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September 2019 Galaxy Release (v 19.09)¶
Highlights¶
- Interactive Tools
A new type of Galaxy tool has been implemented that allows interactive experiences like Galaxy Interactive Environments (via a proxy and Docker containers) but using plugins defined with Galaxy’s XML tool syntax. Dan Blankenberg’s slides on these new features from Galaxy Community Conference 2019 can be found here. More information can be found in the original pull request, including interactive tool versions of all of Galaxy’s bundled interactive environments Pull Request 7494.
- Workflow Invocation Reports
Workflows may now define Markdown templates with Galaxy-specific embedded syntax extensions that can tie together workflow inputs, outputs, jobs, and metadata into rich reports. More information on the motivation for these reports can be found in these slides, implementation details and GUI enhancements are described in the original pull request (#8030), and details on the final syntax selected for embedded Galaxy objects can be found in the pull request that was ultimately merged (#8543).
- New Toolshed Client Interface
The march toward replacing templated backend-generated HTML with modern, reactive components continued in Galaxy 19.09. Galaxy’s tool panel, job properties tables, job management controls, and “Pages” infrastructure were all replaced with VueJS components (with huge help from @scrathat and @inkuzmin). Most notably, Galaxy’s interface to the Tool Shed was also rewritten in VueJS and is now completely API driven. This project drove numerous enhancements to the Tool Shed API, including vastly improved search functionality. This interface has been completely re-imagined and feels much more interactive.
Also check out the 19.09 user release notes.
Get Galaxy¶
The code lives at GitHub and you should have Git to obtain it.
- To get a new Galaxy repository run:
$ git clone -b release_19.09 https://github.com/galaxyproject/galaxy.git
- To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_19.09 && git pull --ff-only origin release_19.09
See the community hub for additional details regarding the source code locations.
Tool configuration file handling changes¶
Shed tool configuration file¶
There have been a few changes to the way that Galaxy loads tool panel configuration files (e.g. tool_conf.xml
and shed_tool_conf.xml
) that deployers should be aware of before upgrading.
A new configuration option named shed_tool_config_file
has been added, with a default value of config/shed_tool_conf.xml
, and that path has been removed from the default value of the tool_config_file
option. This new option makes it possible for Galaxy to create the shed tool configuration file (e.g. shed_tool_conf.xml
) file on demand and moves us one step closer to a Galaxy installation that does not need to be run from the root of its source directory.
If you make no changes to your configuration, you should not encounter any problems. However, if you are using a non-default path to your primary shed tool config file, you should modify these options to remove the path of your primary shed_tool_conf.xml
from tool_config_file
and set it in shed_tool_config_file
. Although Galaxy will continue to operate properly if you do not make this change, failure to do so will result in a second shed tool panel config file being created and loaded at startup time.
Although an unusual configuration, if you have multiple shed tool config files, you can still load them in tool_config_file
, just be sure that one of them is set in shed_tool_config_file
.
Note that Galaxy will fail to start if any of the files specified in tool_conf_file
cannot be read at startup, whereas it will only fail to start if the file specified in shed_tool_config_file
cannot be created (if it does not already exist).
Migrated tools configuration file¶
Galaxy contains a (now unused) system for automatically installing tools from the Tool Shed that had been migrated out of the Galaxy source code after the creation of the Tool Shed. Older deployments that used this system may have tools in the migrated tools config file, config/migrated_tools_conf.xml.sample
(by default). As of this release, an empty migrated_tools_conf.xml
file is not created by default for new installations, but will still be read if it is found at the default path. The path can be changed with the migrated_tools_config
option, and you can force Galaxy to fail startup if the file is missing by adding it to the tool_config_file
option.
Configuration file path defaults¶
Deprecated paths will no longer be searched
The default location for Galaxy’s configuration files has been in the config/
directory for many years, prior to which the default was the root of the Galaxy directory.
As of this release, Galaxy will no longer look in the current directory for configuration files, so you will need to specify the path to galaxy.yml
e.g. with
uwsgi --yaml /path/to/galaxy.yml
, GALAXY_CONFIG_FILE=/path/to/galaxy.yml run.sh
, or similar means, if it is not in the default location.
Default paths to additional configuration files
As of this release, all other configuration files (e.g. datatypes_conf.xml
, job_conf.xml
) are searched for in the same directory as galaxy.yml
.
Prior to this release, the default was in the config/
directory of the current working directory at startup (which has always been, and for the time being continues to be, the root of the Galaxy source).
This means that you do not need to individually configure the paths to these files in galaxy.yml
if you are storing them in non-default locations.
MySQL Support Drop¶
The MySQL database server is no longer officially supported and all deployers are urged to use PostgreSQL.
Deprecation Notice¶
API¶
The following Galaxy API endpoints (related to the Toolshed) are considered deprecated and staged for removal in the next release:
api/toolshed/ { category | repository | search | show | status | tool_json }
api/toolshed_repositories/ { check_for_updates | exported_workflows | get_latest_installable_revision | import_workflow | import_workflows | install | repair_repository_revision | shed_category | shed_repository | shed_search | status }
Python¶
TL;DR Galaxy can be deployed on both Python 2 and 3, with Python 3 expected to be the increasingly encouraged way of deployment.
Python 2 will not be maintained past 2020 which means Galaxy 19.09 is the last release that officially supports Python 2.
Over the past years the Galaxy team has made a substantial effort, spearheaded by @nsoranzo and @mvdbeek, to make Galaxy compatible with Python 3. Thanks to this endeavor the Galaxy Test server has been running on Python 3 since April of this year and Galaxy itself now fully supports Python 3.
Galaxy Tools, that properly declare their Python dependency (using e.g. <requirement type="package" version="2.7">python</requirement>
), will continue to work as expected with Python 2
being provided by Conda. However tools that naively rely on the implicit presence of Python 2 on the PATH may fail on Python3 deployments.
Another corner case are tools that use Python2-specific Cheetah templating syntax in their XML. We have implemented various mitigation
approaches on the Galaxy side, but some old tools using this syntax will not function correctly.
In our testing these problems should affect only a very limited number of tools and the vast majority should work on Python 3 without a change.
GenomeSpace¶
The GenomeSpace project has ended on November 15, 2019 due to expiration of its NHGRI funding. Therefore the GenomeSpace Importer and Exporter Galaxy tools are hereby deprecated and will be removed in 20.01.
Release Notes¶
Enhancements¶
Add InteractiveTools. Pull Request 7494, Pull Request 8506, Pull Request 8574, Pull Request 8589
Implement workflow invocation reports. Pull Request 8543, Pull Request 8664, Pull Request 8683
VueJS rewrite of Toolshed install interface - with substantial API extensions to enable this. Pull Request 7402, Pull Request 8090, Pull Request 8621, Pull Request 8635, Pull Request 8681, Pull Request 7825 Pull Request 8638, Pull Request 8035, Pull Request 8076, Pull Request 8585, Pull Request 8622
VueJS rewrite of admin jobs page (thanks to @scrathat). Pull Request 7790
VueJS rewrite of tools panel (resolves #8262) (thanks to @inkuzmin). Pull Request 8368
VueJS rewrite of dataset job properties tables - with API extensions to enable this. Pull Request 8022, Pull Request 8044
VueJS rewrite of Page management components - with API extensions to enable this. Pull Request 8047
New visualization - free style image annotation (thanks to @anuprulez). Pull Request 6891
New visualization - OpenLayers maps. (thanks to @anuprulez). Pull Request 7888
New visualization - hyphy-vision (thanks to @veg). Pull Request 8227
Implement frameworks for datatype validation and tool-based QC. Pull Request 7913
New Pulsar runner for Kubernetes allowing file staging with Kubernetes. Pull Request 7835, Pull Request 8195
Implement option to delete or preserve Kubernetes pods after completion (thanks to @nuwang). Pull Request 8091
Implement
walltime_limit
option for the Kuberentes jobs (thanks to @telukir). Pull Request 8311Implement UI for Authnz API. Pull Request 7665
Extend dataset search and add search API endpoint (thanks to @mvdbeek). Pull Request 7745
Add Matthias Bernt to the committers group. Pull Request 8446
Add filtering and sorting for folders in data libraries (with help from @bwlang). Pull Request 8281, Pull Request 8287, Pull Request 8277
Implement
xref
tag on the tool structure (with visualization) (thanks to @ValentinMarcon). Pull Request 7905Substantial progress toward refactoring and decomposing Galaxy into properly installable packages. (with help from @dglaetzer, @nsoranzo and @gmauro). Pull Request 921, Pull Request 7992, Pull Request 8114, Pull Request 8234, Pull Request 8241, Pull Request 8266, Pull Request 8276, Pull Request 8284, Pull Request 8293, Pull Request 8306, Pull Request 8305, Pull Request 8307, Pull Request 8308, Pull Request 7971, Pull Request 8051, Pull Request 8062, Pull Request 8280, Pull Request 8310, Pull Request 8302, Pull Request 8298, Pull Request 8098, Pull Request 8208, Pull Request 8235, Pull Request 8365, Pull Request 8357, Pull Request 8342, Pull Request 8345, Pull Request 8431, Pull Request 8269, Pull Request 8314, Pull Request 8687, Pull Request 8702, Pull Request 8610, Pull Request 8315
Enable dynamic reloading of select config options. Pull Request 8475
Improved architecture for Galaxy’s configuration object Pull Request 8502, Pull Request 8526, Pull Request 8462, Pull Request 8433, Pull Request 8545
Allow YAML/JSON job configuration - including embedding right in Galaxy config, validation, better defaults, and better section naming. Pull Request 7854, Pull Request 8616, Pull Request 7882 Pull Request 8609
Allow declaring dependency resolvers right in Galaxy config, validation, and serialization. Pull Request 8118, Pull Request 8152
Add external display application plugin for iCn3D. Pull Request 8347
Enable external display application plugin parameters to declare
allow_cors="true"
. Pull Request 8539Add XML Schema Definition (XSD) for Galaxy External Dispaly Applications (GEDAs). Pull Request 8461
Adding Shapefile composite datatype (thanks to @Alanamosse). Pull Request 7615
Add mcool datatype and extend h5 tool output testing (thanks to @msauria). Pull Request 7993
Add hyphy_results.json datatype (thanks to @veg). Pull Request 8186
Add pgp and osw datatypes as used in OpenSWATH experiments (thanks to @bgruening). Pull Request 8458
Add ckpt datatype (thanks to @astrovsky01). Pull Request 8086
Add dada2 datatypes (thanks to @bernt-matthias). Pull Request 7895
Add rDock active site datatype (thanks to @bgruening). Pull Request 8727
Add Kallistobus datatypes (thanks to @astrovsky01). Pull Request 8229
Sniff fastqsanger more aggressively (thanks to @wm75). Pull Request 8322
Various collection operation tool improvements (thanks to @mvdbeek). Pull Request 8038
Enhance unzip/zip collection collection operation to annotate output format properly (thanks to @bernt-matthias). Pull Request 8239
Implement option to strip whitespace from tool
environment_variables
. Pull Request 8296Add tool output test assertion for
n_lines
(thanks to @bgruening). Pull Request 8440Add zoom reset feature for workflows (thanks to @juleengraham). Pull Request 8301
Fix tool run output to display more data. Pull Request 8018
Track basename at the time of creation for datasets. Pull Request 7670
Remove GFF headers during conversion (backported to 19.05). Pull Request 7808
Enable mulled containers by default for 19.09. Pull Request 8569
Enhanced GitLab integration (thanks to @selten). Pull Request 8455, Issue #8183
Make admin users grid filter on purged Pull Request 8303
Add links to admin entry page. Pull Request 8351
Add ELIXIR OIDC backend, upgrade social-auth-core requirement version (thanks to @kidanem). Pull Request 7852
Run futurize for python2 cheetah templates, fix scope issue for Python 3 comprehensions (thanks to @mvdbeek). Pull Request 7867
Improve look and feel for data libraries (thanks to @inkuzmin). Pull Request 7878
Raise detailed exception for broken citation (thanks to @nsoranzo). Pull Request 7891
Remove
file
attribute of bibtex citation (thanks to @nsoranzo). Pull Request 7911Use transparent background in default welcome page. Pull Request 7929
Cellxgene GIE - use API to get datasets. Pull Request 7945
Change “username” to “public name” throughout the user interface. Pull Request 8009
History menu (cog) UI updates. Pull Request 8024
Delegate config file watching to single handler (thanks to @mvdbeek). Pull Request 8078
Allow admins to disable the visualizations tab in the masthead. Pull Request 8450
Update all Python dependencies (thanks to @nsoranzo). Pull Request 8120, Pull Request 8126
Enable authorization to Google Cloud Platform Pull Request 8123
Update requirements and use pyuwsgi (thanks to @mvdbeek). Pull Request 8489
Update
cloudauthz
dependency to v0.4.0. Pull Request 8155Improve accessibility of certain UI elements. Pull Request 8133
Round-off the time taken for CPU execution (thanks to @janani-prasad). Pull Request 8144
Add API to tag library datasets (thanks to @abretaud). Pull Request 8530
Improve API docs. Pull Request 8541
Update repository issue handling text in docs. Pull Request 8542
Improved tool parameter error reporting (thanks to @bernt-matthias). Pull Request 8163
Configuration API cleanup. Pull Request 8206
New regular expression filter, and efficient sort filter (thanks to @bernt-matthias). Pull Request 8211
Data managers - allow removal of entries (thanks to @selten). Pull Request 8250, Pull Request 8503
Adjust minimum tag length. Pull Request 8256
Some improvements to tool menu styles. Pull Request 8285
Make styleguide work for VueJS components. Pull Request 8291
Library date propagate (thanks to @bwlang). Pull Request 8294
Skip database migrations on entirely clean new databases (thanks to @mvdbeek). Pull Request 8300
Implement undelete and purge API for users (thanks to @cganote). Pull Request 8309
Use lowercase true/false in config_schema.yml (thanks to @nsoranzo). Pull Request 8319
Check correct permission for allowing a user to modify lib folder (thanks to @scholtalbers). Pull Request 8326
Issue`#8105 <https://github.com/galaxyproject/galaxy/issues/8105>`__: Make tool favourite query a toggle (thanks to @janani-prasad). Pull Request 8331
Update anchor tags and enhance navigation cues for screen readers Pull Request 8334
Better config isolation for integration tests. Pull Request 8355
catch exceptions occuring in expression validators (thanks to @bernt-matthias). Pull Request 8359
Update RST files to reflect code structure changes. Pull Request 8363
make cleanup script use logging instead of print (thanks to @bernt-matthias). Pull Request 8394
Mention IGB in the docs Pull Request 8404
Automatically replace dashes by underscores for
argument
attribute on tool parameters. (thanks to @bernt-matthias). Pull Request 8409Add basic unit test for lint_inputs (thanks to @mvdbeek). Pull Request 8410
Various improvements designed to optimize ToolBox loading time. Pull Request 8421, Pull Request 8422, Pull Request 8426
Fix authentication provider exception not logged (thanks to @BioinformaticsPlatformWIV-ISP). Pull Request 8424
Optimize unrestricted library dataset permission checks. Pull Request 8430
Change ‘a when tag has not been defined for’ level to debug (thanks to @mvdbeek). Pull Request 8439
Fix database migrations for MySQL but mention it is unsupported in the docs (thanks to @nsoranzo). Pull Request 8407, Pull Request 8640, Pull Request 8473
Auto convert python 2 code files using 2to3 (thanks to @mvdbeek). Pull Request 8499
Update sass version to support node 12. Pull Request 8507
Integration test for
outputs_to_working_directory
with Pulsar. Pull Request 8335Fix ‘postgres’ dialect name has been renamed to ‘postgresql’ deprecat… (thanks to @mvdbeek). Pull Request 7804
Use
markupsafe.escape
instead ofcgi.escape
(thanks to @mvdbeek). Pull Request 7837Use
getfullargspec
on Python 3 (thanks to @mvdbeek). Pull Request 7838Align popup/dropdown menu templating. Pull Request 7871
Change keyboard input for floats and switch to ES6 features Pull Request 7927
Tool output_checker - fix superficial condition (thanks to @bernt-matthias). Pull Request 7980
Enhance
galaxy.js
and entry folder for ES6. Pull Request 8025, Pull Request 8034Switch
var
tolet
andconst
for VueJS components Pull Request 8028, Pull Request 8036es6 upgrades in entry folder
Remove unresolved function causing console error. Pull Request 8101
Swap out
galaxy.util.odict
for core pythoncollections.OrderedDict
objects. Pull Request 8104Enhance
make config-rebuild
to update config/docs. Pull Request 8220Refactor
setup_user_get_key
method to return the created test user and its API key. Pull Request 8233Fix various small UI issues. Pull Request 8275
Replace in-python quota calc with a SQL query (thanks to @erasche). Pull Request 8452
Remove deprecated scripts (thanks to @erasche). Pull Request 8465
Fix markup in ToolEntryPoints, format client Pull Request 8549
Allow specifying
maxseconds
inverify_tool
(thanks to @mvdbeek). Pull Request 7828Call tool_script.sh with shell (thanks to @mvdbeek). Pull Request 8077
Drop “Manage” from admin workflow Invocation link. Pull Request 8693
Record Galaxy version a job is created with. Pull Request 8414
Git ignore files in
database/shed_tools
directory (thanks to @ashvark). Pull Request 8268Added unit testing section to the client README Pull Request 7890
Update Sphinx RST files for
lib/
. Pull Request 8270Allow re-populating objectstore from
to_dict
form. Pull Request 8213Testing framework fixes (thanks to @nsoranzo). Pull Request 8147
Extend ObjectStore integration tests. Pull Request 8042
Fix link formats for mulled_containers.rst, minor rewording. Pull Request 8075
Add missing files from galaxy-lib (thanks to @nsoranzo). Pull Request 8113
Fixes¶
Add file extensions when downloading from data libraries (thanks to @selten). Pull Request 8456
Fix tool
assert_command
tag test not executed (thanks to @bernt-matthias). Pull Request 7730Fix inconsistent defaults for cleanup scripts - fixing #975 (thanks to @erasche). Pull Request 8470
Allow missing H5 groups in Loom files (thanks to @nsoranzo). Pull Request 8560
Document undocumented
workflow_schedulers_config_file
(thanks to @erasche). Pull Request 8437Use bootstrap classes to fix form css issue. Pull Request 8371
Fix Pulsar job files API to allow transferring directory content. Pull Request 8124
Fix gops_intersect_1 importing galaxy (thanks to @mvdbeek). Pull Request 7805
Quit gsummary script with non-zero exit code upon error (thanks to @mvdbeek). Pull Request 8214
Sort Collection - add missing when tags (thanks to @bernt-matthias). Pull Request 8366
Remove gops from venv list (thanks to @bgruening). Pull Request 8492
Don’t let
parameter_input
steps be workflow outputs (thanks to @mvdbeek). Pull Request 7799Fix column assign bug (thanks to @mvdbeek). Pull Request 8023
Quick hack to allow delayed invocations followed by step that consumes an input parameter (thanks to @mvdbeek). Pull Request 8249
Expression tool fix - include workdir path when reading env var from file (thanks to @mvdbeek). Pull Request 8253
Fix workflow tags lost on save (thanks to @mvdbeek). Pull Request 8398
Fix failure in resubmitting job more than once (thanks to @pcm32). Pull Request 7832
Add file missing from #7694 Pull Request 7873
Strip unicode control characters from TEXT before entering the database (thanks to @mvdbeek). Pull Request 7889
Fix Kubernetes test for job I/O separation. Pull Request 7892
In output_checker, fixed wrong comparison. (thanks to @bernt-matthias). Pull Request 7966
Fix typo grap -> grab. Pull Request 8061
Fix wording for pod retries while maintaining backward compatibility (thanks to @nuwang). Pull Request 8082
Kubernetes / CLI runner integration test fixes (thanks to @mvdbeek). Pull Request 8154
Fail job if queueing job fails (thanks to @mvdbeek). Pull Request 8161
Fix job wrapper fail for queued jobs (thanks to @mvdbeek). Pull Request 8179
Fix failure to fail job when tool is unavailable (thanks to @mvdbeek). Pull Request 8181
Fix external_metadata_set_successfully when metadata file doesn’t exist (thanks to @mvdbeek). Pull Request 8182
Fix portable metadata datatypes config. Pull Request 8207
Fix cancelling jobs with a message from the admin panel (thanks to @mvdbeek). Pull Request 8231
Fix Kubernetes runner on Python 3 (thanks to @mvdbeek). Pull Request 8321
Fix univa runner check for drmaa python module (thanks to @bernt-matthias). Pull Request 8385
Fix memory statement for drmaa (SGE/UNIVA) (thanks to @bernt-matthias). Pull Request 8451
Fix setting metadata externally (thanks to @mvdbeek). Pull Request 8497
Fix Pulsar version checking logic. Pull Request 8524
Hack to fix Pulsar for containerized jobs. Pull Request 8533
Improve and refactor process group handling in the local job runners (thanks to @nsoranzo). Pull Request 8538
Fix container property parsing for Singularity. Pull Request 8614
Data Manager interface - fix to use standard card header styles without extra markup. Pull Request 7811
Allow looking up tool section using label (thanks to @mvdbeek). Pull Request 8225
Backport tool shed and data manager fixes (thanks to @mvdbeek).
Create repository clone path if it doesn’t exist. Pull Request 7770
Remove unused requirejs imports from templates. Pull Request 7810
Small bugfix to GRT for ancient data, deprecated params table (thanks to @erasche). Pull Request 7830
Fix help text in ftp-uploader dialog. Pull Request 7908
Update instructions on conda upgrade (thanks to @nsoranzo). Pull Request 7918
Remove view button, fix library flag in data dialog. Pull Request 7935
Fix non-eager object store with nested object stores (thanks to @mvdbeek). Pull Request 7939
Fix extra newlines in peek code. Pull Request 7952
Fix populators.py workflow testing for non-text inputs. Pull Request 7953
Only show colon when a port exists in URL. Pull Request 7985
Remove href from a tag to prevent backbone page reload and change sometimes. Pull Request 7991
Various datatype I/O fixes (thanks to @mvdbeek). Pull Request 7995
Don’t close popup menu if header item is clicked. Pull Request 8001
Refactor comments in sample object stores to remove nested comments. (thanks to @simpsonw). Pull Request 8016
Fix Selenium DatasetPopulator for more interesting uploads. Pull Request 8046
Fix
stream_to_open_named_file
for non-utf8 text (backported to 19.05) (thanks to @mvdbeek). Pull Request 8050Small testing Dockerfile fixes (thanks to @nsoranzo). Pull Request 8094
Report a lint error if a citation is empty (thanks to @nsoranzo). Pull Request 8112
Ensure
DEFAULT_TOOL_TEST_WAIT
is an integer (thanks to @mvdbeek). Pull Request 8136Fix for tool test data in sub directories (thanks to @bernt-matthias). Pull Request 8162
Increase default font size to 0.85rem. Unify default welcome page fonts. Pull Request 8168
Use
IdEncodingHelper
to encode/decode user ids (thanks to @nsoranzo). Pull Request 8201Fix prefix usage in history copy dialog. Pull Request 8205
Fix UnicodeEncodeError when verifying test results (thanks to @mvdbeek). Pull Request 8221
Fix migration if
WorkflowStepConnection
index not present (thanks to @mvdbeek). Pull Request 8247Fix regex rule count (thanks to @mvdbeek). Pull Request 8254
Fix and unify search bar handling. Pull Request 8257
Typo fix comunity -> community (thanks to @yochannah). Pull Request 8267
Fix typo in run_tests.sh help text. Pull Request 8289
Don’t show the pip progress bar when installing under CI Pull Request 8290
Use temporary file for sniff tests (thanks to @nsoranzo). Pull Request 8304
Adjustments for panel spacing changes Pull Request 8316
Restore docs building (thanks to @nsoranzo). Pull Request 8323
Updates interactor to not ignore numbers in user email address Pull Request 8324
Test removing uwsgi weird python package from circleci Pull Request 8337
Fix use of
PIP_PROGRESS_BAR
env variable (thanks to @nsoranzo). Pull Request 8343Startup fixes (thanks to @nsoranzo). Pull Request 8346
Fix default involucro path (thanks to @mvdbeek). Pull Request 8360
Fix autodetection of zip file format (including xlsx) (thanks to @wm75). Pull Request 8362
Hide references card if array is empty. Pull Request 8373
Fix exception thrown with invalid session key (thanks to @mvdbeek). Pull Request 8377
Better isolation of embedded Pulsar tests. Pull Request 8386
Fix absolutely positioned elements and children from displaying off-screen. Pull Request 8466
Don’t cleanup integration tests twice. Pull Request 8468
Try separate amqp connection from database for integration testing. Pull Request 8469
Fix for NodeJS executable being called
nodejs
in Conda. (thanks to @bgruening). Pull Request 8474Fix startup checks when using a Conda env (thanks to @nsoranzo). Pull Request 8477
Use default backdrop color for modals. Pull Request 8479
Fix shed_tool_conf isolated tool (not in section) removal Pull Request 8485
Do not warn for not configured
user_preferences_extra_conf_path
(thanks to @nsoranzo). Pull Request 8494Use default background for scratchbook. Pull Request 8527
Explicitly declare
expression
assql.text
. Pull Request 8544Update
calculate_or_set_disk_usage
to support sqlite (thanks to @qiagu). Pull Request 8552Fix menu option classes (and thus event bindings) for histories in th… Pull Request 8575
Modify tool panel section text color, size and margin to improve readability. Pull Request 8579
Replaces tabs with spaces in apache.md (thanks to @nsoranzo). Pull Request 8590
Capture missing log messages Pull Request 8605
Regenerate ts search indexes in tmp directory. Pull Request 8611
Only schedule file watching if an observer exists (thanks to @mvdbeek). Pull Request 8629
Fix issue with xml comment handling on python 3 (thanks to @mvdbeek). Pull Request 8643
Fix tool JSON wrapper fail to wrap paths (thanks to @qiagu). Pull Request 8647
Bugfix - kill testing container when test script is killed. Pull Request 8679
Build dependency manager only for galaxy app (thanks to @nsoranzo). Pull Request 8696
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Thanks for using Galaxy!