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January 2017 Galaxy Release (v 17.01)¶
- Conda auto initialization is enabled by default
After updating to 17.01 and upon starting Galaxy the Conda package manager will be installed automatically within the Galaxy’s workspace. This will enable your Galaxy to install tool dependencies from Conda channels such as BioConda. Such channels are already being used for new and updated tools by IUC and we suggest adopting this tool dependency resolution method to all tool developers instead of Tool Shed package recipes - which are now considered deprecated. Please see the details at the admin documentation.
- New interface for user preferences
User preferences menu has been reworked for clarity and consistency. Thanks to @anuprulez and @bgruening. Implemented in Pull Request 3118.
- Support for compressed FASTQ formats
You can now upload compressed (with gzip or bzip2) FASTQ files without them being unpacked automatically (as it was until now). For this to work you have to select the proper type when uploading (e.g. instead of
fastqsanger.bz2for compressed files). Existing tools will work as before and future tools will be able to consume archives and save space in your quota. Thanks to @abretaud, @ashvark, @jvolkening, and @mvdbeek. Implemented in Pull Request 3145, Pull Request 3510 and Pull Request 3514.
The code lives at Github and you should have Git to obtain it.
- To get a new Galaxy repository run:
$ git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git
- To update an existing Galaxy repository run:
$ git checkout release_17.01 && git pull --ff-only origin release_17.01
See our wiki for additional details regarding the source code locations.
Galaxy tools no longer have access to Galaxy’s core framework Python code during tool execution - see Pull Request 3364 for implementation details.
libdirectory would be placed on a tool’s PYTHONPATH - but this can cause different sorts of conflicts with resolved dependencies and should never really have been part of the interface exposed to tools since it makes both reproducibility and distribution of jobs difficult.
Unfortunately, there is a large number of Galaxy tools - both in the core distribution and in the Tool Shed - that depend on Galaxy internals. The ones we know about have been added to a whitelist as part of Pull Request 3364 and we will continue to add there if we find more. If you discover a tool that has problems importing e.g.
galaxy_utilsas a result of this release please let us know by creating an issue with a link to the Tool Shed page of the tool.
If you have local tools that depend on these modules and you do not wish to use a formal dependency resolution mechanism such as Conda, you can change the option
preserve_python_environmentin galaxy.ini from
Galaxy’s ‘repair repository’ feature for installed repositories is deprecated and will be removed/replaced in the next release - details.
Fuzzy search for tools search (thanks to @anuprulez). Pull Request 3356
Add cached dependency manager (was back-ported to 16.10 as well) (thanks to @mvdbeek). Pull Request 3106
Cache dependencies on the fly when first used (thanks to @abretaud). Pull Request 3348
Fix Conda channel order (thanks to @bgruening). Pull Request 3237
Target Miniconda3 for new Conda installs - existing Conda installs will be unaffected but new Conda installs will not be subject to Conda bugs in Miniconda2 such as conda/conda#4492. Pull Request 3419
Use a newer conda version by default (thanks to @bgruening). Pull Request 3378
Resolve Conda dependencies all at once to allow Conda to select compatible builds. Pull Request 3391
Implement dependency resolver mapping files. Pull Request 3444
Add API to install resolver tool dependencies (thanks to @mvdbeek). Pull Request 3222
Various other dependency resolver fixes and improvements. (thanks to @mvdbeek) Pull Request 3454, Pull Request 3461, Pull Request 3483, Pull Request 3482, Pull Request 3427
Enhanced support for failed job re-submission - allow specifying conditions for re-submission as well as improved support, documentation, and testing. Pull Request 3319, Pull Request 3291
Allow specification of a per user total walltime limit. (thanks to @maxf130). Pull Request 3217
Many improvements to the job information page - including exposing certain job metrics to non-admin users (thanks to @hexylena). Pull Request 3344, Pull Request 3256, Pull Request 3340
Formalize decision to increase time between releases to four months. The next release will be 17.05. Pull Request 3271
Add API endpoint to determine who the current user is (thanks to @hexylena). Pull Request 3423
Extend API version information for Docker-based Galaxy instances (thanks to @manabuishii). Pull Request 3411
Implement a more complete Genbank datatype with sniffer (thanks to @hexylena). Pull Request 3339
Add additional image datatypes (thanks to @ThomasWollmann). Pull Request 2679, Pull Request 3380
Add a DIAMOND database datatype (thanks to @bgruening and @bebatut). Pull Request 3379
Add ESTScan scores matrices (smat) datatype (thanks to @gregvonkuster with bug fix from @nsoranzo). Pull Request 3258, Pull Request 3475
Improve GG datatype sniffer to sniff fewer texts files as GG Pull Request 3233
Allow rename dataset post job actions to work on input parameters inside of
repeatblocks (thanks to @scholtalbers). Pull Request 3197
Improve Tour URL routing in the client. Pull Request 3214
Assorted enhancements for the SLURM job runner (thanks to @nsoranzo). Pull Request 3218
Various Galaxy tool schema definition fixes (including adding EDAM topic(s) and operation(s) thanks to @hmenager). Pull Request 3221, Pull Request 3216
Numerous improvements to the test framework including replacing broken CasperJS UI tests with newer Selenium based ones and expanded test coverage with a particular focus on web and integration testing. Pull Request 3285, Pull Request 3286, Pull Request 3291, Pull Request 3342, Pull Request 3367, Pull Request 3381, Pull Request 3239, Pull Request 3371, Pull Request 3190, Pull Request 3264, Pull Request 3288, Pull Request 3387, Pull Request 3400, Pull Request 3401, Pull Request 3228, Pull Request 3365, Pull Request 3368, Pull Request 3370, Pull Request 3482, Pull Request 3185
Bring in fix from galaxy-lib related to Biocontainers and mulled <https://github.com/galaxyproject/galaxy-lib/pull/36>`__ from @bgruening. Pull Request 3304
Large cleanup of datatype converter tools (thanks to @nsoranzo). Pull Request 3305
make chartsMakefile target to make it more obvious how to build these. Pull Request 3306
Implement IGV display for FASTA datatypes (thanks to @Delphine-L). Pull Request 3327
Add an option to specify the port when connecting clients to IEs. (thanks to @bgruening). Pull Request 3328
Allow admins to see API keys under when using remote user authentication from proxies. (thanks to @hexylena). Pull Request 3338
Limit adjusting Galaxy’s Python environment to legacy tools (discussed in Deprecation Notices section of release notes). Pull Request 3364
Workflow run display improvements in particular for data inputs. Pull Request 3369
Adjust menu tooltips to be one line each. Pull Request 3230
Various fixes to escape variables in the client to prevent certain XSS attacks (thanks in large part to @yhoogstrate). Pull Request 3403, Pull Request 3416, Pull Request 3448
Fix import order and Python3 compatibility for lib/galaxy/tools/ (thanks to @nsoranzo). Pull Request 3431
Fix SLURM job re-submission. Pull Request 3290
Dependency resolver documentation fixes (thanks to @nsoranzo). Pull Request 3490
Fix directory existence checks in dependency resolver code (thanks to @bgruening). Pull Request 3301
Fix for mapping tools with paired collection input and a
list:pairedcollections (thanks to @mvdbeek). Pull Request 3209
I201errors from flake8-import-order (thanks to @nsoranzo). Pull Request 3215
Fix user table header in admin view (thanks to @hexylena). Pull Request 3200
Fix to adjust masthead and tool search. Pull Request 3055
Don’t load tools from paths that start with
_(thanks to @mvdbeek). Pull Request 3201
core.galaxy_ui.yamltour. Pull Request 3206
Small fixes to release management script
bootstrap_history.py(thanks to @nsoranzo). Pull Request 3223
Fix tour URLs in welcome sample. Pull Request 3274
Fix logo image when serving Galaxy from a subdirectory. Pull Request 3283
Various fixes for transition from IPython to Jupyter (thanks to @nsoranzo and @annefou). Pull Request 3333, Pull Request 3294
Fix linting of
gff_filter_by_attributewrapper Python code. Pull Request 3324
Fix typo in assertion based testing (thanks to @pvanheus). Pull Request 3384
UCSC_SERVERSlist to include new(ish?) soe subdomain. Pull Request 3345
Fix explicit Docker container resolution (this was backported to 16.10). Pull Request 3346
Fix for connecting webhooks to masthead. (thanks to @anuprulez). Pull Request 3349
Remove seemingly unused file
sort_gtf.py. Pull Request 3362
Fix upload to respect explicit name override on pasted uploads. Pull Request 3377
Do not allow recursive replacements in PJA renames. Pull Request 3395
Fix logout link when using remote user authentication from proxies. Pull Request 3405
Fix typo in webhooks documentation (thanks to @manabuishii). Pull Request 3409
Fix login functionality for RStudio IEs (thanks to @hexylena). Pull Request 3414
Fix accidental email exposure during history sharing (thanks to @hexylena). Pull Request 3417
Fix UX problem when sharing objects with users. Pull Request 3373
Do not wrap
SafeStringWrapper(thanks to @nsoranzo). Pull Request 3429
Fix for determining Condor container id (thanks to @bgruening). Pull Request 3462
Fix linting of
<conditional>tags (thanks to @nsoranzo). Pull Request 3464
Upgrade Python dependency six to 1.10.0. Pull Request 3471
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You can always reach us on Gitter or IRC.
Thanks for using Galaxy!