diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst new file mode 100644 index 000000000000..da30a7417c6e --- /dev/null +++ b/doc/source/releases/17.09.rst @@ -0,0 +1,1019 @@ + +.. to_doc + +17.09 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + + +.. feature + +* Galaxy Workflow support for GenomeSpace + (thanks to `@nuwang `__ and + `@gvlproject `__). + `Pull Request 1814`_ +* Support tags (including new "name" tags) in data libraries. + (thanks to `@bwlang `__). + `Pull Request 4262`_ +* HiCBrowser as Galaxy IE + (thanks to `@bgruening `__). + `Pull Request 3330`_ +* Synnefo/Pithos+ object store backend + (thanks to `@saxtouri `__). + `Pull Request 3611`_ +* Add job runner for `Chronos `__ + (thanks to `@theosotr `__). + `Pull Request 3946`_, `Pull Request 4120`_ +* Many improvements to the shell job runner (including a new Paramiko based + runner with retry support) + (thanks to `@mvdbeek `__). + `Pull Request 4358`_, `Pull Request 4599`_, `Pull Request 4343`_ +* Add entry for ``empty_extra_files_path`` validator + (thanks to `@gregvonkuster `__). + `Pull Request 3994`_ +* Extend async data sources to support dataset collections + (thanks to `@fabio-cumbo `__). + `Pull Request 4198`_ +* Add a repository uninstall endpoint to the tool dependency API + (thanks to `@mvdbeek `__). + `Pull Request 4248`_ +* Display preview feature for Bam datatype + (thanks to `@ashvark `__). + `Pull Request 4279`_ +* Add Unipept taxonomy viewer plugin + (thanks to `@caleb-easterly `__). + `Pull Request 4310`_ +* Created alphabetic and numerical sort tool for collection operations + (thanks to `@glormph `__). + `Pull Request 4329`_ +* Prevent loading tools that require a newer galaxy + (thanks to `@mvdbeek `__). + `Pull Request 4382`_ +* Add explicit support for gzipped VCF files + (thanks to `@ffinfo `__). + `Pull Request 4254`_ +* Add ptkscmp datatype + (thanks to `@gregvonkuster `__). + `Pull Request 4259`_ +* Add imzML datatype + (thanks to `@bgruening `__). + `Pull Request 4370`_ +* Add deepTools datatypes to Galaxy + (thanks to `@bgruening `__). + `Pull Request 4392`_ +* Add support for the MEME psp format + (thanks to `@gregvonkuster `__). + `Pull Request 4430`_ +* Add biom2 datatype + (thanks to `@shiltemann `__). + `Pull Request 4519`_ +* Add Excel97 Datatype + `Pull Request 4410`_ +* Add mz5 datatype + (thanks to `@bgruening `__). + `Pull Request 4466`_ +* Refactor tool error reporting into plugins and implement a new + plugin for `influxdb `__ + (thanks to `@erasche `__). + `Pull Request 4305`_, `Pull Request 4533`_ +* Implement second toolshed installation UX targetting the API. + `Pull Request 3626`_ +* Tool-Describing-Tours + (thanks to `@anatskiy `__). + `Pull Request 4019`_ + +.. enhancement + +* Revamp configuration and default server for tool shed and Galaxy reports application + (these now use a uwsgi server by default configured with a YAML configuration file). + `Pull Request 3179`_ +* Speed up and optimize the process of identifying public libraries. + `Pull Request 4640`_ +* Numerous data library fixes and improvements - both to the frontend and backend. + `Pull Request 4568`_, `Pull Request 4595`_, + `Pull Request 4594`_, `Pull Request 4579`_, `Pull Request 4560`_ + `Pull Request 4512`_, `Pull Request 4621`_, `Pull Request 4752`_ +* Enhance workflow import API endpoint to allow admins to install repositories corresponding + to a supplied workflow + (thanks to `@manabuishii `__). + `Pull Request 3064`_ +* GFF3 support in filter by attribute + (thanks to `@peterjc `__). + `Pull Request 3076`_ +* Add extension point for user preferences + (thanks to `@bgruening `__). + `Pull Request 3383`_ +* Respect ``expose_user_email`` configuration in data libraries permissions list. + `Pull Request 4611`_ +* Explicitly include PyPI as an ``--extra-index-url`` to pip. + `Pull Request 4674`_ +* Improved Kubernetes support (non-privileged filesystem access, updated k8s Job API target) + (thanks to `@phnmnl `__). + `Pull Request 3972`_ +* New Dependency resolver for the LMOD environment modules system + (thanks to `@arbernard `__). + `Pull Request 4489`_ +* Nicer tool click targets for toolbox + (thanks to `@erasche `__). + `Pull Request 4470`_ +* Implement a "plain" bootstrap theme for the UX + (thanks to `@erasche `__). + `Pull Request 4470`_ +* Add Selenium tests for the "saved histories", "published histories", and + "custom builds" + (thanks to `@anatskiy `__). + `Pull Request 4587`_, `Pull Request 4502`_, `Pull Request 4641`_, +* Dozens of Selenium functional test enhancements and fixes + `Pull Request 3993`_, `Pull Request 4523`_, `Pull Request 4524`_, `Pull Request 4549`_, + `Pull Request 4588`_, `Pull Request 4589`_, `Pull Request 4647`_, + `Pull Request 3992`_, `Pull Request 4003`_, `Pull Request 4053`_, + `Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_, + `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_, `Pull Request 4042`_ +* Prevent graphite from dying loudly + (thanks to `@erasche `__). + `Pull Request 4036`_ +* Updated parameters check for OpenID + (thanks to `@VJalili `__). + `Pull Request 4039`_ +* Tooltip translation . Add Deutsch,Spanish + (thanks to `@ValentinChCloud `__). + `Pull Request 4045`_ +* New Workflow Management Screen UI using JavaScript + (thanks to `@bgruening `__). + `Pull Request 4047`_ +* Improve release checklist + `Pull Request 4077`_ +* Fix French translation errors + (thanks to `@yvanlebras `__). + `Pull Request 4080`_ +* remove the content alert from TS response + `Pull Request 4082`_ +* Touchup .gitignore to not ignore new bundles. + `Pull Request 4091`_ +* New Configure Workflow Menu UI + (thanks to `@bgruening `__). + `Pull Request 4092`_ +* get real user name from username and email (for submission as real user with + drmaa) + (thanks to `@bernt-matthias `__). + `Pull Request 4096`_ +* Security policy + (thanks to `@erasche `__). + `Pull Request 4113`_ +* Improved styling of workflow list. + `Pull Request 4138`_ +* Swap over all URLs to new wiki location + (thanks to `@erasche `__). + `Pull Request 4141`_ +* Documentation fixes and improvements + (thanks to `@nsoranzo `__). + `Pull Request 4146`_ +* Slider enhancement, shared event listeners + `Pull Request 4149`_ +* Add the ability to control job conf plugin loading from environment + variables. + `Pull Request 4154`_ +* Replace various mako templates with client side JavaScript rendering. + `Pull Request 4157`_, `Pull Request 4167`_, `Pull Request 4169`_, + `Pull Request 4201`_, `Pull Request 4311`_, `Pull Request 4377`_, + `Pull Request 4411`_, `Pull Request 4334`_, `Pull Request 4305`_, + `Pull Request 4067`_, `Pull Request 4327`_ +* Related to the above mako transition, rework various "grid" rendering code + to do more on the client side as well. + `Pull Request 4302`_, `Pull Request 4291`_, `Pull Request 4293`_, + `Pull Request 4385`_, `Pull Request 4405`_, + `Pull Request 4449`_, `Pull Request 4263`_, `Pull Request 4341`_, + `Pull Request 4163`_, `Pull Request 4101`_ +* Set content type to application/json for JSON text types. + `Pull Request 4160`_ +* Assorted enhancements for container support (both for mulled container generation + and fetching as well as to new Singularity support). + `Pull Request 4173`_, `Pull Request 4179`_, `Pull Request 4180`_, + `Pull Request 4185`_ +* Make updateucsc.sh.sample usable without any change + (thanks to `@nsoranzo `__). + `Pull Request 4192`_ +* deals with .xls older file extension + (thanks to `@FredericBGA `__). + `Pull Request 4200`_ +* add dev requirement + `Pull Request 4008`_ +* Improve search plugin + (thanks to `@bgruening `__). + `Pull Request 4213`_ +* Upgrading Neo4j IE to 3.1 + (thanks to `@thobalose `__). + `Pull Request 4216`_ +* Running a word count on a compressed fastq file now runs wc on the un… + (thanks to `@dpryan79 `__). + `Pull Request 4226`_ +* "Join two Datasets" (join1) preserve column headers + (thanks to `@lecorguille `__). + `Pull Request 4229`_ +* Add public-only filter for data libraries + (thanks to `@pvanheus `__). + `Pull Request 4232`_ +* Fix import order and Python3 compatibility for 51 files + (thanks to `@nsoranzo `__). + `Pull Request 4236`_ +* Sniff fastqsanger and prefer it over fastq if the quality scores match + (thanks to `@dpryan79 `__). + `Pull Request 4237`_ +* Enable skipping comment lines while sniffing files + (thanks to `@dpryan79 `__). + `Pull Request 4239`_ +* Expose 4 more rows from the galaxy_user table to help out sys admins + (thanks to `@XDtim `__). + `Pull Request 4255`_ +* Change 'register or login' to just 'login' if 'allow_user_creation=False' + (thanks to `@scholtalbers `__). + `Pull Request 4258`_ +* Keep tool parameters when rerunning a job + (thanks to `@mvdbeek `__). + `Pull Request 4271`_ +* More uniform backend code for generating page titles + (thanks to `@erasche `__). + `Pull Request 4272`_, `Pull Request 4578`_ +* Fix blockquote>p sizing + (thanks to `@erasche `__). + `Pull Request 4273`_ +* Expose more user properties to admins via the API. + `Pull Request 4274`_ +* Ensure tags are copied and presented when moving collections + (thanks to `@pvanheus `__). + `Pull Request 4277`_ +* Add ``test_errors`` to .gitignore. + `Pull Request 4278`_ +* Implement package locking for node modules. + `Pull Request 4283`_ +* Enhancement for Phylocanvas plugin + (thanks to `@bgruening `__). + `Pull Request 4284`_ +* Improve security via local network access restrictions + (thanks to `@erasche `__). + `Pull Request 4289`_ +* Enhancement for Phyloviz viz plugin + (thanks to `@bgruening `__). + `Pull Request 4292`_ +* Allow submitting the galaxy jobs as a predefined system user using + ``real_system_username`` + (thanks to `@ashvark `__). + `Pull Request 4294`_ +* Update Japanese translation + (thanks to `@manabuishii `__). + `Pull Request 4304`_ +* Allow localization of more UI strings + (thanks to `@manabuishii `__). + `Pull Request 4306`_, `Pull Request 4307`_ +* Allow import of history archives via simple file upload + (thanks to `@mvdbeek `__). + `Pull Request 4326`_ +* Fix some French errors + (thanks to `@loraine-gueguen `__). + `Pull Request 4337`_ +* Updated the version requirements + (thanks to `@VJalili `__). + `Pull Request 4342`_ +* CSRF protection for login, logout, and user registration (most parts of the + Galaxy UI still don't have explicit CSRF protection). + `Pull Request 4365`_, `Pull Request 4710`_ +* Implement ``default_identifier_source`` for tool collection outputs and sort + input keys by default + (thanks to `@mvdbeek `__). + `Pull Request 4368`_, `Pull Request 4380`_ +* Galactic Radio Telescope Update + (thanks to `@erasche `__). + `Pull Request 4376`_ +* Show minimum required galaxy version in tool shed and galaxy installation + process + (thanks to `@mvdbeek `__). + `Pull Request 4386`_ +* Cleanup of Unit Test Code for Loading Tools + `Pull Request 4387`_ +* Refactor ToolOutputCollectionStructure... + `Pull Request 4389`_ +* Slightly improve workflow warnings/errors logging. + `Pull Request 4396`_ +* Better Error Summaries for API Tests + `Pull Request 4397`_ +* Fix import order and Python3 compatibility for lib/galaxy/web/base/ + (thanks to `@nsoranzo `__). + `Pull Request 4403`_ +* Generalize allow_library_path_paste to allow_path_paste. + `Pull Request 4404`_ +* Small GRT bugfixes + (thanks to `@erasche `__). + `Pull Request 4408`_ +* Update conda channel order to sync with Bioconda + (thanks to `@nsoranzo `__). + `Pull Request 4409`_ +* Fixes and enhancements for the upload API + `Pull Request 4417`_ +* Avoid adding `(imported from API)` to workflows + (thanks to `@chambm `__). + `Pull Request 4434`_ +* Enhanced tool options for dataset discovery + `Pull Request 4437`_ +* Augment form module separation + `Pull Request 4438`_ +* Fix E201 and E202 style errors + (thanks to `@nsoranzo `__). + `Pull Request 4440`_ +* Add autopep8 script to help rebasing branches after `#4440 + `__. + `Pull Request 4447`_ +* Uniform indentation of multiline if conditionals + (thanks to `@nsoranzo `__). + `Pull Request 4455`_ +* Small logging improvements + (thanks to `@nsoranzo `__). + `Pull Request 4456`_ +* Improvements to `Sentry `__ integration + (thanks to `@erasche `__). + `Pull Request 4457`_, `Pull Request 4471`_ +* Fix for GIEs to not automatically uppercase environment variables + (thanks to `@xgaia `__). + `Pull Request 4458`_, `Pull Request 4454`_ +* Fix security checking of WorkflowInvocation for published workflows + (thanks to `@mvdbeek `__). + `Pull Request 4465`_ +* Show more items per page in saved history view and directly show tags + (thanks to `@mvdbeek `__). + `Pull Request 4467`_ +* A variety of usability improvements to the workflow index page (show tags, + allow import by drag-and-drop, and avoid unneeded page refreshs) + (thanks to `@mvdbeek `__). + `Pull Request 4476`_, `Pull Request 4369`_ +* Use pysam instead of samtools binary when discovering BAM metadata in one + place (samtools is still required by Galaxy) + (thanks to `@nsoranzo `__). + `Pull Request 4479`_ +* Replace exclamation with a clock icon for "new" datasets in the history panel. + `Pull Request 4485`_ +* Minor copy datasets dialog improvement. + `Pull Request 4486`_ +* 41% reduction in freiburg galaxy startup time + (thanks to `@erasche `__). + `Pull Request 4495`_ +* Allow paramiko cli to recover from ssh timeout + (thanks to `@mvdbeek `__). + `Pull Request 4503`_ +* Tests and clarifications for composite uploads. + `Pull Request 4505`_ +* Load tools with collection type source attributes into the workflow editor + `Pull Request 4514`_ +* Display d3 hierarchy datatype in upload interface + `Pull Request 4522`_ +* Sync non-CWL galaxy-lib changes. + `Pull Request 4535`_ +* Add a small howto on profiling galaxy code + (thanks to `@mvdbeek `__). + `Pull Request 4542`_ +* allow linking, posix and spaces conversions in datalib imports + `Pull Request 4547`_ +* Allow exporting workflows when tool is uninstalled + (thanks to `@mvdbeek `__). + `Pull Request 4553`_ +* Lower threshold for auto-matching dataset pairs in the collection builder + `Pull Request 4555`_ +* Allow working with pbzip2 compressed files + (thanks to `@mvdbeek `__). + `Pull Request 4559`_ +* add logging to ts index building + `Pull Request 4567`_ +* Add show/hide deleted/hidden links when history is filtered... + (thanks to `@chambm `__). + `Pull Request 4581`_ +* Python 3 fixes for set_metadata.py + `Pull Request 4607`_ +* Allow adding new data tables without restart + (thanks to `@mvdbeek `__). + `Pull Request 4617`_ +* remove .git and .hg from recursive file search + (thanks to `@bgruening `__). + `Pull Request 4636`_ +* Better handling of long id secrets when generating per-kind encryption keys. + `Pull Request 4713`_ + +.. small_enhancement + +* Add test case clarifying datasets do get "renamed" by rename PJA in + collections. + `Pull Request 3983`_ +* Add some test tools for collection job failures. + `Pull Request 4044`_ +* Merge ShedToolLineage and StockLineage to ToolLineage + (thanks to `@mvdbeek `__). + `Pull Request 4119`_ +* Move PlantTribes datatypes to a separate file with enhancements and fixes + (thanks to `@gregvonkuster `__). + `Pull Request 4137`_ +* Move ``galaxy.tools.toolbox.cache`` to ``galaxy.tools.cache``. + `Pull Request 4155`_ +* Small code style and error message fixes for data library code + (thanks to `@bwlang `__). + `Pull Request 4250`_ +* Refactors tag manager to not consume the unneeded ``app`` argument + (thanks to `@bwlang `__). + `Pull Request 4253`_ +* Use contextmanager when using ``compression_util.get_fileobj()`` + (thanks to `@mvdbeek `__). + `Pull Request 4270`_ +* Swap the deprecated ``unescape()`` for ``decodeURIComponent``. + `Pull Request 4321`_ +* More consistent formatting for model mapping code + (thanks to `@VJalili `__). + `Pull Request 4333`_ +* Merge configure menu with main workflow view + (thanks to `@bgruening `__). + `Pull Request 4353`_ +* Delete ``conda_exec_home`` instead of ``env['HOME']`` + (thanks to `@mvdbeek `__). + `Pull Request 4360`_ +* Replace list with generator when iterating headers in datatypes code + (thanks to `@mvdbeek `__). + `Pull Request 4388`_ +* Get tools with ``tool_version`` in more places + (thanks to `@mvdbeek `__). + `Pull Request 4391`_ +* Fix issues identified by the JavaScript linting application + `lgtm `__. + (thanks to `@xiemaisi `__). + `Pull Request 4421`_ +* Remove /mobile and associated templates (the code was unused and broken). + `Pull Request 4494`_ +* Workflow loading speedup + (thanks to `@mvdbeek `__). + `Pull Request 4500`_ +* Prevent transient job state API test failures from failing the build. + `Pull Request 4510`_ +* More robust workflow invocation testing. + `Pull Request 4530`_ +* Refactor history import/export tests to allow collection testing. + `Pull Request 4534`_ +* Refactor test modules toward cleaner dependencies + `Pull Request 4536`_ +* Prevent in-place editing of uploaded files if files are imported from the + FTP folder + (thanks to `@mvdbeek `__). + `Pull Request 4539`_ +* Speedup toolform building + (thanks to `@mvdbeek `__). + `Pull Request 4541`_ +* Check user roles only once if user has no roles + (thanks to `@mvdbeek `__). + `Pull Request 4546`_ +* Remove unused bam to bai converter + (thanks to `@mvdbeek `__). + `Pull Request 4598`_ +* Remove various unreachable statements + (thanks to `@erasche `__). + `Pull Request 4603`_ +* Refactored a dataset variable to HDA + (thanks to `@VJalili `__). + `Pull Request 4630`_ +* Disable MacOS tests on TravisCI. + `Pull Request 4631`_ + + +Fixes +------------------------------- + +.. major_bug + +.. bug + +* Various hashtag (or name tag) fixes (also backported to 17.05). + `Pull Request 4139`_, `Pull Request 4188`_ +* Simplify RC creation in Makefile. + `Pull Request 4011`_ +* Do not recurse in ``ensure_installed()`` + (thanks to `@bernt-matthias `__). + `Pull Request 4049`_ +* Minor fixes for new locales, rebuild of client. + `Pull Request 4050`_ +* French translation error + (thanks to `@yvanlebras `__). + `Pull Request 4051`_ +* Minor history tour tweaks. + `Pull Request 4061`_ +* Improve tour button logic + (thanks to `@bagnacan `__). + `Pull Request 4062`_ +* Bug fix to prevent fetching the file path of purged files + (thanks to `@dpryan79 `__). + `Pull Request 4066`_ +* ToolShed tool dependency install fixes + (thanks to `@nsoranzo `__). + `Pull Request 4105`_ +* Fix legacy Python path for genome diversity tools from miller lab. + `Pull Request 4117`_ +* Avoid locale specific string.letters for job_name + (thanks to `@peterjc `__). + `Pull Request 4121`_ +* Fix typo in job_conf.xml.sample + (thanks to `@manabuishii `__). + `Pull Request 4126`_ +* Hide error highlighting if user interacts with highlighted field + `Pull Request 4147`_ +* Fix webhooks loading URL. + `Pull Request 4158`_ +* Fix older GIE config sample description. + `Pull Request 4164`_ +* Fix `#3990 `__, don't + chown non-galaxy files + (thanks to `@dpryan79 `__). + `Pull Request 4186`_ +* Debug of script library_upload_dir.py + (thanks to `@FredericBGA `__). + `Pull Request 4199`_ +* Correct name of neo4j datatype class + (thanks to `@pvanheus `__). + `Pull Request 4223`_ +* Fix ``Registry.get_datatype_by_extension()`` to return ``None`` if ``ext`` is unknown + (thanks to `@nsoranzo `__). + `Pull Request 4224`_ +* Avoid broken version of Mercurial in conda + (thanks to `@bwlang `__). + `Pull Request 4227`_ +* Fix empty tabular output error when using discover_datasets. + (thanks to `@pkrog `__). + `Pull Request 4240`_ +* Fix importing old exported histories. + (thanks to `@cche `__). + `Pull Request 4268`_ +* Update ``tool_conf.xml.main`` to reflect usegalaxy.org's current state. + `Pull Request 4295`_ +* Fix ``TypeError`` when uploading large files from FTP to S3. + (thanks to `@jlhg `__). + `Pull Request 4315`_ +* Fix for loading tools when ``tool.lineage is None``. + `Pull Request 4317`_ +* Fix for the caching of location filenames when they are broken symlinks. + `Pull Request 4318`_ +* Remove print debug option from toolshed. + `Pull Request 4332`_ +* Fix default output labels for subworkflows + (thanks to `@mvdbeek `__). + `Pull Request 4346`_ +* Search overlay plugin bug fix + (thanks to `@bgruening `__). + `Pull Request 4348`_ +* Tool version and lineage fixes + (thanks to `@mvdbeek `__). + `Pull Request 4375`_ +* Fix bug in ``scripts/extract_dataset_part.py`` during task splitting. + `Pull Request 4383`_ +* Fix ``get_tool`` returning list when it shouldn't. + `Pull Request 4390`_ +* Bug fix for loading subworkflows from workflow descriptions. + `Pull Request 4394`_ +* Bug fix ``__str__`` method on tool parsers that previously would throw an ``Exception``. + `Pull Request 4395`_ +* Add missing chemical formats to ``datatypes_conf.xml.sample`` + (thanks to `@nsoranzo `__). + `Pull Request 4413`_ +* Don't cast ``tool_version`` to string if ``tool_version`` is None-type + (thanks to `@mvdbeek `__). + `Pull Request 4420`_ +* Some unicoding for local runner + (thanks to `@erasche `__). + `Pull Request 4426`_ +* Break connection in workflow editor if necessary + (thanks to `@mvdbeek `__). + `Pull Request 4431`_ +* Fix private role validation. + `Pull Request 4432`_ +* Remove print of non-existent attribute 'content' + (thanks to `@chambm `__). + `Pull Request 4439`_ +* Fix quota function name + `Pull Request 4469`_ +* Fixes for VCF/BCF datatypes + (thanks to `@nsoranzo `__). + `Pull Request 4477`_ +* Validate workflow step after step argument injection. + `Pull Request 4483`_ +* Fix drag and drop from history for Firefox + `Pull Request 4496`_ +* 2017-08 Security Patch + (thanks to `@erasche `__). + `Pull Request 4501`_ +* Fix history import if using symlink in database directory + (thanks to `@FredericBGA `__). + `Pull Request 4511`_ +* Fix missing tools in the workflow editor + (thanks to `@mvdbeek `__). + `Pull Request 4552`_ +* Prevent unbound variable error history controller. + `Pull Request 4557`_ +* Backport uwsgi fix from `#2836 + `__. + `Pull Request 4565`_ +* Bug fix startup of galaxy when webhooks dir is empty + (thanks to `@mvdbeek `__). + `Pull Request 4570`_ +* Fix delete option in history menu. + `Pull Request 4574`_ +* Cancel workflow invocations when histories are deleted. + `Pull Request 4580`_ +* Multiview missing histories fix + `Pull Request 4610`_ +* Fix virtualenv activation for some scripts + (thanks to `@nsoranzo `__). + `Pull Request 4616`_ +* Pulsar remote metadata fixes + `Pull Request 4622`_ +* Swap sanitize whitelist form to use a post. + `Pull Request 4625`_ +* Fix various spelling and grammatical error fixes. + `Pull Request 4626`_ +* Typo fix + (thanks to `@VJalili `__). + `Pull Request 4628`_ +* Updated function description and fix some typos + (thanks to `@VJalili `__). + `Pull Request 4629`_ +* Fix display of data in "custom builds" page + (thanks to `@anatskiy `__). + `Pull Request 4634`_ +* Do not wrap lines in the upload URL fetch. + `Pull Request 4639`_ +* Explicitly write registry.xml when creating a job for the upload tool + (thanks to `@mvdbeek `__). + `Pull Request 4644`_, `Pull Request 4600`_ +* Fix links on workflow, history items. + `Pull Request 4656`_ +* Fix for modules resolver. + `Pull Request 4663`_ +* Remove overly chatty debug statement. + `Pull Request 4671`_ +* Client side fixes for GIEs. + `Pull Request 4680`_ +* Update target versions of conda and conda-build + (thanks to `@nsoranzo `__). + `Pull Request 4701`_ +* Correct base route for workflows, allowing proxy-prefix to work. + `Pull Request 4705`_ +* Cachebust IE require'd files (jupyter.js, etc). + `Pull Request 4714`_ +* Add message (error and info) display to workflows display list. + `Pull Request 4716`_ +* If the newest version of a tool is hidden, load the newest older version, if + any, into the tool panel. + `Pull Request 4726`_ +* Fix missing support for command_inject when using containers lib in GIEs. + `Pull Request 4740`_ +* Fix t, a, g, s returned in to_dict() method + (thanks to `@mvdbeek `__). + `Pull Request 4742`_ +* Fix joiner tool to inherit datatype from the input format + `Pull Request 4745`_ +* Fix auth with ``ldaps://`` + (thanks to `@abretaud `__). + `Pull Request 4748`_ +* Force onload webhooks to wait for Galaxy object (and root) resolution. + `Pull Request 4750`_ +* GIEs: Grandfather automatic uppercasing of some env_override variables + `Pull Request 4760`_ + +.. github_links +.. _Pull Request 1814: https://github.com/galaxyproject/galaxy/pull/1814 +.. _Pull Request 3064: https://github.com/galaxyproject/galaxy/pull/3064 +.. _Pull Request 3076: https://github.com/galaxyproject/galaxy/pull/3076 +.. _Pull Request 3179: https://github.com/galaxyproject/galaxy/pull/3179 +.. _Pull Request 3330: https://github.com/galaxyproject/galaxy/pull/3330 +.. _Pull Request 3383: https://github.com/galaxyproject/galaxy/pull/3383 +.. _Pull Request 3611: https://github.com/galaxyproject/galaxy/pull/3611 +.. _Pull Request 3626: https://github.com/galaxyproject/galaxy/pull/3626 +.. _Pull Request 3946: https://github.com/galaxyproject/galaxy/pull/3946 +.. _Pull Request 3972: https://github.com/galaxyproject/galaxy/pull/3972 +.. _Pull Request 3983: https://github.com/galaxyproject/galaxy/pull/3983 +.. _Pull Request 3992: https://github.com/galaxyproject/galaxy/pull/3992 +.. _Pull Request 3993: https://github.com/galaxyproject/galaxy/pull/3993 +.. _Pull Request 3994: https://github.com/galaxyproject/galaxy/pull/3994 +.. _Pull Request 3995: https://github.com/galaxyproject/galaxy/pull/3995 +.. _Pull Request 4003: https://github.com/galaxyproject/galaxy/pull/4003 +.. _Pull Request 4008: https://github.com/galaxyproject/galaxy/pull/4008 +.. _Pull Request 4010: https://github.com/galaxyproject/galaxy/pull/4010 +.. _Pull Request 4011: https://github.com/galaxyproject/galaxy/pull/4011 +.. _Pull Request 4019: https://github.com/galaxyproject/galaxy/pull/4019 +.. _Pull Request 4036: https://github.com/galaxyproject/galaxy/pull/4036 +.. _Pull Request 4039: https://github.com/galaxyproject/galaxy/pull/4039 +.. _Pull Request 4042: https://github.com/galaxyproject/galaxy/pull/4042 +.. _Pull Request 4044: https://github.com/galaxyproject/galaxy/pull/4044 +.. _Pull Request 4045: https://github.com/galaxyproject/galaxy/pull/4045 +.. _Pull Request 4047: https://github.com/galaxyproject/galaxy/pull/4047 +.. _Pull Request 4049: https://github.com/galaxyproject/galaxy/pull/4049 +.. _Pull Request 4050: https://github.com/galaxyproject/galaxy/pull/4050 +.. _Pull Request 4051: https://github.com/galaxyproject/galaxy/pull/4051 +.. _Pull Request 4053: https://github.com/galaxyproject/galaxy/pull/4053 +.. _Pull Request 4061: https://github.com/galaxyproject/galaxy/pull/4061 +.. _Pull Request 4062: https://github.com/galaxyproject/galaxy/pull/4062 +.. _Pull Request 4066: https://github.com/galaxyproject/galaxy/pull/4066 +.. _Pull Request 4067: https://github.com/galaxyproject/galaxy/pull/4067 +.. _Pull Request 4077: https://github.com/galaxyproject/galaxy/pull/4077 +.. _Pull Request 4080: https://github.com/galaxyproject/galaxy/pull/4080 +.. _Pull Request 4081: https://github.com/galaxyproject/galaxy/pull/4081 +.. _Pull Request 4082: https://github.com/galaxyproject/galaxy/pull/4082 +.. _Pull Request 4087: https://github.com/galaxyproject/galaxy/pull/4087 +.. _Pull Request 4088: https://github.com/galaxyproject/galaxy/pull/4088 +.. _Pull Request 4091: https://github.com/galaxyproject/galaxy/pull/4091 +.. _Pull Request 4092: https://github.com/galaxyproject/galaxy/pull/4092 +.. _Pull Request 4093: https://github.com/galaxyproject/galaxy/pull/4093 +.. _Pull Request 4096: https://github.com/galaxyproject/galaxy/pull/4096 +.. _Pull Request 4098: https://github.com/galaxyproject/galaxy/pull/4098 +.. _Pull Request 4101: https://github.com/galaxyproject/galaxy/pull/4101 +.. _Pull Request 4105: https://github.com/galaxyproject/galaxy/pull/4105 +.. _Pull Request 4112: https://github.com/galaxyproject/galaxy/pull/4112 +.. _Pull Request 4113: https://github.com/galaxyproject/galaxy/pull/4113 +.. _Pull Request 4117: https://github.com/galaxyproject/galaxy/pull/4117 +.. _Pull Request 4119: https://github.com/galaxyproject/galaxy/pull/4119 +.. _Pull Request 4120: https://github.com/galaxyproject/galaxy/pull/4120 +.. _Pull Request 4121: https://github.com/galaxyproject/galaxy/pull/4121 +.. _Pull Request 4124: https://github.com/galaxyproject/galaxy/pull/4124 +.. _Pull Request 4126: https://github.com/galaxyproject/galaxy/pull/4126 +.. _Pull Request 4137: https://github.com/galaxyproject/galaxy/pull/4137 +.. _Pull Request 4138: https://github.com/galaxyproject/galaxy/pull/4138 +.. _Pull Request 4139: https://github.com/galaxyproject/galaxy/pull/4139 +.. _Pull Request 4141: https://github.com/galaxyproject/galaxy/pull/4141 +.. _Pull Request 4146: https://github.com/galaxyproject/galaxy/pull/4146 +.. _Pull Request 4147: https://github.com/galaxyproject/galaxy/pull/4147 +.. _Pull Request 4149: https://github.com/galaxyproject/galaxy/pull/4149 +.. _Pull Request 4154: https://github.com/galaxyproject/galaxy/pull/4154 +.. _Pull Request 4155: https://github.com/galaxyproject/galaxy/pull/4155 +.. _Pull Request 4156: https://github.com/galaxyproject/galaxy/pull/4156 +.. _Pull Request 4157: https://github.com/galaxyproject/galaxy/pull/4157 +.. _Pull Request 4158: https://github.com/galaxyproject/galaxy/pull/4158 +.. _Pull Request 4160: https://github.com/galaxyproject/galaxy/pull/4160 +.. _Pull Request 4163: https://github.com/galaxyproject/galaxy/pull/4163 +.. _Pull Request 4164: https://github.com/galaxyproject/galaxy/pull/4164 +.. _Pull Request 4167: https://github.com/galaxyproject/galaxy/pull/4167 +.. _Pull Request 4169: https://github.com/galaxyproject/galaxy/pull/4169 +.. _Pull Request 4173: https://github.com/galaxyproject/galaxy/pull/4173 +.. _Pull Request 4175: https://github.com/galaxyproject/galaxy/pull/4175 +.. _Pull Request 4179: https://github.com/galaxyproject/galaxy/pull/4179 +.. _Pull Request 4180: https://github.com/galaxyproject/galaxy/pull/4180 +.. _Pull Request 4185: https://github.com/galaxyproject/galaxy/pull/4185 +.. _Pull Request 4186: https://github.com/galaxyproject/galaxy/pull/4186 +.. _Pull Request 4188: https://github.com/galaxyproject/galaxy/pull/4188 +.. _Pull Request 4192: https://github.com/galaxyproject/galaxy/pull/4192 +.. _Pull Request 4198: https://github.com/galaxyproject/galaxy/pull/4198 +.. _Pull Request 4199: https://github.com/galaxyproject/galaxy/pull/4199 +.. _Pull Request 4200: https://github.com/galaxyproject/galaxy/pull/4200 +.. _Pull Request 4201: https://github.com/galaxyproject/galaxy/pull/4201 +.. _Pull Request 4207: https://github.com/galaxyproject/galaxy/pull/4207 +.. _Pull Request 4208: https://github.com/galaxyproject/galaxy/pull/4208 +.. _Pull Request 4210: https://github.com/galaxyproject/galaxy/pull/4210 +.. _Pull Request 4213: https://github.com/galaxyproject/galaxy/pull/4213 +.. _Pull Request 4216: https://github.com/galaxyproject/galaxy/pull/4216 +.. _Pull Request 4223: https://github.com/galaxyproject/galaxy/pull/4223 +.. _Pull Request 4224: https://github.com/galaxyproject/galaxy/pull/4224 +.. _Pull Request 4226: https://github.com/galaxyproject/galaxy/pull/4226 +.. _Pull Request 4227: https://github.com/galaxyproject/galaxy/pull/4227 +.. _Pull Request 4229: https://github.com/galaxyproject/galaxy/pull/4229 +.. _Pull Request 4232: https://github.com/galaxyproject/galaxy/pull/4232 +.. _Pull Request 4236: https://github.com/galaxyproject/galaxy/pull/4236 +.. _Pull Request 4237: https://github.com/galaxyproject/galaxy/pull/4237 +.. _Pull Request 4239: https://github.com/galaxyproject/galaxy/pull/4239 +.. _Pull Request 4240: https://github.com/galaxyproject/galaxy/pull/4240 +.. _Pull Request 4248: https://github.com/galaxyproject/galaxy/pull/4248 +.. _Pull Request 4250: https://github.com/galaxyproject/galaxy/pull/4250 +.. _Pull Request 4253: https://github.com/galaxyproject/galaxy/pull/4253 +.. _Pull Request 4254: https://github.com/galaxyproject/galaxy/pull/4254 +.. _Pull Request 4255: https://github.com/galaxyproject/galaxy/pull/4255 +.. _Pull Request 4258: https://github.com/galaxyproject/galaxy/pull/4258 +.. _Pull Request 4259: https://github.com/galaxyproject/galaxy/pull/4259 +.. _Pull Request 4262: https://github.com/galaxyproject/galaxy/pull/4262 +.. _Pull Request 4263: https://github.com/galaxyproject/galaxy/pull/4263 +.. _Pull Request 4268: https://github.com/galaxyproject/galaxy/pull/4268 +.. _Pull Request 4270: https://github.com/galaxyproject/galaxy/pull/4270 +.. _Pull Request 4271: https://github.com/galaxyproject/galaxy/pull/4271 +.. _Pull Request 4272: https://github.com/galaxyproject/galaxy/pull/4272 +.. _Pull Request 4273: https://github.com/galaxyproject/galaxy/pull/4273 +.. _Pull Request 4274: https://github.com/galaxyproject/galaxy/pull/4274 +.. _Pull Request 4277: https://github.com/galaxyproject/galaxy/pull/4277 +.. _Pull Request 4278: https://github.com/galaxyproject/galaxy/pull/4278 +.. _Pull Request 4279: https://github.com/galaxyproject/galaxy/pull/4279 +.. _Pull Request 4281: https://github.com/galaxyproject/galaxy/pull/4281 +.. _Pull Request 4283: https://github.com/galaxyproject/galaxy/pull/4283 +.. _Pull Request 4284: https://github.com/galaxyproject/galaxy/pull/4284 +.. _Pull Request 4285: https://github.com/galaxyproject/galaxy/pull/4285 +.. _Pull Request 4289: https://github.com/galaxyproject/galaxy/pull/4289 +.. _Pull Request 4291: https://github.com/galaxyproject/galaxy/pull/4291 +.. _Pull Request 4292: https://github.com/galaxyproject/galaxy/pull/4292 +.. _Pull Request 4293: https://github.com/galaxyproject/galaxy/pull/4293 +.. _Pull Request 4294: https://github.com/galaxyproject/galaxy/pull/4294 +.. _Pull Request 4295: https://github.com/galaxyproject/galaxy/pull/4295 +.. _Pull Request 4302: https://github.com/galaxyproject/galaxy/pull/4302 +.. _Pull Request 4304: https://github.com/galaxyproject/galaxy/pull/4304 +.. _Pull Request 4305: https://github.com/galaxyproject/galaxy/pull/4305 +.. _Pull Request 4306: https://github.com/galaxyproject/galaxy/pull/4306 +.. _Pull Request 4307: https://github.com/galaxyproject/galaxy/pull/4307 +.. _Pull Request 4309: https://github.com/galaxyproject/galaxy/pull/4309 +.. _Pull Request 4310: https://github.com/galaxyproject/galaxy/pull/4310 +.. _Pull Request 4311: https://github.com/galaxyproject/galaxy/pull/4311 +.. _Pull Request 4315: https://github.com/galaxyproject/galaxy/pull/4315 +.. _Pull Request 4317: https://github.com/galaxyproject/galaxy/pull/4317 +.. _Pull Request 4318: https://github.com/galaxyproject/galaxy/pull/4318 +.. _Pull Request 4321: https://github.com/galaxyproject/galaxy/pull/4321 +.. _Pull Request 4326: https://github.com/galaxyproject/galaxy/pull/4326 +.. _Pull Request 4327: https://github.com/galaxyproject/galaxy/pull/4327 +.. _Pull Request 4329: https://github.com/galaxyproject/galaxy/pull/4329 +.. _Pull Request 4332: https://github.com/galaxyproject/galaxy/pull/4332 +.. _Pull Request 4333: https://github.com/galaxyproject/galaxy/pull/4333 +.. _Pull Request 4334: https://github.com/galaxyproject/galaxy/pull/4334 +.. _Pull Request 4337: https://github.com/galaxyproject/galaxy/pull/4337 +.. _Pull Request 4341: https://github.com/galaxyproject/galaxy/pull/4341 +.. _Pull Request 4342: https://github.com/galaxyproject/galaxy/pull/4342 +.. _Pull Request 4343: https://github.com/galaxyproject/galaxy/pull/4343 +.. _Pull Request 4346: https://github.com/galaxyproject/galaxy/pull/4346 +.. _Pull Request 4348: https://github.com/galaxyproject/galaxy/pull/4348 +.. _Pull Request 4353: https://github.com/galaxyproject/galaxy/pull/4353 +.. _Pull Request 4357: https://github.com/galaxyproject/galaxy/pull/4357 +.. _Pull Request 4358: https://github.com/galaxyproject/galaxy/pull/4358 +.. _Pull Request 4360: https://github.com/galaxyproject/galaxy/pull/4360 +.. _Pull Request 4365: https://github.com/galaxyproject/galaxy/pull/4365 +.. _Pull Request 4368: https://github.com/galaxyproject/galaxy/pull/4368 +.. _Pull Request 4369: https://github.com/galaxyproject/galaxy/pull/4369 +.. _Pull Request 4370: https://github.com/galaxyproject/galaxy/pull/4370 +.. _Pull Request 4371: https://github.com/galaxyproject/galaxy/pull/4371 +.. _Pull Request 4373: https://github.com/galaxyproject/galaxy/pull/4373 +.. _Pull Request 4375: https://github.com/galaxyproject/galaxy/pull/4375 +.. _Pull Request 4376: https://github.com/galaxyproject/galaxy/pull/4376 +.. _Pull Request 4377: https://github.com/galaxyproject/galaxy/pull/4377 +.. _Pull Request 4380: https://github.com/galaxyproject/galaxy/pull/4380 +.. _Pull Request 4382: https://github.com/galaxyproject/galaxy/pull/4382 +.. _Pull Request 4383: https://github.com/galaxyproject/galaxy/pull/4383 +.. _Pull Request 4385: https://github.com/galaxyproject/galaxy/pull/4385 +.. _Pull Request 4386: https://github.com/galaxyproject/galaxy/pull/4386 +.. _Pull Request 4387: https://github.com/galaxyproject/galaxy/pull/4387 +.. _Pull Request 4388: https://github.com/galaxyproject/galaxy/pull/4388 +.. _Pull Request 4389: https://github.com/galaxyproject/galaxy/pull/4389 +.. _Pull Request 4390: https://github.com/galaxyproject/galaxy/pull/4390 +.. _Pull Request 4391: https://github.com/galaxyproject/galaxy/pull/4391 +.. _Pull Request 4392: https://github.com/galaxyproject/galaxy/pull/4392 +.. _Pull Request 4394: https://github.com/galaxyproject/galaxy/pull/4394 +.. _Pull Request 4395: https://github.com/galaxyproject/galaxy/pull/4395 +.. _Pull Request 4396: https://github.com/galaxyproject/galaxy/pull/4396 +.. _Pull Request 4397: https://github.com/galaxyproject/galaxy/pull/4397 +.. _Pull Request 4403: https://github.com/galaxyproject/galaxy/pull/4403 +.. _Pull Request 4404: https://github.com/galaxyproject/galaxy/pull/4404 +.. _Pull Request 4405: https://github.com/galaxyproject/galaxy/pull/4405 +.. _Pull Request 4408: https://github.com/galaxyproject/galaxy/pull/4408 +.. _Pull Request 4409: https://github.com/galaxyproject/galaxy/pull/4409 +.. _Pull Request 4410: https://github.com/galaxyproject/galaxy/pull/4410 +.. _Pull Request 4411: https://github.com/galaxyproject/galaxy/pull/4411 +.. _Pull Request 4413: https://github.com/galaxyproject/galaxy/pull/4413 +.. _Pull Request 4417: https://github.com/galaxyproject/galaxy/pull/4417 +.. _Pull Request 4420: https://github.com/galaxyproject/galaxy/pull/4420 +.. _Pull Request 4421: https://github.com/galaxyproject/galaxy/pull/4421 +.. _Pull Request 4426: https://github.com/galaxyproject/galaxy/pull/4426 +.. _Pull Request 4427: https://github.com/galaxyproject/galaxy/pull/4427 +.. _Pull Request 4430: https://github.com/galaxyproject/galaxy/pull/4430 +.. _Pull Request 4431: https://github.com/galaxyproject/galaxy/pull/4431 +.. _Pull Request 4432: https://github.com/galaxyproject/galaxy/pull/4432 +.. _Pull Request 4434: https://github.com/galaxyproject/galaxy/pull/4434 +.. _Pull Request 4437: https://github.com/galaxyproject/galaxy/pull/4437 +.. _Pull Request 4438: https://github.com/galaxyproject/galaxy/pull/4438 +.. _Pull Request 4439: https://github.com/galaxyproject/galaxy/pull/4439 +.. _Pull Request 4440: https://github.com/galaxyproject/galaxy/pull/4440 +.. _Pull Request 4445: https://github.com/galaxyproject/galaxy/pull/4445 +.. _Pull Request 4446: https://github.com/galaxyproject/galaxy/pull/4446 +.. _Pull Request 4447: https://github.com/galaxyproject/galaxy/pull/4447 +.. _Pull Request 4449: https://github.com/galaxyproject/galaxy/pull/4449 +.. _Pull Request 4454: https://github.com/galaxyproject/galaxy/pull/4454 +.. _Pull Request 4455: https://github.com/galaxyproject/galaxy/pull/4455 +.. _Pull Request 4456: https://github.com/galaxyproject/galaxy/pull/4456 +.. _Pull Request 4457: https://github.com/galaxyproject/galaxy/pull/4457 +.. _Pull Request 4458: https://github.com/galaxyproject/galaxy/pull/4458 +.. _Pull Request 4465: https://github.com/galaxyproject/galaxy/pull/4465 +.. _Pull Request 4466: https://github.com/galaxyproject/galaxy/pull/4466 +.. _Pull Request 4467: https://github.com/galaxyproject/galaxy/pull/4467 +.. _Pull Request 4469: https://github.com/galaxyproject/galaxy/pull/4469 +.. _Pull Request 4470: https://github.com/galaxyproject/galaxy/pull/4470 +.. _Pull Request 4471: https://github.com/galaxyproject/galaxy/pull/4471 +.. _Pull Request 4476: https://github.com/galaxyproject/galaxy/pull/4476 +.. _Pull Request 4477: https://github.com/galaxyproject/galaxy/pull/4477 +.. _Pull Request 4479: https://github.com/galaxyproject/galaxy/pull/4479 +.. _Pull Request 4483: https://github.com/galaxyproject/galaxy/pull/4483 +.. _Pull Request 4485: https://github.com/galaxyproject/galaxy/pull/4485 +.. _Pull Request 4486: https://github.com/galaxyproject/galaxy/pull/4486 +.. _Pull Request 4489: https://github.com/galaxyproject/galaxy/pull/4489 +.. _Pull Request 4492: https://github.com/galaxyproject/galaxy/pull/4492 +.. _Pull Request 4494: https://github.com/galaxyproject/galaxy/pull/4494 +.. _Pull Request 4495: https://github.com/galaxyproject/galaxy/pull/4495 +.. _Pull Request 4496: https://github.com/galaxyproject/galaxy/pull/4496 +.. _Pull Request 4500: https://github.com/galaxyproject/galaxy/pull/4500 +.. _Pull Request 4501: https://github.com/galaxyproject/galaxy/pull/4501 +.. _Pull Request 4502: https://github.com/galaxyproject/galaxy/pull/4502 +.. _Pull Request 4503: https://github.com/galaxyproject/galaxy/pull/4503 +.. _Pull Request 4505: https://github.com/galaxyproject/galaxy/pull/4505 +.. _Pull Request 4508: https://github.com/galaxyproject/galaxy/pull/4508 +.. _Pull Request 4510: https://github.com/galaxyproject/galaxy/pull/4510 +.. _Pull Request 4511: https://github.com/galaxyproject/galaxy/pull/4511 +.. _Pull Request 4512: https://github.com/galaxyproject/galaxy/pull/4512 +.. _Pull Request 4514: https://github.com/galaxyproject/galaxy/pull/4514 +.. _Pull Request 4515: https://github.com/galaxyproject/galaxy/pull/4515 +.. _Pull Request 4519: https://github.com/galaxyproject/galaxy/pull/4519 +.. _Pull Request 4522: https://github.com/galaxyproject/galaxy/pull/4522 +.. _Pull Request 4523: https://github.com/galaxyproject/galaxy/pull/4523 +.. _Pull Request 4524: https://github.com/galaxyproject/galaxy/pull/4524 +.. _Pull Request 4530: https://github.com/galaxyproject/galaxy/pull/4530 +.. _Pull Request 4531: https://github.com/galaxyproject/galaxy/pull/4531 +.. _Pull Request 4533: https://github.com/galaxyproject/galaxy/pull/4533 +.. _Pull Request 4534: https://github.com/galaxyproject/galaxy/pull/4534 +.. _Pull Request 4535: https://github.com/galaxyproject/galaxy/pull/4535 +.. _Pull Request 4536: https://github.com/galaxyproject/galaxy/pull/4536 +.. _Pull Request 4539: https://github.com/galaxyproject/galaxy/pull/4539 +.. _Pull Request 4541: https://github.com/galaxyproject/galaxy/pull/4541 +.. _Pull Request 4542: https://github.com/galaxyproject/galaxy/pull/4542 +.. _Pull Request 4546: https://github.com/galaxyproject/galaxy/pull/4546 +.. _Pull Request 4547: https://github.com/galaxyproject/galaxy/pull/4547 +.. _Pull Request 4549: https://github.com/galaxyproject/galaxy/pull/4549 +.. _Pull Request 4552: https://github.com/galaxyproject/galaxy/pull/4552 +.. _Pull Request 4553: https://github.com/galaxyproject/galaxy/pull/4553 +.. _Pull Request 4555: https://github.com/galaxyproject/galaxy/pull/4555 +.. _Pull Request 4556: https://github.com/galaxyproject/galaxy/pull/4556 +.. _Pull Request 4557: https://github.com/galaxyproject/galaxy/pull/4557 +.. _Pull Request 4559: https://github.com/galaxyproject/galaxy/pull/4559 +.. _Pull Request 4560: https://github.com/galaxyproject/galaxy/pull/4560 +.. _Pull Request 4561: https://github.com/galaxyproject/galaxy/pull/4561 +.. _Pull Request 4562: https://github.com/galaxyproject/galaxy/pull/4562 +.. _Pull Request 4564: https://github.com/galaxyproject/galaxy/pull/4564 +.. _Pull Request 4565: https://github.com/galaxyproject/galaxy/pull/4565 +.. _Pull Request 4567: https://github.com/galaxyproject/galaxy/pull/4567 +.. _Pull Request 4568: https://github.com/galaxyproject/galaxy/pull/4568 +.. _Pull Request 4570: https://github.com/galaxyproject/galaxy/pull/4570 +.. _Pull Request 4574: https://github.com/galaxyproject/galaxy/pull/4574 +.. _Pull Request 4576: https://github.com/galaxyproject/galaxy/pull/4576 +.. _Pull Request 4577: https://github.com/galaxyproject/galaxy/pull/4577 +.. _Pull Request 4578: https://github.com/galaxyproject/galaxy/pull/4578 +.. _Pull Request 4579: https://github.com/galaxyproject/galaxy/pull/4579 +.. _Pull Request 4580: https://github.com/galaxyproject/galaxy/pull/4580 +.. _Pull Request 4581: https://github.com/galaxyproject/galaxy/pull/4581 +.. _Pull Request 4582: https://github.com/galaxyproject/galaxy/pull/4582 +.. _Pull Request 4586: https://github.com/galaxyproject/galaxy/pull/4586 +.. _Pull Request 4587: https://github.com/galaxyproject/galaxy/pull/4587 +.. _Pull Request 4588: https://github.com/galaxyproject/galaxy/pull/4588 +.. _Pull Request 4589: https://github.com/galaxyproject/galaxy/pull/4589 +.. _Pull Request 4592: https://github.com/galaxyproject/galaxy/pull/4592 +.. _Pull Request 4594: https://github.com/galaxyproject/galaxy/pull/4594 +.. _Pull Request 4595: https://github.com/galaxyproject/galaxy/pull/4595 +.. _Pull Request 4598: https://github.com/galaxyproject/galaxy/pull/4598 +.. _Pull Request 4599: https://github.com/galaxyproject/galaxy/pull/4599 +.. _Pull Request 4600: https://github.com/galaxyproject/galaxy/pull/4600 +.. _Pull Request 4603: https://github.com/galaxyproject/galaxy/pull/4603 +.. _Pull Request 4607: https://github.com/galaxyproject/galaxy/pull/4607 +.. _Pull Request 4610: https://github.com/galaxyproject/galaxy/pull/4610 +.. _Pull Request 4611: https://github.com/galaxyproject/galaxy/pull/4611 +.. _Pull Request 4616: https://github.com/galaxyproject/galaxy/pull/4616 +.. _Pull Request 4617: https://github.com/galaxyproject/galaxy/pull/4617 +.. _Pull Request 4619: https://github.com/galaxyproject/galaxy/pull/4619 +.. _Pull Request 4621: https://github.com/galaxyproject/galaxy/pull/4621 +.. _Pull Request 4622: https://github.com/galaxyproject/galaxy/pull/4622 +.. _Pull Request 4625: https://github.com/galaxyproject/galaxy/pull/4625 +.. _Pull Request 4626: https://github.com/galaxyproject/galaxy/pull/4626 +.. _Pull Request 4628: https://github.com/galaxyproject/galaxy/pull/4628 +.. _Pull Request 4629: https://github.com/galaxyproject/galaxy/pull/4629 +.. _Pull Request 4630: https://github.com/galaxyproject/galaxy/pull/4630 +.. _Pull Request 4631: https://github.com/galaxyproject/galaxy/pull/4631 +.. _Pull Request 4632: https://github.com/galaxyproject/galaxy/pull/4632 +.. _Pull Request 4634: https://github.com/galaxyproject/galaxy/pull/4634 +.. _Pull Request 4636: https://github.com/galaxyproject/galaxy/pull/4636 +.. _Pull Request 4639: https://github.com/galaxyproject/galaxy/pull/4639 +.. _Pull Request 4640: https://github.com/galaxyproject/galaxy/pull/4640 +.. _Pull Request 4641: https://github.com/galaxyproject/galaxy/pull/4641 +.. _Pull Request 4644: https://github.com/galaxyproject/galaxy/pull/4644 +.. _Pull Request 4647: https://github.com/galaxyproject/galaxy/pull/4647 +.. _Pull Request 4648: https://github.com/galaxyproject/galaxy/pull/4648 +.. _Pull Request 4650: https://github.com/galaxyproject/galaxy/pull/4650 +.. _Pull Request 4652: https://github.com/galaxyproject/galaxy/pull/4652 +.. _Pull Request 4656: https://github.com/galaxyproject/galaxy/pull/4656 +.. _Pull Request 4663: https://github.com/galaxyproject/galaxy/pull/4663 +.. _Pull Request 4671: https://github.com/galaxyproject/galaxy/pull/4671 +.. _Pull Request 4674: https://github.com/galaxyproject/galaxy/pull/4674 +.. _Pull Request 4680: https://github.com/galaxyproject/galaxy/pull/4680 +.. _Pull Request 4701: https://github.com/galaxyproject/galaxy/pull/4701 +.. _Pull Request 4705: https://github.com/galaxyproject/galaxy/pull/4705 +.. _Pull Request 4710: https://github.com/galaxyproject/galaxy/pull/4710 +.. _Pull Request 4713: https://github.com/galaxyproject/galaxy/pull/4713 +.. _Pull Request 4714: https://github.com/galaxyproject/galaxy/pull/4714 +.. _Pull Request 4715: https://github.com/galaxyproject/galaxy/pull/4715 +.. _Pull Request 4716: https://github.com/galaxyproject/galaxy/pull/4716 +.. _Pull Request 4726: https://github.com/galaxyproject/galaxy/pull/4726 +.. _Pull Request 4740: https://github.com/galaxyproject/galaxy/pull/4740 +.. _Pull Request 4742: https://github.com/galaxyproject/galaxy/pull/4742 +.. _Pull Request 4743: https://github.com/galaxyproject/galaxy/pull/4743 +.. _Pull Request 4745: https://github.com/galaxyproject/galaxy/pull/4745 +.. _Pull Request 4748: https://github.com/galaxyproject/galaxy/pull/4748 +.. _Pull Request 4750: https://github.com/galaxyproject/galaxy/pull/4750 +.. _Pull Request 4752: https://github.com/galaxyproject/galaxy/pull/4752 +.. _Pull Request 4760: https://github.com/galaxyproject/galaxy/pull/4760 + diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index e32481ef2401..2a536dad649c 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -3,8 +3,127 @@ September 2017 Galaxy Release (v 17.09) =========================================================== +.. include:: _header.rst -Schedule +Highlights =========================================================== - * Planned Freeze Date: 2017-09-04 - * Planned Release Date: 2017-09-25 + +**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). For more information + checkout `this presentation `__ from the 2017 Galaxy Community Conference. + `Pull Request 4175`_ + +**Download entire collection** + Downloading whole colections is now possible from the history interface. `Pull Request 4098`_ + Thanks to `@mvdbeek `__. + +**Switch tool versions in workflows** + You can now select exactly what version of tool you want to use when building workflows. `Pull Request 4373`_ + Thanks to `@mvdbeek `__. + +Get Galaxy +========== + +The code lives at `Github `__ and you should have `Git `__ to obtain it. + +To get a new Galaxy repository run: + .. code-block:: shell + + $ git clone -b release_17.09 https://github.com/galaxyproject/galaxy.git + +To update an existing Galaxy repository run: + .. code-block:: shell + + $ git checkout release_17.09 && git pull --ff-only origin release_17.09 + +See `the community hub `__ for additional details regarding the source code locations. + + +Security +======== + +Together with the 17.09 Galaxy version we release the following three security patches. Per our `Security Policy `__ these has been already applied to all Galaxy releases in the last 12 months. + +If you maintain a publicly accessible Galaxy please consider signing up for this [mailing list](https://lists.galaxyproject.org/listinfo/galaxy-public-servers) to receive the future security patches in advance of the public disclosure. + +Limited Galaxy Data Library unauthorized filesystem access +---------------------------------------------------------- + +Tracked as `GX-2017-0001 `__ + +A medium severity security vulnerability in Galaxy Data Libraries was +recently discovered by `Jelle Scholtalbers `__. +This vulnerability allows the following unauthorized actions: + +1. Any user that has been granted the permission to add datasets to a + library, library folder, or to modify an existing library dataset (an + "authorized user"), is able to import any file on the system that is + readable by the user running the Galaxy server. + +2. Anyone can create libraries and library folders (but not add datasets to them) + +The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit `__ + +Arbitrary code execution for Galaxy servers with Galaxy Interactive Environments enabled +---------------------------------------------------------------------------------------- + +Tracked as `GX-2017-0002 `__ + +A high severity security vulnerability was recently discovered in Galaxy +Interactive Environments (GIEs) by the Galaxy Committers Team. Anyone with +a Galaxy account can exploit this vulnerability to execute arbitrary code +on the Galaxy server as the user running the Galaxy server process. + +The vulnerability only affects Galaxy servers on which Galaxy Interactive +Environments are enabled (by setting the +`interactive_environment_plugins_directory` +option in `galaxy.ini`). Because the vulnerability can be exploited to +execute arbitrary code, the impact for affected servers is severe. + +Administrators of Galaxy servers where GIEs *are* enabled should update +immediately. + +The fix for this issue has been applied to Galaxy releases back to 17.05 and can be found in this `commit `__ + +Unauthorized filesystem access via data source tools +---------------------------------------------------- + +Tracked as `GX-2017-0003 `__ + +A medium severity security vulnerability in tools utilizing the Galaxy data +source protocol was recently discovered by the Galaxy Committers Team. +Anyone who is able to run an external data source tool can access +any file that is readable by the user running Galaxy jobs +on the host where the job runs. + +Many such "external data source" tools are provided with the Galaxy +distribution and are enabled by default (most tools under the "Get Data" +section of the tool panel), meaning that its exploitability is fairly high, +as only one such tool needs to be enabled to be vulnerable, including any +custom data source tools (any tool that uses +`tools/data_source/data_source.py`). +What files are readable depends entirely upon what the job's user has +access to read on the host(s) where jobs run. + +The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit `__ + +Deprecation Notices +=================== + +* The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In future releases we will strip down the related + user interface and introduce configuration option to keep relevant API controllers active if desired. `Related PR `__. +* The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release. +* Workflows API: When exposing WorkflowInvocationSteps ``state`` will no longer be available. +* The ``refresh_on_change`` attribute of a ```` tag in the tool syntax can no longer be set to a value of another parameter. Use boolean instead (e.g.``refresh_on_change="True"``). `Details `__ + + +Release Notes +=========================================================== + +.. include:: 17.09.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/18.01_announce.rst b/doc/source/releases/18.01_announce.rst new file mode 100644 index 000000000000..b62092b1e063 --- /dev/null +++ b/doc/source/releases/18.01_announce.rst @@ -0,0 +1,10 @@ + +=========================================================== +January 2018 Galaxy Release (v 18.01) +=========================================================== + + +Schedule +=========================================================== + * Planned Freeze Date: 2018-01-08 + * Planned Release Date: 2018-01-29 diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst index c57cbc5e46d1..448ab9bfbd00 100644 --- a/doc/source/releases/index.rst +++ b/doc/source/releases/index.rst @@ -4,6 +4,7 @@ Releases .. toctree:: :maxdepth: 1 + 17.09_announce 17.05_announce 17.01_announce 16.10_announce