January 2018 Galaxy Release (v 18.01)
Highlights
- Performance and User Experience Improvements
We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time. We achieved this by optimizing database queries, implementing cache, rethinking presentation, and adding progress bars and loading indicators where needed. See the list of related performance pull requests.
- Web Server and Configuration
The default web server used by Galaxy has changed from Paste to uWSGI and the default configuration file for Galaxy is now
config/galaxy.yml
instead ofconfig/galaxy.ini
. To minimize the impact of this change on existing Galaxy instances, if a Galaxy has agalaxy.ini
file configured, it will continue to use Paste by default unless additional steps are taken by the administrator. uWSGI is more production ready and allows Galaxy to scale better in its default configuration. Read more about the server, configuration, and documentation changes in the uWSGI details section of this document.- Dataset Collection Usability
This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements to collections have been made, some of the key highlights include:
Data library folders can now be sent to histories as a dataset collection. Pull Request 4998, Pull Request 5080
Failed dataset collection elements can now be fixed using job re-running (thanks to @mvdbeek). Pull Request 5321, Pull Request 5247, Pull Request 5270
Collections now appear with state and progress bars in the history panel and contained datasets are hidden by default (with help from @mvdbeek). Pull Request 5013, Pull Request 5078
We added intuitive workflow post job actions for dataset collections. Pull Request 5416, Pull Request 5418, Pull Request 5414
The web interface now supports collections with arbitrary nesting and size (with help from @mvdbeek). Pull Request 4942, Pull Request 4934, Pull Request 5091
More robust nametag discovery and propagation when using collections. Pull Request 5403
- Client Architecture
The architecture for the client code that powers the Galaxy user interface has been significantly overhauled. The code base has been converted to ES6, Yarn now powers the build and dependency management of the code, Prettier is now used to ensure consistent code formatting, and the VueJS framework has been integrated. Taken together, these changes are enabling Galaxy developers to write usable, responsive client code more quickly and concisely than previously possible. A big thanks goes out to community contributions from @anuprulez and @anatskiy that are already converting existing Galaxy components to reactive VueJS ones. See the list of related client pull requests.
- New BAM datatypes
Previously Galaxy only supported coordinate sorted BAM files by default (the
bam
datatype). In addition, this release of Galaxy now supports three new types of BAM:qname_sorted.bam
, that ensures that the file is queryname sorted (e.g.SO:queryname
);qname_input_sorted.bam
, that can be used to describe the output of aligners which generally keep mate pairs adjacentunsorted.bam
, that makes no assumptions about the sort order of the file.
A huge thanks goes out to @bgruening and @mvdbeek who implemented these datatypes.
Pull Request 5180, Pull Request 5589, Pull Request 5532, Pull Request 5644, Pull Request 5674
- Experimental Job Caching
Galaxy can now be configured to allow users the option of skipping duplicated jobs if one with identical parameters has been previously executed and simply reuse the previously generated outputs. This contribution is 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:
$ git clone -b release_18.01 https://github.com/galaxyproject/galaxy.git
- To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_18.01 && git pull --ff-only origin release_18.01
See the community hub for additional details regarding the source code locations.
Security
Unsecure GenomeSpace token exposure
Tracked as GX-2018-0002
.
We have found and fixed a medium-level security issue concering the GenomeSpace importer/exporter tools that were updated in the Galaxy release 17.09. These tools did not handle the GenomeSpace access token securely and stored it as a job parameter which made it accessible to anybody with access to the datasets created by these tools. This means that any user that used a GenomeSpace token to access these tools and subsequently shared the output dataset (or history that contains it) with another user shared their GenomeSpace token also.
These tools are both included in the tool_conf.xml.sample
and are therefore enabled on every new Galaxy by default.
Administrators please see the GenomeSpace security sanitization section of this document for the details on how to sanitize the tokens stored in the Galaxy database created prior to this fix.
The vulnerability has been resolved by removing the token functionality until a proper implementation is in place. The GenomeSpace tools continue to work using the OpenID authentication as before.
The fix for this issue has been applied back to Galaxy release 17.09 and can be found in this pull request.
Breaking Changes
We have reworked the Galaxy Webhook interface so if you have custom webhooks at your instance you need to take the following steps in order to make them work:
Rename the main config file: <name>.yml -> config.yml
In the config file, rename the name attribute: name -> id
Put all files into the plugin’s root folder, which should contain only four files:
config.yml
(mandatory),__init__.py
(optional),script.js
(optional),styles.css
(optional)
Deprecation Notices
This is the last release we are shipping JavaScript source maps for Galaxy client.
Removal Notices
The following features that have been deprecated in the past releases are being removed in 18.01:
Sample tracking
Sample request and external services management
Legacy library interface for Administrators
In addition to that, the PlantTribes datatypes have been commented out in the source code. Uncomment them if you want to re-enable it.
uWSGI details
Galaxy can be forced to start under uWSGI even with an older configuration file
by setting APP_WEBSERVER=uwsgi
in the environment. As part of the transition to YAML-based
configuration files, we have implemented a schema to validate Galaxy configuration files. Run
make config-validate
from Galaxy’s root directory to validate a schema and make config-lint
to
check for best practices. While there is no need to convert your configuration file (galaxy.ini
hasn’t
been deprecated), you can run make config-convert-dry-run
and make config-convert
to respectively test and perform the conversion of an ini
configuration file to a YAML one.
In the future uWSGI will allow Galaxy to setup GIE proxies without additional configuration and use modern web technologies such as web sockets.
These are big changes that affect many parts of Galaxy’s administration documentation and makes
this documentation very dependent on which Galaxy version they are targeting. To address this, we have
moved a significant amount of administration documentation into Galaxy’s code
base and made it available on a per-release basis. The latest administration documentation for
the previous release of Galaxy (17.09) which reference galaxy.ini
files and Paste servers can
be found here, while documentation for this release can be found here.
Pull Request 4475, Pull Request 5135, Pull Request 5390, Pull Request 5373, Pull Request 5105, Pull Request 5441
Release Notes
Enhancements
Add option to clone tool steps in the workflow editor (thanks to @anatskiy). Pull Request 5087, Pull Request 5124, Pull Request 5185
Implement a generic Cloud ObjectStore using multi-cloud support from cloudbridge (thanks to @VJalili). Pull Request 4487
Reload tools immediately if a macro changes (thanks to @mvdbeek). Pull Request 4635
Add an interactive environment for AskOmics a visual SPARQL query builder for RDF databases (thanks to @xgaia). Pull Request 4737
Implement a Github error report backend for (thanks to @hexylena). Pull Request 4765
Add maintenance script to simplify setting up a cleanup cron job (thanks to @scholtalbers). Pull Request 4916
Create the
$GALAXY_MEMORY_MB
job environment variable for tools. Pull Request 4958Improved home and temp directory handling for tools and jobs. Pull Request 5193
Tool-based annotation of out of memory errors. Pull Request 5196
Added support for recursively discovering output datasets (thanks to @nuwang). Pull Request 5240
Add an API endpoint that allows admins to decode galaxy object IDs. Pull Request 5018
Add sorting options for data library folders. Pull Request 4877
Add option to auto create
user_library_import_dir
directories upon user login. (thanks to @scholtalbers). Pull Request 5138Add option to check file permissions for the user library imports (thanks to @scholtalbers). Pull Request 5154
Add an admin form to pre-populate an LDAP user (thanks to @scholtalbers). Pull Request 5238
Add a CRAM to BAM datatype converter (thanks to @mvdbeek). Pull Request 4939
Add infernal-cm datatype (thanks to @mmiladi). Pull Request 4977
Add ICM datatype for glimmer (thanks to @abretaud). Pull Request 5042
Add Analyze75 datatype (thanks to @bgruening). Pull Request 4841
Add Classical linkage and haplotype datatypes (thanks to @mtekman). Pull Request 4894
Add ideaspre datatype (thanks to @gregvonkuster). Pull Request 5445
Add compressed fasta support. Pull Request 5561
Add
cool
datatype (thanks to @bgruening). Pull Request 5023Add neostore zip datatype (thanks to @zipho). Pull Request 4178
Add fast5_archive datatype (thanks to @jvolkening). Pull Request 4569
Add postgresql datatype (thanks to @bgruening). Pull Request 4730
Add IQtree datatypes (thanks to @mtekman). Pull Request 4849
Add Phylip datatype (thanks to @khillion). Pull Request 5301
Option to group Galaxy Tours for viewing clarity (thanks to @selten). Pull Request 4829
Allow users to upload multiple FTP files within a single request Pull Request 4513
Replaces the admin form builder grid and forms Pull Request 4480
Update pysam dependency to 0.14 and eliminate the need to have samtools on Galaxy’s
PATH
(with huge help from @mvdbeek) Pull Request 4497, Pull Request 5512, Pull Request 5037Expand and improve Selenium testing of the web UI (with help from @anatskiy). Pull Request 4543, Pull Request 4655, Pull Request 4676, Pull Request 4753, Pull Request 4732, Pull Request 4909, Pull Request 4935, Pull Request 4925, Pull Request 4687, Pull Request 4660, Pull Request 5333, Pull Request 5068, Pull Request 4757, Pull Request 4971, Pull Request 4653
Allow multiple simultaneous uploads via single POST. Pull Request 4563
Various bits of proactive security-related hardening (thanks to @hexylena). Pull Request 4604
Move test helper
wait_for_dataset_collection
for reuse (thanks to @mvdbeek). Pull Request 4658Extend job search for hdcas (thanks to @mvdbeek). Pull Request 4665
Add a custom
TRACE
log level for even more verbosity. Pull Request 4672Migrate various mako templates to modern JavaScript driven views. Pull Request 4681, Pull Request 4682, Pull Request 4711, Pull Request 4755, Pull Request 4661, Pull Request 4993, Pull Request 4664, Pull Request 4996, Pull Request 5014, Pull Request 4833, Pull Request 5212, Pull Request 5114
More HDCA copying tests, add option to copy HDAs into new history. Pull Request 5004
Use only latest publication in
CITATION
(thanks to @nsoranzo). Pull Request 4688Nicer logging message for sentry (thanks to @hexylena). Pull Request 4693
Use enumeration to provide history input index names. Pull Request 4700
Cleanup delayed action in
history-view.js
. Pull Request 4704Add logging during for script integrity exceptions (thanks to @hexylena). Pull Request 4720
Fix to respect
galaxy.json
supplied metadata for empty outputs. Pull Request 4722Update
reports.md
with a link to the community hub (thanks to @scholtalbers). Pull Request 4723Typo fixes and small cleanups (thanks to @nsoranzo). Pull Request 4725
Fix that implements stricter checks for SDF datatype sniffing (thanks to @nsoranzo). Pull Request 4729
When reloading the toolbox, use the existing dependency manager if possible (thanks to @mvdbeek). Pull Request 4739
Many more upload tests - big improvements to uploads will be coming to Galaxy 18.05. Pull Request 4746, Pull Request 4762, Pull Request 4790, Pull Request 4863, Pull Request 5266, Pull Request 5209
Kubernetes resources requests/limits support (thanks to @pcm32 and the @phnmnl project). Pull Request 4751
Send all influxdb stats to a single bucket (thanks to @hexylena). Pull Request 4758
PEP-8 fixes in random doctests. Pull Request 4764
Avoid circular import when determining max metadata value size. Pull Request 4770
Remove unused concept of dataset children. Pull Request 4771
Allow dataset attribute changes without refreshing the page. Pull Request 4779
Include check for updates to dependencies in tox, Makefile, Travis. Pull Request 4788
Add labels to selection options of the collection flattening tool. Pull Request 4791
Expose
state
,stdout
,stderr
,uuid
in the library API Pull Request 4839Significant improvements to client QUnit tests including new Karma based test driver. Pull Request 4855, Pull Request 5066, Pull Request 5063, Pull Request 5074
Remove tool reloading buttons and packaging endpoint, revise admin labels Pull Request 4866
Add various elements to the Tool XML doc page (thanks to @nsoranzo). Pull Request 4871
Absolute pins on linting dependencies. Pull Request 4876
Update various Galaxy requirements. Pull Request 4884
Updates and enhancements for the testing
Dockerfile
. Pull Request 4885, Pull Request 4879, Pull Request 4900Add nicer composite dataset names by default (thanks to @bgruening). Pull Request 4886
Improved initialization and isolation of Postgres databases used in integration testing. Pull Request 4887, Pull Request 4914
Rework dev dependencies to be Pipfile generated, locked, and hashed. Pull Request 4891
Install dev and regular dependencies at the same time. Pull Request 4903
More structured app shutdown. Pull Request 4910
Touch up issue labels in repository procedures document. Pull Request 4912
Improve error handling for incorrect datatype upload. Pull Request 4922
Activate mulled dependencies once per job (thanks to @nsoranzo). Pull Request 4945
Remove invalid user preferences beta (no longer a beta, always enabled) Pull Request 4957
Add
DELETE /api/jobs/<job_id>
as a job cancellation API endpoint. Pull Request 4961Kill off processes when stopping the local job runner. Pull Request 4962
Test both endpoints for collection creation in history contents API. Pull Request 4965
Add @flakey test annotation and “skip” them if the fail on Jenkins. Pull Request 4972
Include path in job script integrity errors (thanks to @nsoranzo). Pull Request 4991
Fix tox envlist to contain all envs that should pass (thanks to @nsoranzo). Pull Request 4992
Changes made while working on uWSGI mules that don’t belong in the mules PR Pull Request 4994
Add warning for sort-of-defunct workflow options in galaxy.ini. Pull Request 5002
Fix Python import order everywhere (thanks to @nsoranzo). Pull Request 4697, Pull Request 5005
dataset info: present decoded IDs for admins and add peek Pull Request 5006
Removed unneeded skip_install tags in tox.ini. Pull Request 5011
Add metric to the core plugin to collect $GALAXY_MEMORY_MB Pull Request 5016
Test renaming multiple different outputs in workflows. Pull Request 5017
Render arbitrarily nested lists in the UI Pull Request 5038
Expose proper element_identifier in tool action template expansions Pull Request 5049
Document fastest way to iterate on client & client tests together. Pull Request 5051
Support separate DSN for job sentry error reports (thanks to @hexylena). Pull Request 5056
Build endpoint separation Pull Request 5058
Remove
wchartype
dependency andis_multi_byte
attribute (thanks to @nsoranzo). Pull Request 5062, Pull Request 5088Implement multilingualization support on workflow page (thanks to @manabuishii). Pull Request 5077
Update Jupyter IE default image (thanks to @galaxyproject). Pull Request 5095
Determine dynamically if an extension corresponds to an unsniffable binary datatype (thanks to @nsoranzo). Pull Request 5109
Update to flake8-import-order 0.16 (thanks to @nsoranzo). Pull Request 4869, Pull Request 5110
Change the default to not add tags based on filename Pull Request 5115
Improve tool validation and metadata generation (thanks to @mvdbeek). Pull Request 5119
Download button fixes. Pull Request 5125
Datatype conversion check optimization (thanks to @nsoranzo). Pull Request 5137
Test resubmit for dynamic JobDestination structures. Pull Request 5139
Various dataset hashtag display improvements. Pull Request 5155
i18n improvements for French localization (thanks to @ValentinChCloud). Pull Request 5089, Pull Request 5157
Change hicexplorer image name (thanks to @bgruening). Pull Request 5177
Fix #3002 with update to newer version of virtualenv. (thanks to @selten). Pull Request 5202
Huge steps toward Python 3 compatiblity (thanks to @nsoranzo). Pull Request 5215, Pull Request 5221, Pull Request 5225, Pull Request 5228, Pull Request 5200, Pull Request 5199, Pull Request 4799, Pull Request 4811
Add chinese support (thanks to @istevenshen). Pull Request 5232
Make
pam
a conditional dependency (thanks to @nsoranzo). Pull Request 5251Update api quickstart doc to use default port, with a little bit of extra guidance. Pull Request 5260
Allow sorting collection elements based on file (thanks to @mvdbeek). Pull Request 5273
Add Biostar configuration options to the configuration sample file. Pull Request 5276
Update Japanese translation (thanks to @istevenshen). Pull Request 5288
Improve the migration message when having to downgrade the database (thanks to @mvdbeek). Pull Request 5299
Allow
message
attribute to be modified on a library dataset. Pull Request 5312Enforce a size constraint on the tag editor. Pull Request 5337
Various webhooks improvements. Pull Request 5342
Make
TabularToolDataTable._deduplicate_data()
faster (thanks to @nsoranzo). Pull Request 5383Add
--skip_flakey_fails
flag to CI script for API tests Pull Request 5455Fix for toolbox filters (thanks to @bgruening). Pull Request 5526
Fix missing job stdout/stderr on Pulsar transfer failures. Pull Request 5535
Optimization to fix repeated fetching dataset permissions in dynamic output collection. Pull Request 5578
Backport toolbox cache Pull Request 5583
Replace distutils.version with packaging.version (fixing lineage handling for freebayes among other things). Pull Request 5588
Move the cache from toolbox level to the tool level. Pull Request 5600
Removes Sample request and External services makos/controllers Pull Request 4526, Pull Request 4872, Pull Request 5103, Pull Request 5204
Remove unused abstraction layers from Visualizations Registry. Pull Request 4620
Visible keys standardization in model classes. Pull Request 4744
Remove legacy library interface Pull Request 4908
ES6 client/galaxy/scripts/utils/ajax-queue.js Pull Request 4933
Remove unused galaxy-side set_tool_version code (thanks to @mvdbeek). Pull Request 4986
Fix
allow-register
option inauth
module (thanks to @nsoranzo). Pull Request 4989Tried to fix issue with Conda environment building failing jobs that had to be rolled back. (thanks to @mvdbeek). Pull Request 5036, Pull Request 5470
Add packed symlink back pending a deprecation cycle. Pull Request 5094
Onload webhook toggles. Pull Request 5116
Re-organize edge case upload options for greater readability. Pull Request 5206
Refactor
upload.py
toward reuse. Pull Request 5229JavaScript router cleanup. Pull Request 5235
Comment PlantTribes datatypes (thanks to @gregvonkuster). Pull Request 5254
Dataset error interface cleanup. Pull Request 5279
Mention how to specify the config file location (thanks to @mvdbeek). Pull Request 5297
Uninstall a tool by default (vs. deactivating it). Pull Request 5300
Fixes
Allow mapping over collections when discovering dataset collections in tools (thanks to @mvdbeek). Pull Request 5413
Make liftover tool use data tables (thanks to @mvdbeek). Pull Request 4645
Pass job output file unqualified names to Pulsar so that it can create them before running the job. Pull Request 4662
Fix transiently failing saved histories due to success message disappearing. Pull Request 4669
Update CITATION file with 2016 paper (thanks to @mvdbeek). Pull Request 4686
Stop running common_startup.sh twice when starting from run.sh Pull Request 4759
Fix docstring linting. Pull Request 4766
Mothur.freq sniffer more stringent (thanks to @yhoogstrate). Pull Request 4781
MacOS X fix for a test tool. Pull Request 4806
Minor architecture slides fixes for typos/grammar. Pull Request 4822
Fix two invalid targets in dataset list item. Pull Request 4823
Fix double return in form-parameters. Pull Request 4826
Fix the case where ‘Labels’ in a docker node inspect exists but is null. Pull Request 4838
Fix all E722 errors and ignore E741 (thanks to @nsoranzo). Pull Request 4847
Fix jsutils time - fixes charts visualize. Pull Request 4852
Bugfix during error handling with linked files during upload (thanks to @ieguinoa). Pull Request 4858
Add a gulp plumber. Pull Request 4867
Minor admin panel fixes. Pull Request 4895
Fix list collection creator dragdrop event bindings. Pull Request 4901
Fix status handling for grids. Pull Request 4913
Fix revision selection during (beta) repository installation (thanks to @mvdbeek). Pull Request 4944
Fix Trackster styles bleeding into the app (the slightly off-center upload .icon buttons). Pull Request 4948
Fix multiple selections for grid operations redirecting to center panel. Pull Request 4951
Fix visualization link in import success message. Pull Request 4952
Fix up reports JavaScript. Pull Request 4967
Run
hg clone
in a subprocess instead of using the Mercurial API (thanks to @nsoranzo). Pull Request 4979Tolerate
IOError
in tool and data table watcher (thanks to @mvdbeek). Pull Request 4981Install numpy before bx-python in case you are installing from sdists Pull Request 4982
Specify
TagAssociation
class when copying a tag (thanks to @mvdbeek). Pull Request 4984Fix initialization of named ajax queue. Pull Request 4985
Encode file content with utf-8 (thanks to @mvdbeek). Pull Request 4987
Revert export to file. Pull Request 4988
Remove extraneous subclass for DMND datatype (thanks to @nsoranzo). Pull Request 4990
Fix to allow
get_history
calls withcreate=False
when evaluating workflows. Pull Request 4997Add missing
ipaddress
requirement (thanks to @nsoranzo). Pull Request 5000Use github instead of NCBI for problematic data manager test FASTA. Pull Request 5007
Fix for history contents API to remove the default flag override. Pull Request 5008
Fix to avoid visiting child inputs of invalid conditionals. Pull Request 5010
Fix for
parse_interpreter
- log a warning only if interpreter is set (thanks to @nsoranzo). Pull Request 5015Fix a few stray wiki links. Pull Request 5020
Workflow editor outputs fixes. Pull Request 5021
Fix workflow editor output attributes. Pull Request 5022
Metadata parameters rely on their own optional setting not on the field attribute. Pull Request 5027
A Python 3 fix for the gsummary tool (thanks to @bernt-matthias). Pull Request 5043
Cleanup SA objects between workflow invocation scheduling attempts. Pull Request 5045
Safely handle possible
None
value encountered in processing and execution of post-job action arguments (thanks to @hexylena). Pull Request 5050Restore admin form routes. Pull Request 5065
Fixes galaxy startup when
LC_TYPE=UTF-8
on OS X (thanks to @mvdbeek). Pull Request 5070Ignore
OSError
when chmod’ing integrated_tool_panel_conf.xml (thanks to @mvdbeek). Pull Request 5071Fix metadata setting for
otu
datatypes (thanks to @mvdbeek). Pull Request 5072Fix exception in admin panel (thanks to @mvdbeek). Pull Request 5079
Always fill
message
to avoidKeyError
for sentryERROR_TEMPLATE
(thanks to @mvdbeek). Pull Request 5086Attempt to make data manager integration test more robust. Pull Request 5098
Toolshed install stability improvements (thanks to @mvdbeek). Pull Request 5099
Fix Trackster link to custom builds view. Pull Request 5104
Improve resilience of filter detection, add error messages, fix identifiers. Pull Request 5106
Fix ICM datatype sniffer config (thanks to @mvdbeek). Pull Request 5121
Fix attribute error that was missed during refactor of sentry (thanks to @hexylena). Pull Request 5122
Fix connecting non-input modules to subworkflow inputs. Pull Request 5140
Fix for history copy. Pull Request 5144
Fixes for handling delayed steps within subworkflows. Pull Request 5145
Fix localization and build client. Pull Request 5156
Resolve broken link for “all workflows” (thanks to @mmiladi). Pull Request 5161
Fix workflow collection attachments. Pull Request 5166
Provide UI collection output information for subworkflows. Pull Request 5172
Remove legacy request controller from reports app. Pull Request 5182
Fixes genome decode handling. Pull Request 5198
Remove broken Yahoo OpenID support (thanks to @VJalili). Pull Request 5208
Force window jQuery access for charts. Pull Request 5210
Mark transiently failing
test_run_data
as flakey. Pull Request 5211Fail job if tools that use
galaxy.json
write to stderr (thanks to @mvdbeek). Pull Request 5217Allow shell plugins with different parameters to co-exist (thanks to @mvdbeek). Pull Request 5223
paster.pid/log to galaxy.pid/log reference update (thanks to @nsoranzo). Pull Request 5226
Refine Conda version numbers allowed for using
--offline
flag again (thanks to @NCEichner). Pull Request 5233Workflow list show-in-tool-panel callback bugfix. Pull Request 5234
Fix image proxy prefix in tool form. Pull Request 5237
Fix wrong tool id after switching versions (thanks to @mvdbeek). Pull Request 5249
Catch and display error when displaying broken BAM file (thanks to @mvdbeek). Pull Request 5253
Fix for getmicrobedata tool (thanks to @bernt-matthias). Pull Request 5258
Adjust note about nginx enabled sites configuration (thanks to @scholtalbers). Pull Request 5259
Mark the test
rerun_with_use_cached_job
as flakey (thanks to @mvdbeek). Pull Request 5286Fix dataset edit link. Pull Request 5289
Fix link to getgalaxy.org (thanks to @selten). Pull Request 5295
Fix tool report submission with sentry (thanks to @mvdbeek). Pull Request 5303
Fix
common_startup.sh
bash-isms (thanks to @nsoranzo). Pull Request 5304Fix Galaxy instance startup error (thanks to @bgruening). Pull Request 5306
Fix link to library from history structure view. Pull Request 5327
Prevent reloading when data table is being modified (thanks to @mvdbeek). Pull Request 5331
Work around (temporarily) wrong
getsize()
output (thanks to @mvdbeek). Pull Request 5335Disable galaxy tour ‘path’ navigation. Pull Request 5340
Fix
tool-shed-config-validate
Makefile
target. (thanks to @ValentinChCloud). Pull Request 5343History import fixes (thanks to @mvdbeek). Pull Request 5344
Fix dataset purging, dataset cleanup script and db_shell script (thanks to @mvdbeek). Pull Request 5346
Fix BAM conversion test tool (thanks to @mvdbeek). Pull Request 5351
Remove charlimit for fetching URLs. Pull Request 5353
Use
print()
function in common_startup.sh (thanks to @mvdbeek). Pull Request 5357Handle
None
in job owner in API (thanks to @hexylena). Pull Request 5358Fix form logic in deactivate or uninstall. Pull Request 5363
History multipanel fixes. Pull Request 5364
Remove additional checkbox workarounds. Pull Request 5367
Workflow tool menu fix for deleted workflows. Pull Request 5368
Bump conditional
Pygments
version to 2.2.0 so it matches the dev. Pull Request 5376Fix
make docs
when the virtualenv is not.venv
. Pull Request 5377Force a fixed node image version when building client for Jenkins. Pull Request 5382
Install latest Conda and don’t use
shell=True
(thanks to @nsoranzo). Pull Request 5397Fix for subworkflow creation (thanks to @mvdbeek). Pull Request 5398
Follow IUC and drop
r
channel from the default Conda channels (thanks to @mvdbeek). Pull Request 5406Implement workaround for extra metadata revision creation. Pull Request 5433
Don’t silently fail rest of multi-action queue when attempting to purge a collection. Pull Request 5443
Ensure
jobStateSummariesCollection
exists. Pull Request 5444Fix
server_name
when config is adict
. Pull Request 5447Fixes for workflow sharing links. Pull Request 5467
Fix workflow execution post action - rename (thanks to @scholtalbers). Pull Request 5485
Fix
common_startup.sh
for galaxy tarballs (thanks to @nsoranzo). Pull Request 5491Close
tempfile
handles. Pull Request 5506, Pull Request 5552Do not allow
codefiles
during tool shed tool loading. Pull Request 5510Fix for GenomeSpace importer/exporter (thanks to @nuwang). Pull Request 5528
Fix search overlay JS errors (thanks to @bgruening). Pull Request 5531
Allow LDAP options not starting with
OPT_
(thanks to @nsoranzo). Pull Request 5556Fix broken admin
create new user
whenregistration =='challenge'
(thanks to @scholtalbers). Pull Request 5569Do not remove external path files during library uploads (thanks to @nsoranzo). Pull Request 5573
Bump sqlite3 dependency for web proxy. Pull Request 5575
Fix small bam (header-only) infinite fetching. Pull Request 5579
Fix migration 0137’s downgrade. Pull Request 5605
Conda fix for commands using stdout redirection. Pull Request 5620
Move Extract genomic DNA 1 to list of versioned galaxy tools requiring galaxy to be importable (thanks to @mvdbeek). Pull Request 5626
Changed GenomeSpace token handling to use manual OpenID association only. Pull Request 5631
Use sample file path when adding missing indexes (thanks to @mvdbeek). Pull Request 5650
Fix exception if user preference value undefined (thanks to @mvdbeek). Pull Request 5662
Fix exception if email is not specified or email is wrong (thanks to @mvdbeek). Pull Request 5663
Show error message if user tries purging datasets (thanks to @mvdbeek). Pull Request 5664
Show error message if history structure can’t be shown (thanks to @mvdbeek). Pull Request 5665
Consistent sniffing regardless of in_place. Pull Request 5643
GenomeSpace security sanitization
Outputs of these tools may require sanitization: genomespace_importer
and genomespace_exporter
The following SQL commands will help you identify the datasets in your Galaxy’s database.
Finding bad GenomeSpace importer params:
SELECT j.id,
j.create_time,
j.user_id,
jp.value
FROM job_parameter jp
JOIN job j ON j.id = jp.job_id
WHERE jp.job_id IN
(SELECT id
FROM job
WHERE tool_id = 'genomespace_importer')
AND jp.name = 'URL'
AND jp.value LIKE '%^%'
ORDER BY j.id DESC;
Finding bad GenomeSpace exporter params:
SELECT j.id,
j.create_time,
j.user_id,
jp.value
FROM job_parameter jp
JOIN job j ON j.id = jp.job_id
WHERE jp.job_id IN
(SELECT id
FROM job
WHERE tool_id = 'genomespace_exporter')
AND jp.name = 'genomespace_browser'
AND jp.value LIKE '%^%'
ORDER BY j.id DESC;
The following SQL commands will help you sanitize the datasets in your Galaxy’s database.
Sanitizing GenomeSpace importer params:
UPDATE job_parameter jp
SET value = split_part(jp.value, '^', 1) || '"'
FROM job j
WHERE jp.job_id = j.id
AND j.tool_id = 'genomespace_importer'
AND jp.name = 'URL'
AND jp.value LIKE '%^%';
Sanitizing GenomeSpace exporter params:
UPDATE job_parameter jp
SET value = split_part(jp.value, '^', 1) || '"'
FROM job j
WHERE jp.job_id = j.id
AND j.tool_id = 'genomespace_exporter'
AND jp.name = 'genomespace_browser'
AND jp.value LIKE '%^%';
To stay up to date with Galaxy’s progress, watch our screencasts; visit our community Hub; and follow us on Bluesky, Mastodon, and LinkedIn.
You can always chat with us on Matrix.
Thanks for using Galaxy!