galaxy/doc/source/releases/17.01.rst

.. to_doc

17.01
===============================

.. announce_start

Enhancements
-------------------------------

* Fuzzy search for tools search
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 3356`_
* Add cached dependency manager (was back-ported to 16.10 as well)
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3106`_
* Cache dependencies on the fly when first used
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 3348`_
* Fix Conda channel order
  (thanks to `@bgruening <https://github.com/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 <https://github.com/conda/conda/issues/4492>`__.
  `Pull Request 3419`_
* Use a newer conda version by default
  (thanks to `@bgruening <https://github.com/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 <https://github.com/mvdbeek>`__).
  `Pull Request 3222`_
* Various other dependency resolver fixes and improvements.
  (thanks to `@mvdbeek <https://github.com/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 <https://github.com/maxf130>`__).
  `Pull Request 3217`_
* Many improvements to the job information page - including
  exposing certain job metrics to non-admin users
  (thanks to `@hexylena <https://github.com/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 <https://github.com/hexylena>`__).
  `Pull Request 3423`_
* Extend API version information for Docker-based Galaxy instances
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 3411`_
* Implement a more complete Genbank datatype with sniffer
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3339`_
* Add additional image datatypes
  (thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__).
  `Pull Request 2679`_, `Pull Request 3380`_
* Add a DIAMOND database datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__ and `@bebatut <https://github.com/bebatut>`__).
  `Pull Request 3379`_
* Add ESTScan scores matrices (smat) datatype
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__
  with bug fix from `@nsoranzo <https://github.com/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 ``repeat`` blocks
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 3197`_
* Improve Tour URL routing in the client.
  `Pull Request 3214`_
* Assorted enhancements for the SLURM job runner
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3218`_
* Various Galaxy tool schema definition fixes (including adding
  EDAM topic(s) and operation(s) thanks to `@hmenager <https://github.com/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 <https://github.com/nsoranzo>`__).
  `Pull Request 3305`_
* Adds a ``make charts`` Makefile target to make it more obvious how to build
  these.
  `Pull Request 3306`_
* Implement IGV display for FASTA datatypes
  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
  `Pull Request 3327`_
* Add an option to specify the port when connecting clients to IEs.
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3328`_
* Allow admins to see API keys under when using remote user authentication from proxies.
  (thanks to `@hexylena <https://github.com/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`_

Fixes
-------------------------------

* Various fixes to escape variables in the client to prevent certain XSS attacks
  (thanks in large part to `@yhoogstrate <https://github.com/yhoogstrate>`__).
  `Pull Request 3403`_, `Pull Request 3416`_, `Pull Request 3448`_
* Fix import order and Python3 compatibility for lib/galaxy/tools/
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3431`_
* Fix SLURM job re-submission.
  `Pull Request 3290`_
* Dependency resolver documentation fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3490`_
* Fix directory existence checks in dependency resolver code
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3301`_
* Fix for mapping tools with paired collection input and a ``structured_like`` tag
  over ``list:paired`` collections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3209`_
* Fix ``I201`` errors from flake8-import-order
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3215`_
* Fix user table header in admin view
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3200`_
* Fix to adjust masthead and tool search.
  `Pull Request 3055`_
* Don't load tools from paths that start with ``.`` or ``_``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3201`_
* Fixes for ``core.galaxy_ui.yaml`` tour.
  `Pull Request 3206`_
* Small fixes to release management script ``bootstrap_history.py``
  (thanks to `@nsoranzo <https://github.com/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 <https://github.com/nsoranzo>`__
  and `@annefou <https://github.com/annefou>`__).
  `Pull Request 3333`_, `Pull Request 3294`_
* Fix linting of ``gff_filter_by_attribute`` wrapper Python code.
  `Pull Request 3324`_
* Fix typo in assertion based testing
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 3384`_
* Update ``UCSC_SERVERS`` list 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 <https://github.com/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 <https://github.com/manabuishii>`__).
  `Pull Request 3409`_
* Fix login functionality for RStudio IEs
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3414`_
* Fix accidental email exposure during history sharing
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3417`_
* Fix UX problem when sharing objects with users.
  `Pull Request 3373`_
* Do not wrap ``__class__`` attribute of ``SafeStringWrapper``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3429`_
* Fix for determining Condor container id
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3462`_
* Fix linting of ``<conditional>`` tags
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3464`_
* Upgrade Python dependency six to 1.10.0.
  `Pull Request 3471`_

.. github_links
.. _Pull Request 2679: https://github.com/galaxyproject/galaxy/pull/2679
.. _Pull Request 3055: https://github.com/galaxyproject/galaxy/pull/3055
.. _Pull Request 3106: https://github.com/galaxyproject/galaxy/pull/3106
.. _Pull Request 3118: https://github.com/galaxyproject/galaxy/pull/3118
.. _Pull Request 3145: https://github.com/galaxyproject/galaxy/pull/3145
.. _Pull Request 3185: https://github.com/galaxyproject/galaxy/pull/3185
.. _Pull Request 3189: https://github.com/galaxyproject/galaxy/pull/3189
.. _Pull Request 3190: https://github.com/galaxyproject/galaxy/pull/3190
.. _Pull Request 3192: https://github.com/galaxyproject/galaxy/pull/3192
.. _Pull Request 3197: https://github.com/galaxyproject/galaxy/pull/3197
.. _Pull Request 3200: https://github.com/galaxyproject/galaxy/pull/3200
.. _Pull Request 3201: https://github.com/galaxyproject/galaxy/pull/3201
.. _Pull Request 3206: https://github.com/galaxyproject/galaxy/pull/3206
.. _Pull Request 3209: https://github.com/galaxyproject/galaxy/pull/3209
.. _Pull Request 3214: https://github.com/galaxyproject/galaxy/pull/3214
.. _Pull Request 3215: https://github.com/galaxyproject/galaxy/pull/3215
.. _Pull Request 3216: https://github.com/galaxyproject/galaxy/pull/3216
.. _Pull Request 3217: https://github.com/galaxyproject/galaxy/pull/3217
.. _Pull Request 3218: https://github.com/galaxyproject/galaxy/pull/3218
.. _Pull Request 3221: https://github.com/galaxyproject/galaxy/pull/3221
.. _Pull Request 3222: https://github.com/galaxyproject/galaxy/pull/3222
.. _Pull Request 3223: https://github.com/galaxyproject/galaxy/pull/3223
.. _Pull Request 3228: https://github.com/galaxyproject/galaxy/pull/3228
.. _Pull Request 3230: https://github.com/galaxyproject/galaxy/pull/3230
.. _Pull Request 3233: https://github.com/galaxyproject/galaxy/pull/3233
.. _Pull Request 3237: https://github.com/galaxyproject/galaxy/pull/3237
.. _Pull Request 3239: https://github.com/galaxyproject/galaxy/pull/3239
.. _Pull Request 3240: https://github.com/galaxyproject/galaxy/pull/3240
.. _Pull Request 3253: https://github.com/galaxyproject/galaxy/pull/3253
.. _Pull Request 3256: https://github.com/galaxyproject/galaxy/pull/3256
.. _Pull Request 3258: https://github.com/galaxyproject/galaxy/pull/3258
.. _Pull Request 3264: https://github.com/galaxyproject/galaxy/pull/3264
.. _Pull Request 3271: https://github.com/galaxyproject/galaxy/pull/3271
.. _Pull Request 3274: https://github.com/galaxyproject/galaxy/pull/3274
.. _Pull Request 3283: https://github.com/galaxyproject/galaxy/pull/3283
.. _Pull Request 3285: https://github.com/galaxyproject/galaxy/pull/3285
.. _Pull Request 3286: https://github.com/galaxyproject/galaxy/pull/3286
.. _Pull Request 3288: https://github.com/galaxyproject/galaxy/pull/3288
.. _Pull Request 3290: https://github.com/galaxyproject/galaxy/pull/3290
.. _Pull Request 3291: https://github.com/galaxyproject/galaxy/pull/3291
.. _Pull Request 3294: https://github.com/galaxyproject/galaxy/pull/3294
.. _Pull Request 3301: https://github.com/galaxyproject/galaxy/pull/3301
.. _Pull Request 3304: https://github.com/galaxyproject/galaxy/pull/3304
.. _Pull Request 3305: https://github.com/galaxyproject/galaxy/pull/3305
.. _Pull Request 3306: https://github.com/galaxyproject/galaxy/pull/3306
.. _Pull Request 3313: https://github.com/galaxyproject/galaxy/pull/3313
.. _Pull Request 3319: https://github.com/galaxyproject/galaxy/pull/3319
.. _Pull Request 3324: https://github.com/galaxyproject/galaxy/pull/3324
.. _Pull Request 3325: https://github.com/galaxyproject/galaxy/pull/3325
.. _Pull Request 3327: https://github.com/galaxyproject/galaxy/pull/3327
.. _Pull Request 3328: https://github.com/galaxyproject/galaxy/pull/3328
.. _Pull Request 3333: https://github.com/galaxyproject/galaxy/pull/3333
.. _Pull Request 3338: https://github.com/galaxyproject/galaxy/pull/3338
.. _Pull Request 3339: https://github.com/galaxyproject/galaxy/pull/3339
.. _Pull Request 3340: https://github.com/galaxyproject/galaxy/pull/3340
.. _Pull Request 3342: https://github.com/galaxyproject/galaxy/pull/3342
.. _Pull Request 3344: https://github.com/galaxyproject/galaxy/pull/3344
.. _Pull Request 3345: https://github.com/galaxyproject/galaxy/pull/3345
.. _Pull Request 3346: https://github.com/galaxyproject/galaxy/pull/3346
.. _Pull Request 3348: https://github.com/galaxyproject/galaxy/pull/3348
.. _Pull Request 3349: https://github.com/galaxyproject/galaxy/pull/3349
.. _Pull Request 3356: https://github.com/galaxyproject/galaxy/pull/3356
.. _Pull Request 3358: https://github.com/galaxyproject/galaxy/pull/3358
.. _Pull Request 3362: https://github.com/galaxyproject/galaxy/pull/3362
.. _Pull Request 3364: https://github.com/galaxyproject/galaxy/pull/3364
.. _Pull Request 3365: https://github.com/galaxyproject/galaxy/pull/3365
.. _Pull Request 3367: https://github.com/galaxyproject/galaxy/pull/3367
.. _Pull Request 3368: https://github.com/galaxyproject/galaxy/pull/3368
.. _Pull Request 3369: https://github.com/galaxyproject/galaxy/pull/3369
.. _Pull Request 3370: https://github.com/galaxyproject/galaxy/pull/3370
.. _Pull Request 3371: https://github.com/galaxyproject/galaxy/pull/3371
.. _Pull Request 3373: https://github.com/galaxyproject/galaxy/pull/3373
.. _Pull Request 3377: https://github.com/galaxyproject/galaxy/pull/3377
.. _Pull Request 3378: https://github.com/galaxyproject/galaxy/pull/3378
.. _Pull Request 3379: https://github.com/galaxyproject/galaxy/pull/3379
.. _Pull Request 3380: https://github.com/galaxyproject/galaxy/pull/3380
.. _Pull Request 3381: https://github.com/galaxyproject/galaxy/pull/3381
.. _Pull Request 3384: https://github.com/galaxyproject/galaxy/pull/3384
.. _Pull Request 3387: https://github.com/galaxyproject/galaxy/pull/3387
.. _Pull Request 3391: https://github.com/galaxyproject/galaxy/pull/3391
.. _Pull Request 3395: https://github.com/galaxyproject/galaxy/pull/3395
.. _Pull Request 3397: https://github.com/galaxyproject/galaxy/pull/3397
.. _Pull Request 3400: https://github.com/galaxyproject/galaxy/pull/3400
.. _Pull Request 3401: https://github.com/galaxyproject/galaxy/pull/3401
.. _Pull Request 3403: https://github.com/galaxyproject/galaxy/pull/3403
.. _Pull Request 3404: https://github.com/galaxyproject/galaxy/pull/3404
.. _Pull Request 3405: https://github.com/galaxyproject/galaxy/pull/3405
.. _Pull Request 3406: https://github.com/galaxyproject/galaxy/pull/3406
.. _Pull Request 3409: https://github.com/galaxyproject/galaxy/pull/3409
.. _Pull Request 3411: https://github.com/galaxyproject/galaxy/pull/3411
.. _Pull Request 3412: https://github.com/galaxyproject/galaxy/pull/3412
.. _Pull Request 3414: https://github.com/galaxyproject/galaxy/pull/3414
.. _Pull Request 3416: https://github.com/galaxyproject/galaxy/pull/3416
.. _Pull Request 3417: https://github.com/galaxyproject/galaxy/pull/3417
.. _Pull Request 3419: https://github.com/galaxyproject/galaxy/pull/3419
.. _Pull Request 3423: https://github.com/galaxyproject/galaxy/pull/3423
.. _Pull Request 3427: https://github.com/galaxyproject/galaxy/pull/3427
.. _Pull Request 3429: https://github.com/galaxyproject/galaxy/pull/3429
.. _Pull Request 3431: https://github.com/galaxyproject/galaxy/pull/3431
.. _Pull Request 3439: https://github.com/galaxyproject/galaxy/pull/3439
.. _Pull Request 3444: https://github.com/galaxyproject/galaxy/pull/3444
.. _Pull Request 3447: https://github.com/galaxyproject/galaxy/pull/3447
.. _Pull Request 3448: https://github.com/galaxyproject/galaxy/pull/3448
.. _Pull Request 3454: https://github.com/galaxyproject/galaxy/pull/3454
.. _Pull Request 3461: https://github.com/galaxyproject/galaxy/pull/3461
.. _Pull Request 3462: https://github.com/galaxyproject/galaxy/pull/3462
.. _Pull Request 3464: https://github.com/galaxyproject/galaxy/pull/3464
.. _Pull Request 3470: https://github.com/galaxyproject/galaxy/pull/3470
.. _Pull Request 3471: https://github.com/galaxyproject/galaxy/pull/3471
.. _Pull Request 3475: https://github.com/galaxyproject/galaxy/pull/3475
.. _Pull Request 3476: https://github.com/galaxyproject/galaxy/pull/3476
.. _Pull Request 3482: https://github.com/galaxyproject/galaxy/pull/3482
.. _Pull Request 3483: https://github.com/galaxyproject/galaxy/pull/3483
.. _Pull Request 3490: https://github.com/galaxyproject/galaxy/pull/3490
.. _Pull Request 3510: https://github.com/galaxyproject/galaxy/pull/3510
.. _Pull Request 3514: https://github.com/galaxyproject/galaxy/pull/3514