||
* Docker swarm support for interactive environments
|
||||
`Pull Request 2386`_
|
||||
* Add support for EDAM data annotations to datatypes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2387`_
|
||||
* Ever more informative, explicit, and complete release checklist.
|
||||
`Pull Request 2388`_
|
||||
* Add a new workflow building mode variation which does access the history
|
||||
`Pull Request 2390`_
|
||||
* Fixes pep8 issues from `#2386
|
||||
<https://github.com/galaxyproject/galaxy/issues/2386>`__
|
||||
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__.)
|
||||
`Pull Request 2392`_
|
||||
* Add conda search function
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__.)
|
||||
`Pull Request 2395`_
|
||||
* Add history navigation options for dataset frames to scratch book
|
||||
`Pull Request 2396`_
|
||||
* Add EDAM topics to tools and expose in API
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2397`_
|
||||
* SLURM: when scontrol fails, try to get job state with sacct
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2403`_
|
||||
* Enhancements to tool test output verification.
|
||||
`Pull Request 2409`_
|
||||
* UI, datasets: show hid in 'view details' page
|
||||
`Pull Request 2411`_
|
||||
* Update galaxy-lib related modules to latest in that project.
|
||||
`Pull Request 2414`_
|
||||
* Updates and fixes for the run workflow ui elements
|
||||
`Pull Request 2416`_
|
||||
* Raise Exception if watch_tools has an unrecognized value
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2418`_
|
||||
* Python3: use log.warning() instead of deprecated log.warn()
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2420`_
|
||||
* minor docs touch
|
||||
`Pull Request 2427`_
|
||||
* Correct various EDAM data/format annotations in datatypes
|
||||
(thanks to `@hmenager <https://github.com/hmenager>`__.)
|
||||
`Pull Request 2428`_
|
||||
* small updates to Mothur datatypes
|
||||
(thanks to `@shiltemann <https://github.com/shiltemann>`__.)
|
||||
`Pull Request 2429`_
|
||||
* Update Galaxy testing to target latest galaxy-lib.
|
||||
`Pull Request 2436`_
|
||||
* fixed $defaults according to `#2430
|
||||
<https://github.com/galaxyproject/galaxy/issues/2430>`__
|
||||
(thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__.)
|
||||
`Pull Request 2438`_
|
||||
* Properly list subworkflows in run workflow form
|
||||
`Pull Request 2440`_
|
||||
* Python3: Make some files compatible with Python3
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2453`_
|
||||
* Add parameter expansion caller and test cases as preparation for workflow
|
||||
api extension
|
||||
`Pull Request 2464`_
|
||||
* Set a default for tool_dependencies_dir.
|
||||
`Pull Request 2480`_
|
||||
* Add a password expiration config option (resolves `#2485
|
||||
<https://github.com/galaxyproject/galaxy/issues/2485>`__)
|
||||
(thanks to `@benfulton <https://github.com/benfulton>`__.)
|
||||
`Pull Request 2486`_
|
||||
* Update against latest galaxy-lib.
|
||||
`Pull Request 2494`_
|
||||
* display TIFF in upload
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__.)
|
||||
`Pull Request 2516`_
|
||||
* Use self.decode_id instead of trans.security.decode_id
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2529`_
|
||||
* Charts revision
|
||||
`Pull Request 2531`_
|
||||
* Add Makefile target for fetching updated bower dependencies.
|
||||
`Pull Request 2534`_
|
||||
* Make conda autoinstall of packages safer:
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__.)
|
||||
`Pull Request 2538`_
|
||||
* Updates to Interactive Environment docs
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__.)
|
||||
`Pull Request 2543`_
|
||||
* bigWig files displayed in IGV
|
||||
(thanks to `@dpryan79 <https://github.com/dpryan79>`__.)
|
||||
`Pull Request 2545`_
|
||||
* Allow users to purge datasets by default
|
||||
`Pull Request 2553`_
|
||||
* Kubernetes runner: improves handling of failed jobs
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__.)
|
||||
`Pull Request 2559`_
|
||||
* Fixes `#2442 <https://github.com/galaxyproject/galaxy/issues/2442>`__
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2572`_
|
||||
* Python3: port 215 files
|
||||
(thanks to `@bxlab <https://github.com/bxlab>`__.)
|
||||
`Pull Request 2574`_
|
||||
* Add python-ldap module to conditional requirements
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__.)
|
||||
`Pull Request 2576`_
|
||||
* Kubernetes runner: authenticate through service account
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__.)
|
||||
`Pull Request 2578`_
|
||||
* Update gsummary.xml
|
||||
(thanks to `@lecorguille <https://github.com/lecorguille>`__.)
|
||||
`Pull Request 2590`_
|
||||
* Add Warning when Conda is installed
|
||||
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
|
||||
`Pull Request 2596`_
|
||||
* Added the neostore (neo4j db) for noe4jdb dataset
|
||||
(thanks to `@zipho <https://github.com/zipho>`__.)
|
||||
`Pull Request 2605`_
|
||||
* Fix smart_str for Python 3. Add doctests
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2608`_
|
||||
* Added Neo4j IE
|
||||
(thanks to `@thobalose <https://github.com/thobalose>`__.)
|
||||
`Pull Request 2610`_
|
||||
* Committing format changes to the user impersonation dropdown.
|
||||
(thanks to `@sszakony <https://github.com/sszakony>`__.)
|
||||
`Pull Request 2612`_
|
||||
* Use pagination and filtering for select2 fields
|
||||
`Pull Request 2615`_
|
||||
* Update workflow share dropdown width
|
||||
(thanks to `@sszakony <https://github.com/sszakony>`__.)
|
||||
`Pull Request 2617`_
|
||||
* Graph visualization: add parsers, change datatypes
|
||||
`Pull Request 2620`_
|
||||
* Fix certain combos of dynamic deeply nested collections in workflows.
|
||||
`Pull Request 2634`_
|
||||
* add tar to datatypes_conf.xml
|
||||
(thanks to `@mariabernard <https://github.com/mariabernard>`__.)
|
||||
`Pull Request 2636`_
|
||||
* Optimize get_file_peek()
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2637`_
|
||||
* Move workflow run and history options to top, add loading indicator
|
||||
`Pull Request 2643`_
|
||||
* Enhance workflow run button to indicate workflow loading progress, keep
|
||||
header fixed
|
||||
`Pull Request 2647`_
|
||||
* Allow uploading strict BED datatypes.
|
||||
`Pull Request 2648`_
|
||||
* Reduce server sided refresh requests to changes in data associated input
|
||||
fields
|
||||
`Pull Request 2652`_
|
||||
* Add import order linting using tox and flake8-import-order.
|
||||
`Pull Request 2661`_
|
||||
* Add hg38 to main for ucsc_build_sites.txt.sample
|
||||
`Pull Request 2670`_
|
||||
* Extend the list of files tested with flake8-import-order to all files
|
||||
already passing
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2682`_
|
||||
* List resolver toolshed packages
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
|
||||
`Pull Request 2750`_
|
||||
|
||||
|
||||
.. small_enhancement
|
||||
|
||||
* remove buildbot remnants
|
||||
`Pull Request 2125`_
|
||||
* try pushing again when we get unexpected exception...
|
||||
`Pull Request 2130`_
|
||||
* Refactor checking tool files toward reuse with workflows in planemo.
|
||||
`Pull Request 2183`_
|
||||
* Rename/refactor Utils.validate() to Utils.isEmpty()
|
||||
`Pull Request 2239`_
|
||||
* Cleanup of the install and test framework.
|
||||
`Pull Request 2249`_
|
||||
* cleanup TS and Reports configs
|
||||
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__.)
|
||||
`Pull Request 2267`_
|
||||
* Move specific methods from shed_util_common.py to specific_util.py
|
||||
`Pull Request 2269`_
|
||||
* Revise selection, options and drilldown wrappers, add tests
|
||||
`Pull Request 2305`_
|
||||
* Visualizations: remove graphview
|
||||
`Pull Request 2329`_
|
||||
* Update qunit and sinon
|
||||
`Pull Request 2338`_
|
||||
* Build job success messages within tool form view
|
||||
`Pull Request 2355`_
|
||||
* Cleanup of E203 primarily, and some other misc formatting encountered…
|
||||
`Pull Request 2364`_
|
||||
* isolate the data libraries css to affect only the libraries app
|
||||
`Pull Request 2444`_
|
||||
* Re-add get_updated_changeset_revisions_from_tool_shed() method
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2472`_
|
||||
* Workaround for circular import. Refactor.
|
||||
`Pull Request 2477`_
|
||||
* run_tests.sh: Clarify when/where the report file is created.
|
||||
(thanks to `@NickSto <https://github.com/NickSto>`__.)
|
||||
`Pull Request 2564`_
|
||||
* Reroute consistent workflow endpoint to internal api
|
||||
`Pull Request 2622`_
|
||||
* Add tool test for what happens when output filter throws exception.
|
||||
`Pull Request 2631`_
|
||||
* Ignore .tox directory. Used to be ignored by default w/ flake8 appar…
|
||||
`Pull Request 2650`_
|
||||
* Reorder base templates meta tags
|
||||
`Pull Request 2651`_
|
||||
* Import pyparsing in testing so twill's older version doesn't get loaded.
|
||||
`Pull Request 2656`_
|
||||
* Change default refresh mode for form views
|
||||
`Pull Request 2667`_
|
||||
* Fix unit tests
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2691`_
|
||||
* Create a uWSGI postfork function registry and start the tool conf watcher
|
||||
thread post-fork
|
||||
`Pull Request 2774`_
|
||||
|
||||
|
||||
Fixes
|
||||
-------------------------------
|
||||
|
||||
.. major_bug
|
||||
|
||||
* Do not encode dict items that start with 'metadata_' in return value of
|
||||
api/tools/create.
|
||||
`Pull Request 2459`_
|
||||
|
||||
.. bug
|
||||
|
||||
* fix blocking issue check
|
||||
`Pull Request 2113`_
|
||||
* Correctly check set_environment declarations when updating repository.
|
||||
`Pull Request 2116`_
|
||||
* Hide hidden data parameters in workflow editor
|
||||
`Pull Request 2120`_
|
||||
* Place $headers before integrity_check
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
|
||||
`Pull Request 2146`_
|
||||
* Fix bug when determining locale
|
||||
(thanks to `@xiaojay <https://github.com/xiaojay>`__.)
|
||||
`Pull Request 2213`_
|
||||
* Add pyparsing dependency of svgwrite. Unpin mercurial.
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2223`_
|
||||
* Fixes `#2230 <https://github.com/galaxyproject/galaxy/issues/2230>`__
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2231`_
|
||||
* Multi-data collection reductions in repeat blocks are broken.
|
||||
`Pull Request 2233`_
|
||||
* Encode collection reduce in serializable fashion
|
||||
`Pull Request 2241`_
|
||||
* Cast everything to a string
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2252`_
|
||||
* Use standard model.orm.now for toolshed's password reset token dateti…
|
||||
`Pull Request 2261`_
|
||||
* fixed ui bugs in tours
|
||||
(thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__.)
|
||||
`Pull Request 2262`_
|
||||
* Preliminary fix for displaying raw text/html
|
||||
`Pull Request 2263`_
|
||||
* Correctly use defaults specified in galaxy.ini.sample for statsd.
|
||||
`Pull Request 2268`_
|
||||
* Fix encoding issues in test/unit/test_objectstore.py.
|
||||
`Pull Request 2280`_
|
||||
* Workflow sharing slug edit fix.
|
||||
`Pull Request 2293`_
|
||||
* Always remove the working directory after creating the capsule archive.
|
||||
`Pull Request 2294`_
|
||||
* update check for Conda env.
|
||||
(thanks to `@matthdsm <https://github.com/matthdsm>`__.)
|
||||
`Pull Request 2295`_
|
||||
* Make grunt watch (for scripts) work again, settings were being overwr…
|
||||
`Pull Request 2296`_
|
||||
* Monkeypatch Whoosh to use mkdtemp rather than a fixed temporary directory
|
||||
`Pull Request 2310`_
|
||||
* Build: remove redundant webpack step in makefile
|
||||
`Pull Request 2327`_
|
||||
* Unicodify has different semantics to str, causing bug reporter bug
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2336`_
|
||||
* Wrap statsd timing middleware more closely around the core applicatio…
|
||||
`Pull Request 2342`_
|
||||
* UI & API: fix display of inaccessible datasets
|
||||
`Pull Request 2351`_
|
||||
* Update README to remove 2.6
|
||||
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
|
||||
`Pull Request 2367`_
|
||||
* Revise asserts triggering false exceptions for dynamic parameters
|
||||
`Pull Request 2374`_
|
||||
* Fix the installed conda version to 3.19.3.
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__.)
|
||||
`Pull Request 2394`_
|
||||
* Check variable's presence before calling str methods
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2408`_
|
||||
* UI, history: correctly handle index API defaults
|
||||
`Pull Request 2413`_
|
||||
* Fix to 4a61a4c: add hids for dataset inputs
|
||||
`Pull Request 2415`_
|
||||
* wrap bare str raises with generic Exception()
|
||||
`Pull Request 2421`_
|
||||
* Fix raven.js import order in galaxy.panels.mako
|
||||
`Pull Request 2445`_
|
||||
* Fix usage of super() in the mothur datatypes.
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__.)
|
||||
`Pull Request 2457`_
|
||||
* Make pykube an optional dependency since we don't have wheels for it.
|
||||
`Pull Request 2468`_
|
||||
* fix markup for button links on sharing template
|
||||
`Pull Request 2481`_
|
||||
* fix image generation for workflows with missing tools
|
||||
`Pull Request 2488`_
|
||||
* mothur datatypes: don't generate error for pairwise distance matrices
|
||||
(thanks to `@shiltemann <https://github.com/shiltemann>`__.)
|
||||
`Pull Request 2489`_
|
||||
* Kubernetes runner: fixes result files from work directory not being
|
||||
recovered issue
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__.)
|
||||
`Pull Request 2498`_
|
||||
* Toolbox filter fixes
|
||||
`Pull Request 2499`_
|
||||
* This is an extra hammer swing at `#1531
|
||||
<https://github.com/galaxyproject/galaxy/issues/1531>`__ / `#1542
|
||||
<https://github.com/galaxyproject/galaxy/issues/1542>`__
|
||||
`Pull Request 2505`_
|
||||
* Copy PJAs when importing a workflow.
|
||||
`Pull Request 2508`_
|
||||
* Fix two errors in sff_extract.py detected by flake8
|
||||
`Pull Request 2509`_
|
||||
* Fix HTML errors on 2 templates
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
|
||||
`Pull Request 2524`_
|
||||
* Fix tabular display chunking
|
||||
`Pull Request 2527`_
|
||||
* Writes Kubernetes logs files in UTF-8
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__.)
|
||||
`Pull Request 2528`_
|
||||
* Fix dataset matcher when no tool available.
|
||||
(thanks to `@zipho <https://github.com/zipho>`__.)
|
||||
`Pull Request 2540`_
|
||||
* Initialize objectstore for fix_set_dataset_sizes script
|
||||
`Pull Request 2544`_
|
||||
* Fix old bug in non-allowed_images.yml GIEs
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2548`_
|
||||
* More defensive GIE Proxying
|
||||
(thanks to `@erasche <https://github.com/erasche>`__.)
|
||||
`Pull Request 2552`_
|
||||
* Fixes for showing min/max labels in Trackster.
|
||||
`Pull Request 2555`_
|
||||
* Fix tag_autocomplete issue in workflow editor.
|
||||
`Pull Request 2569`_
|
||||
* Fix element_identifier unavailable with data_collection input param
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__.)
|
||||
`Pull Request 2570`_
|
||||
* Ignore W503 (line break before binary operator) as PEP 8 has reversed its
|
||||
position on this.
|
||||
`Pull Request 2594`_
|
||||
* Fix hex vs float parsing in request body
|
||||
`Pull Request 2597`_
|
||||
* Kubernetes runner corrects working directory not passed to container
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__.)
|
||||
`Pull Request 2616`_
|
||||
* Fixes for workflow extraction of mapping collection jobs.
|
||||
`Pull Request 2625`_
|
||||
* Workflow SVG generation fix
|
||||
`Pull Request 2628`_
|
||||
* Smart string handling on the wsgi response -- this fixes uwsgi blanki…
|
||||
`Pull Request 2630`_
|
||||
* Properly initialize datasets when workflow is loaded for execution
|
||||
`Pull Request 2632`_
|
||||
* typo in summary statistics tool
|
||||
(thanks to `@nturaga <https://github.com/nturaga>`__.)
|
||||
`Pull Request 2639`_
|
||||
* Set allow_duplicate_entries="False" for built-in Tool Data Tables.
|
||||
`Pull Request 2644`_
|
||||
* Ensure Galaxy's python binary is used for metadata generation.
|
||||
`Pull Request 2660`_
|
||||
* Fix an error with getting the size of an object from Azure. Attempte…
|
||||
`Pull Request 2678`_
|
||||
* Limit creation of multitudes of default, empty histories.
|
||||
`Pull Request 2684`_
|
||||
* Fix the sanitization of None values in utils. This had previously no…
|
||||
`Pull Request 2693`_
|
||||
* Fix: Remove the old HubAssembly class
|
||||
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
|
||||
`Pull Request 2701`_
|
||||
* Fix metadata collection on workdir outputs for Pulsar.
|
||||
`Pull Request 2721`_
|
||||
* Allow link buttons to trigger regular click events
|
||||
`Pull Request 2743`_
|
||||
* Fix unused href parameter when adding scratchbook frames
|
||||
`Pull Request 2744`_
|
||||
* Update common_startup.sh to require python2.7 in .venv
|
||||
(thanks to `@BenjaminHCCarr <https://github.com/BenjaminHCCarr>`__.)
|
||||
`Pull Request 2756`_
|
||||
* separate styles of new and old libraries fixing various ui bugs
|
||||
`Pull Request 2780`_
|
||||
* Make conda install and resolver status more robust
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
|
||||
`Pull Request 2789`_
|
||||
* Do not instantiate the raven (sentry) client or tool conf watchdog threads
|
||||
until uWSGI postfork
|
||||
`Pull Request 2792`_
|
||||
* API, history contents: allow 'source' in payload
|
||||
`Pull Request 2809`_
|
||||
|
||||
.. github_links
|
||||
.. _Pull Request 2038: https://github.com/galaxyproject/galaxy/pull/2038
|
||||
.. _Pull Request 2077: https://github.com/galaxyproject/galaxy/pull/2077
|
||||
.. _Pull Request 2079: https://github.com/galaxyproject/galaxy/pull/2079
|
||||
.. _Pull Request 2110: https://github.com/galaxyproject/galaxy/pull/2110
|
||||
.. _Pull Request 2113: https://github.com/galaxyproject/galaxy/pull/2113
|
||||
.. _Pull Request 2116: https://github.com/galaxyproject/galaxy/pull/2116
|
||||
.. _Pull Request 2117: https://github.com/galaxyproject/galaxy/pull/2117
|
||||
.. _Pull Request 2119: https://github.com/galaxyproject/galaxy/pull/2119
|
||||
.. _Pull Request 2120: https://github.com/galaxyproject/galaxy/pull/2120
|
||||
.. _Pull Request 2121: https://github.com/galaxyproject/galaxy/pull/2121
|
||||
.. _Pull Request 2124: https://github.com/galaxyproject/galaxy/pull/2124
|
||||
.. _Pull Request 2125: https://github.com/galaxyproject/galaxy/pull/2125
|
||||
.. _Pull Request 2130: https://github.com/galaxyproject/galaxy/pull/2130
|
||||
.. _Pull Request 2142: https://github.com/galaxyproject/galaxy/pull/2142
|
||||
.. _Pull Request 2143: https://github.com/galaxyproject/galaxy/pull/2143
|
||||
.. _Pull Request 2144: https://github.com/galaxyproject/galaxy/pull/2144
|
||||
.. _Pull Request 2145: https://github.com/galaxyproject/galaxy/pull/2145
|
||||
.. _Pull Request 2146: https://github.com/galaxyproject/galaxy/pull/2146
|
||||
.. _Pull Request 2157: https://github.com/galaxyproject/galaxy/pull/2157
|
||||
.. _Pull Request 2158: https://github.com/galaxyproject/galaxy/pull/2158
|
||||
.. _Pull Request 2165: https://github.com/galaxyproject/galaxy/pull/2165
|
||||
.. _Pull Request 2168: https://github.com/galaxyproject/galaxy/pull/2168
|
||||
.. _Pull Request 2171: https://github.com/galaxyproject/galaxy/pull/2171
|
||||
.. _Pull Request 2173: https://github.com/galaxyproject/galaxy/pull/2173
|
||||
.. _Pull Request 2183: https://github.com/galaxyproject/galaxy/pull/2183
|
||||
.. _Pull Request 2213: https://github.com/galaxyproject/galaxy/pull/2213
|
||||
.. _Pull Request 2215: https://github.com/galaxyproject/galaxy/pull/2215
|
||||
.. _Pull Request 2223: https://github.com/galaxyproject/galaxy/pull/2223
|
||||
.. _Pull Request 2231: https://github.com/galaxyproject/galaxy/pull/2231
|
||||
.. _Pull Request 2233: https://github.com/galaxyproject/galaxy/pull/2233
|
||||
.. _Pull Request 2239: https://github.com/galaxyproject/galaxy/pull/2239
|
||||
.. _Pull Request 2241: https://github.com/galaxyproject/galaxy/pull/2241
|
||||
.. _Pull Request 2243: https://github.com/galaxyproject/galaxy/pull/2243
|
||||
.. _Pull Request 2248: https://github.com/galaxyproject/galaxy/pull/2248
|
||||
.. _Pull Request 2249: https://github.com/galaxyproject/galaxy/pull/2249
|
||||
.. _Pull Request 2252: https://github.com/galaxyproject/galaxy/pull/2252
|
||||
.. _Pull Request 2253: https://github.com/galaxyproject/galaxy/pull/2253
|
||||
.. _Pull Request 2254: https://github.com/galaxyproject/galaxy/pull/2254
|
||||
.. _Pull Request 2256: https://github.com/galaxyproject/galaxy/pull/2256
|
||||
.. _Pull Request 2257: https://github.com/galaxyproject/galaxy/pull/2257
|
||||
.. _Pull Request 2258: https://github.com/galaxyproject/galaxy/pull/2258
|
||||
.. _Pull Request 2261: https://github.com/galaxyproject/galaxy/pull/2261
|
||||
.. _Pull Request 2262: https://github.com/galaxyproject/galaxy/pull/2262
|
||||
.. _Pull Request 2263: https://github.com/galaxyproject/galaxy/pull/2263
|
||||
.. _Pull Request 2267: https://github.com/galaxyproject/galaxy/pull/2267
|
||||
.. _Pull Request 2268: https://github.com/galaxyproject/galaxy/pull/2268
|
||||
.. _Pull Request 2269: https://github.com/galaxyproject/galaxy/pull/2269
|
||||
.. _Pull Request 2271: https://github.com/galaxyproject/galaxy/pull/2271
|
||||
.. _Pull Request 2273: https://github.com/galaxyproject/galaxy/pull/2273
|
||||
.. _Pull Request 2274: https://github.com/galaxyproject/galaxy/pull/2274
|
||||
.. _Pull Request 2276: https://github.com/galaxyproject/galaxy/pull/2276
|
||||
.. _Pull Request 2278: https://github.com/galaxyproject/galaxy/pull/2278
|
||||
.. _Pull Request 2279: https://github.com/galaxyproject/galaxy/pull/2279
|
||||
.. _Pull Request 2280: https://github.com/galaxyproject/galaxy/pull/2280
|
||||
.. _Pull Request 2286: https://github.com/galaxyproject/galaxy/pull/2286
|
||||
.. _Pull Request 2289: https://github.com/galaxyproject/galaxy/pull/2289
|
||||
.. _Pull Request 2292: https://github.com/galaxyproject/galaxy/pull/2292
|
||||
.. _Pull Request 2293: https://github.com/galaxyproject/galaxy/pull/2293
|
||||
.. _Pull Request 2294: https://github.com/galaxyproject/galaxy/pull/2294
|
||||
.. _Pull Request 2295: https://github.com/galaxyproject/galaxy/pull/2295
|
||||
.. _Pull Request 2296: https://github.com/galaxyproject/galaxy/pull/2296
|
||||
.. _Pull Request 2302: https://github.com/galaxyproject/galaxy/pull/2302
|
||||
.. _Pull Request 2305: https://github.com/galaxyproject/galaxy/pull/2305
|
||||
.. _Pull Request 2307: https://github.com/galaxyproject/galaxy/pull/2307
|
||||
.. _Pull Request 2308: https://github.com/galaxyproject/galaxy/pull/2308
|
||||
.. _Pull Request 2310: https://github.com/galaxyproject/galaxy/pull/2310
|
||||
.. _Pull Request 2314: https://github.com/galaxyproject/galaxy/pull/2314
|
||||
.. _Pull Request 2326: https://github.com/galaxyproject/galaxy/pull/2326
|
||||
.. _Pull Request 2327: https://github.com/galaxyproject/galaxy/pull/2327
|
||||
.. _Pull Request 2328: https://github.com/galaxyproject/galaxy/pull/2328
|
||||
.. _Pull Request 2329: https://github.com/galaxyproject/galaxy/pull/2329
|
||||
.. _Pull Request 2330: https://github.com/galaxyproject/galaxy/pull/2330
|
||||
.. _Pull Request 2335: https://github.com/galaxyproject/galaxy/pull/2335
|
||||
.. _Pull Request 2336: https://github.com/galaxyproject/galaxy/pull/2336
|
||||
.. _Pull Request 2338: https://github.com/galaxyproject/galaxy/pull/2338
|
||||
.. _Pull Request 2340: https://github.com/galaxyproject/galaxy/pull/2340
|
||||
.. _Pull Request 2342: https://github.com/galaxyproject/galaxy/pull/2342
|
||||
.. _Pull Request 2348: https://github.com/galaxyproject/galaxy/pull/2348
|
||||
.. _Pull Request 2351: https://github.com/galaxyproject/galaxy/pull/2351
|
||||
.. _Pull Request 2354: https://github.com/galaxyproject/galaxy/pull/2354
|
||||
.. _Pull Request 2355: https://github.com/galaxyproject/galaxy/pull/2355
|
||||
.. _Pull Request 2358: https://github.com/galaxyproject/galaxy/pull/2358
|
||||
.. _Pull Request 2360: https://github.com/galaxyproject/galaxy/pull/2360
|
||||
.. _Pull Request 2361: https://github.com/galaxyproject/galaxy/pull/2361
|
||||
.. _Pull Request 2363: https://github.com/galaxyproject/galaxy/pull/2363
|
||||
.. _Pull Request 2364: https://github.com/galaxyproject/galaxy/pull/2364
|
||||
.. _Pull Request 2366: https://github.com/galaxyproject/galaxy/pull/2366
|
||||
.. _Pull Request 2367: https://github.com/galaxyproject/galaxy/pull/2367
|
||||
.. _Pull Request 2368: https://github.com/galaxyproject/galaxy/pull/2368
|
||||
.. _Pull Request 2370: https://github.com/galaxyproject/galaxy/pull/2370
|
||||
.. _Pull Request 2372: https://github.com/galaxyproject/galaxy/pull/2372
|
||||
.. _Pull Request 2374: https://github.com/galaxyproject/galaxy/pull/2374
|
||||
.. _Pull Request 2378: https://github.com/galaxyproject/galaxy/pull/2378
|
||||
.. _Pull Request 2379: https://github.com/galaxyproject/galaxy/pull/2379
|
||||
.. _Pull Request 2380: https://github.com/galaxyproject/galaxy/pull/2380
|
||||
.. _Pull Request 2381: https://github.com/galaxyproject/galaxy/pull/2381
|
||||
.. _Pull Request 2383: https://github.com/galaxyproject/galaxy/pull/2383
|
||||
.. _Pull Request 2386: https://github.com/galaxyproject/galaxy/pull/2386
|
||||
.. _Pull Request 2387: https://github.com/galaxyproject/galaxy/pull/2387
|
||||
.. _Pull Request 2388: https://github.com/galaxyproject/galaxy/pull/2388
|
||||
.. _Pull Request 2390: https://github.com/galaxyproject/galaxy/pull/2390
|
||||
.. _Pull Request 2391: https://github.com/galaxyproject/galaxy/pull/2391
|
||||
.. _Pull Request 2392: https://github.com/galaxyproject/galaxy/pull/2392
|
||||
.. _Pull Request 2394: https://github.com/galaxyproject/galaxy/pull/2394
|
||||
.. _Pull Request 2395: https://github.com/galaxyproject/galaxy/pull/2395
|
||||
.. _Pull Request 2396: https://github.com/galaxyproject/galaxy/pull/2396
|
||||
.. _Pull Request 2397: https://github.com/galaxyproject/galaxy/pull/2397
|
||||
.. _Pull Request 2403: https://github.com/galaxyproject/galaxy/pull/2403
|
||||
.. _Pull Request 2408: https://github.com/galaxyproject/galaxy/pull/2408
|
||||
.. _Pull Request 2409: https://github.com/galaxyproject/galaxy/pull/2409
|
||||
.. _Pull Request 2410: https://github.com/galaxyproject/galaxy/pull/2410
|
||||
.. _Pull Request 2411: https://github.com/galaxyproject/galaxy/pull/2411
|
||||
.. _Pull Request 2412: https://github.com/galaxyproject/galaxy/pull/2412
|
||||
.. _Pull Request 2413: https://github.com/galaxyproject/galaxy/pull/2413
|
||||
.. _Pull Request 2414: https://github.com/galaxyproject/galaxy/pull/2414
|
||||
.. _Pull Request 2415: https://github.com/galaxyproject/galaxy/pull/2415
|
||||
.. _Pull Request 2416: https://github.com/galaxyproject/galaxy/pull/2416
|
||||
.. _Pull Request 2418: https://github.com/galaxyproject/galaxy/pull/2418
|
||||
.. _Pull Request 2420: https://github.com/galaxyproject/galaxy/pull/2420
|
||||
.. _Pull Request 2421: https://github.com/galaxyproject/galaxy/pull/2421
|
||||
.. _Pull Request 2427: https://github.com/galaxyproject/galaxy/pull/2427
|
||||
.. _Pull Request 2428: https://github.com/galaxyproject/galaxy/pull/2428
|
||||
.. _Pull Request 2429: https://github.com/galaxyproject/galaxy/pull/2429
|
||||
.. _Pull Request 2434: https://github.com/galaxyproject/galaxy/pull/2434
|
||||
.. _Pull Request 2436: https://github.com/galaxyproject/galaxy/pull/2436
|
||||
.. _Pull Request 2438: https://github.com/galaxyproject/galaxy/pull/2438
|
||||
.. _Pull Request 2440: https://github.com/galaxyproject/galaxy/pull/2440
|
||||
.. _Pull Request 2444: https://github.com/galaxyproject/galaxy/pull/2444
|
||||
.. _Pull Request 2445: https://github.com/galaxyproject/galaxy/pull/2445
|
||||
.. _Pull Request 2452: https://github.com/galaxyproject/galaxy/pull/2452
|
||||
.. _Pull Request 2453: https://github.com/galaxyproject/galaxy/pull/2453
|
||||
.. _Pull Request 2455: https://github.com/galaxyproject/galaxy/pull/2455
|
||||
.. _Pull Request 2457: https://github.com/galaxyproject/galaxy/pull/2457
|
||||
.. _Pull Request 2459: https://github.com/galaxyproject/galaxy/pull/2459
|
||||
.. _Pull Request 2464: https://github.com/galaxyproject/galaxy/pull/2464
|
||||
.. _Pull Request 2468: https://github.com/galaxyproject/galaxy/pull/2468
|
||||
.. _Pull Request 2469: https://github.com/galaxyproject/galaxy/pull/2469
|
||||
.. _Pull Request 2472: https://github.com/galaxyproject/galaxy/pull/2472
|
||||
.. _Pull Request 2476: https://github.com/galaxyproject/galaxy/pull/2476
|
||||
.. _Pull Request 2477: https://github.com/galaxyproject/galaxy/pull/2477
|
||||
.. _Pull Request 2480: https://github.com/galaxyproject/galaxy/pull/2480
|
||||
.. _Pull Request 2481: https://github.com/galaxyproject/galaxy/pull/2481
|
||||
.. _Pull Request 2486: https://github.com/galaxyproject/galaxy/pull/2486
|
||||
.. _Pull Request 2488: https://github.com/galaxyproject/galaxy/pull/2488
|
||||
.. _Pull Request 2489: https://github.com/galaxyproject/galaxy/pull/2489
|
||||
.. _Pull Request 2494: https://github.com/galaxyproject/galaxy/pull/2494
|
||||
.. _Pull Request 2498: https://github.com/galaxyproject/galaxy/pull/2498
|
||||
.. _Pull Request 2499: https://github.com/galaxyproject/galaxy/pull/2499
|
||||
.. _Pull Request 2505: https://github.com/galaxyproject/galaxy/pull/2505
|
||||
.. _Pull Request 2508: https://github.com/galaxyproject/galaxy/pull/2508
|
||||
.. _Pull Request 2509: https://github.com/galaxyproject/galaxy/pull/2509
|
||||
.. _Pull Request 2515: https://github.com/galaxyproject/galaxy/pull/2515
|
||||
.. _Pull Request 2516: https://github.com/galaxyproject/galaxy/pull/2516
|
||||
.. _Pull Request 2524: https://github.com/galaxyproject/galaxy/pull/2524
|
||||
.. _Pull Request 2527: https://github.com/galaxyproject/galaxy/pull/2527
|
||||
.. _Pull Request 2528: https://github.com/galaxyproject/galaxy/pull/2528
|
||||
.. _Pull Request 2529: https://github.com/galaxyproject/galaxy/pull/2529
|
||||
.. _Pull Request 2531: https://github.com/galaxyproject/galaxy/pull/2531
|
||||
.. _Pull Request 2534: https://github.com/galaxyproject/galaxy/pull/2534
|
||||
.. _Pull Request 2538: https://github.com/galaxyproject/galaxy/pull/2538
|
||||
.. _Pull Request 2540: https://github.com/galaxyproject/galaxy/pull/2540
|
||||
.. _Pull Request 2543: https://github.com/galaxyproject/galaxy/pull/2543
|
||||
.. _Pull Request 2544: https://github.com/galaxyproject/galaxy/pull/2544
|
||||
.. _Pull Request 2545: https://github.com/galaxyproject/galaxy/pull/2545
|
||||
.. _Pull Request 2548: https://github.com/galaxyproject/galaxy/pull/2548
|
||||
.. _Pull Request 2552: https://github.com/galaxyproject/galaxy/pull/2552
|
||||
.. _Pull Request 2553: https://github.com/galaxyproject/galaxy/pull/2553
|
||||
.. _Pull Request 2554: https://github.com/galaxyproject/galaxy/pull/2554
|
||||
.. _Pull Request 2555: https://github.com/galaxyproject/galaxy/pull/2555
|
||||
.. _Pull Request 2559: https://github.com/galaxyproject/galaxy/pull/2559
|
||||
.. _Pull Request 2564: https://github.com/galaxyproject/galaxy/pull/2564
|
||||
.. _Pull Request 2569: https://github.com/galaxyproject/galaxy/pull/2569
|
||||
.. _Pull Request 2570: https://github.com/galaxyproject/galaxy/pull/2570
|
||||
.. _Pull Request 2572: https://github.com/galaxyproject/galaxy/pull/2572
|
||||
.. _Pull Request 2574: https://github.com/galaxyproject/galaxy/pull/2574
|
||||
.. _Pull Request 2576: https://github.com/galaxyproject/galaxy/pull/2576
|
||||
.. _Pull Request 2578: https://github.com/galaxyproject/galaxy/pull/2578
|
||||
.. _Pull Request 2579: https://github.com/galaxyproject/galaxy/pull/2579
|
||||
.. _Pull Request 2590: https://github.com/galaxyproject/galaxy/pull/2590
|
||||
.. _Pull Request 2594: https://github.com/galaxyproject/galaxy/pull/2594
|
||||
.. _Pull Request 2595: https://github.com/galaxyproject/galaxy/pull/2595
|
||||
.. _Pull Request 2596: https://github.com/galaxyproject/galaxy/pull/2596
|
||||
.. _Pull Request 2597: https://github.com/galaxyproject/galaxy/pull/2597
|
||||
.. _Pull Request 2599: https://github.com/galaxyproject/galaxy/pull/2599
|
||||
.. _Pull Request 2605: https://github.com/galaxyproject/galaxy/pull/2605
|
||||
.. _Pull Request 2608: https://github.com/galaxyproject/galaxy/pull/2608
|
||||
.. _Pull Request 2610: https://github.com/galaxyproject/galaxy/pull/2610
|
||||
.. _Pull Request 2612: https://github.com/galaxyproject/galaxy/pull/2612
|
||||
.. _Pull Request 2613: https://github.com/galaxyproject/galaxy/pull/2613
|
||||
.. _Pull Request 2615: https://github.com/galaxyproject/galaxy/pull/2615
|
||||
.. _Pull Request 2616: https://github.com/galaxyproject/galaxy/pull/2616
|
||||
.. _Pull Request 2617: https://github.com/galaxyproject/galaxy/pull/2617
|
||||
.. _Pull Request 2620: https://github.com/galaxyproject/galaxy/pull/2620
|
||||
.. _Pull Request 2621: https://github.com/galaxyproject/galaxy/pull/2621
|
||||
.. _Pull Request 2622: https://github.com/galaxyproject/galaxy/pull/2622
|
||||
.. _Pull Request 2625: https://github.com/galaxyproject/galaxy/pull/2625
|
||||
.. _Pull Request 2628: https://github.com/galaxyproject/galaxy/pull/2628
|
||||
.. _Pull Request 2630: https://github.com/galaxyproject/galaxy/pull/2630
|
||||
.. _Pull Request 2631: https://github.com/galaxyproject/galaxy/pull/2631
|
||||
.. _Pull Request 2632: https://github.com/galaxyproject/galaxy/pull/2632
|
||||
.. _Pull Request 2634: https://github.com/galaxyproject/galaxy/pull/2634
|
||||
.. _Pull Request 2636: https://github.com/galaxyproject/galaxy/pull/2636
|
||||
.. _Pull Request 2637: https://github.com/galaxyproject/galaxy/pull/2637
|
||||
.. _Pull Request 2639: https://github.com/galaxyproject/galaxy/pull/2639
|
||||
.. _Pull Request 2643: https://github.com/galaxyproject/galaxy/pull/2643
|
||||
.. _Pull Request 2644: https://github.com/galaxyproject/galaxy/pull/2644
|
||||
.. _Pull Request 2646: https://github.com/galaxyproject/galaxy/pull/2646
|
||||
.. _Pull Request 2647: https://github.com/galaxyproject/galaxy/pull/2647
|
||||
.. _Pull Request 2648: https://github.com/galaxyproject/galaxy/pull/2648
|
||||
.. _Pull Request 2650: https://github.com/galaxyproject/galaxy/pull/2650
|
||||
.. _Pull Request 2651: https://github.com/galaxyproject/galaxy/pull/2651
|
||||
.. _Pull Request 2652: https://github.com/galaxyproject/galaxy/pull/2652
|
||||
.. _Pull Request 2656: https://github.com/galaxyproject/galaxy/pull/2656
|
||||
.. _Pull Request 2660: https://github.com/galaxyproject/galaxy/pull/2660
|
||||
.. _Pull Request 2661: https://github.com/galaxyproject/galaxy/pull/2661
|
||||
.. _Pull Request 2664: https://github.com/galaxyproject/galaxy/pull/2664
|
||||
.. _Pull Request 2667: https://github.com/galaxyproject/galaxy/pull/2667
|
||||
.. _Pull Request 2670: https://github.com/galaxyproject/galaxy/pull/2670
|
||||
.. _Pull Request 2678: https://github.com/galaxyproject/galaxy/pull/2678
|
||||
.. _Pull Request 2680: https://github.com/galaxyproject/galaxy/pull/2680
|
||||
.. _Pull Request 2681: https://github.com/galaxyproject/galaxy/pull/2681
|
||||
.. _Pull Request 2682: https://github.com/galaxyproject/galaxy/pull/2682
|
||||
.. _Pull Request 2684: https://github.com/galaxyproject/galaxy/pull/2684
|
||||
.. _Pull Request 2685: https://github.com/galaxyproject/galaxy/pull/2685
|
||||
.. _Pull Request 2691: https://github.com/galaxyproject/galaxy/pull/2691
|
||||
.. _Pull Request 2693: https://github.com/galaxyproject/galaxy/pull/2693
|
||||
.. _Pull Request 2701: https://github.com/galaxyproject/galaxy/pull/2701
|
||||
.. _Pull Request 2721: https://github.com/galaxyproject/galaxy/pull/2721
|
||||
.. _Pull Request 2723: https://github.com/galaxyproject/galaxy/pull/2723
|
||||
.. _Pull Request 2737: https://github.com/galaxyproject/galaxy/pull/2737
|
||||
.. _Pull Request 2743: https://github.com/galaxyproject/galaxy/pull/2743
|
||||
.. _Pull Request 2744: https://github.com/galaxyproject/galaxy/pull/2744
|
||||
.. _Pull Request 2749: https://github.com/galaxyproject/galaxy/pull/2749
|
||||
.. _Pull Request 2750: https://github.com/galaxyproject/galaxy/pull/2750
|
||||
.. _Pull Request 2756: https://github.com/galaxyproject/galaxy/pull/2756
|
||||
.. _Pull Request 2759: https://github.com/galaxyproject/galaxy/pull/2759
|
||||
.. _Pull Request 2773: https://github.com/galaxyproject/galaxy/pull/2773
|
||||
.. _Pull Request 2774: https://github.com/galaxyproject/galaxy/pull/2774
|
||||
.. _Pull Request 2780: https://github.com/galaxyproject/galaxy/pull/2780
|
||||
.. _Pull Request 2789: https://github.com/galaxyproject/galaxy/pull/2789
|
||||
.. _Pull Request 2792: https://github.com/galaxyproject/galaxy/pull/2792
|
||||
.. _Pull Request 2809: https://github.com/galaxyproject/galaxy/pull/2809
|
||||
.. _Pull Request 2810: https://github.com/galaxyproject/galaxy/pull/2810
|
||||
|
||||
@@ -3,8 +3,53 @@
|
||||
July 2016 Galaxy Release (v 16.07)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Schedule
|
||||
Highlights
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2016-07-04
|
||||
* Planned Release Date: 2016-07-25
|
||||
|
||||
**Shift of Galaxy tool dependencies to Conda**
|
||||
Galaxy admins obtained the ability to install Galaxy tool's
|
||||
dependencies using the Conda package manager. Also starting
|
||||
with this release Galaxy will automatically install
|
||||
Conda at startup.
|
||||
See `PR #2554 <https://github.com/galaxyproject/galaxy/pull/2554>`__
|
||||
and `PR #2759 <https://github.com/galaxyproject/galaxy/pull/2759>`__
|
||||
|
||||
**Feature2**
|
||||
Feature description.
|
||||
|
||||
**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.
|
||||
See `PR #2515 <https://github.com/galaxyproject/galaxy/pull/2515>`__
|
||||
|
||||
`Github <https://github.com/galaxyproject/galaxy>`__
|
||||
===========================================================
|
||||
|
||||
New installs
|
||||
.. code-block:: shell
|
||||
|
||||
% git clone -b release_16.07 https://github.com/galaxyproject/galaxy.git
|
||||
|
||||
Optionally update to latest stable release
|
||||
.. code-block:: shell
|
||||
|
||||
% git checkout master && pull --ff-only origin master
|
||||
|
||||
See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
|
||||
|
||||
Deprecation Notices
|
||||
===========================================================
|
||||
|
||||
The following URLs will be removed and should be considered deprecated:
|
||||
* ``<galaxy>\history\as_xml``
|
||||
* ``<galaxy>\history\list_as_xml``
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
.. include:: 16.07.rst
|
||||
:start-after: announce_start
|
||||
|
||||
.. include:: _thanks.rst
|
||||
|
||||
@@ -0,0 +1,10 @@
|
||||
|
||||
===========================================================
|
||||
October 2016 Galaxy Release (v 16.10)
|
||||
===========================================================
|
||||
|
||||
|
||||
Schedule
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2016-10-03
|
||||
* Planned Release Date: 2016-10-24
|
||||
Reference in New Issue
Block a user