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
- 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.
- 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.
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
Resolve Conda dependencies all at once to allow Conda to select compatible builds. Pull Request 3391
Implement dependency resolver mapping files. Pull Request 3444
Formalize decision to increase time between releases to four months. The next release will be 17.05. Pull Request 3271
Improve GG datatype sniffer to sniff fewer texts files as GG Pull Request 3233
Improve Tour URL routing in the client. Pull Request 3214
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
make chartsMakefile target to make it more obvious how to build these. Pull Request 3306
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
Fix SLURM job re-submission. Pull Request 3290
Fix to adjust masthead and tool search. Pull Request 3055
core.galaxy_ui.yamltour. Pull Request 3206
Fix tour URLs in welcome sample. Pull Request 3274
Fix logo image when serving Galaxy from a subdirectory. Pull Request 3283
Fix linting of
gff_filter_by_attributewrapper Python code. Pull Request 3324
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
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 UX problem when sharing objects with users. Pull Request 3373
Upgrade Python dependency six to 1.10.0. Pull Request 3471
Thanks for using Galaxy!