.. to_doc 17.01 =============================== .. announce_start Enhancements ------------------------------- * 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 ``repeat`` blocks (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 `__ from @bgruening. `Pull Request 3304`_ * Large cleanup of datatype converter tools (thanks to `@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 `__). `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`_ Fixes ------------------------------- * 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 ``structured_like`` tag over ``list:paired`` collections (thanks to `@mvdbeek `__). `Pull Request 3209`_ * Fix ``I201`` errors 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 ``.`` or ``_`` (thanks to `@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 `__). `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_attribute`` wrapper Python code. `Pull Request 3324`_ * Fix typo in assertion based testing (thanks to `@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 `__). `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 ``__class__`` attribute of ``SafeStringWrapper`` (thanks to `@nsoranzo `__). `Pull Request 3429`_ * Fix for determining Condor container id (thanks to `@bgruening `__). `Pull Request 3462`_ * Fix linting of ```` tags (thanks to `@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