.. to_doc ------------------------------- 15.05 ------------------------------- .. enhancements Enhancements ------------------------------- * Pluggable framework to custom authentication (including new LDAP/Active Directory integration). Thanks to many including Andrew Robinson, Nicola Soranzo, and David Trudgian. `Pull Request 1`_, `Pull Request 33`_, `Pull Request 51`_, `Pull Request 75`_, `Pull Request 98`_, `Pull Request 216`_ * Implement a new ``section`` tag for tool parameters. `Pull Request 35`_, `Trello `__ * New UI widgets allowing much more flexibility when creating simple dataset pair and list collections. `Pull Request 134`_, `Trello `__ * Improved JavaScript build system for client code and libraries (now using uglify_ and featuring `Source Maps`_). 72c876c_, 9a7f5fc_, 648a623_, 22f280f_, `Trello `__ * Add an `External Display Application`_ for viewing GFF/GTF files with IGV_. `Pull Request 70`_, `Trello `__ * Use TravisCI_ and Tox_ for continuous integration testing. `Pull Request 40`_, `Pull Request 62`_, `Pull Request 97`_, `Pull Request 99`_, `Pull Request 123`_, `Pull Request 222`_, `Pull Request 235`_, * Infrastructure for improved toolbox and Tool Shed searching. `Pull Request 9`_, `Pull Request 116`_, `Pull Request 142`_, `Pull Request 226`_, c2eb74c_, 2bf52fe_, ec549db_, `Trello `__, `Trello `__ * Enhance UI to allow renaming dataset collections. 21d1d6b_ * Improve highlighting of current/active content history panel. `Pull Request 126`_ * Improvements to UI and API for histories and collections. e36e51e_, 1e55206_, 0c79680_ * Update history dataset API to account for job re-submission. b4cf49a_ * Allow recalculating user disk usage from the admin interface. 964e081_ * Collect significantly more metadata for BAM files. `Pull Request 107`_, `Pull Request 108`_ * Implement ``detect_errors`` attribute on command of tool XML. `Pull Request 117`_ * Allow setting ``auto_format="True"`` on tool ``output`` tags. `Pull Request 130`_ * Allow testing tool outputs based on MD5 hashes. `Pull Request 125`_ * Improved Cheetah type casting for int/float values. `Pull Request 121`_ * Add option to pass arbitrary parameters to gem install as part of the tool shed ``setup_ruby_environment`` Tool Shed install action - thanks to Björn Grüning. `Pull Request 118`_ * Add ``argument`` attribute to tool parameters. `Pull Request 8`_ * Improve link and message that appears after workflows are run. `Pull Request 143`_ * Add NCBI SRA datatype - thanks to Matt Shirley. `Pull Request 87`_ * Stronger toolbox filtering. `Pull Request 119`_ * Allow updating Tool Shed repositories via the API - thanks to Eric Rasche. `Pull Request 30`_ * Expose category list in show call for Tool Shed repositories - thanks to Eric Rasche. `Pull Request 29`_ * Add API endpoint to create Tool Shed repositories. `Pull Request 2`_ * Do not configure Galaxy to use the test Tool Shed by default. `Pull Request 38`_ * Add fields and improve display of Tool Shed repositories. a24e206_, d6d61bc_, `Trello `__ * Enhance multi-selection widgets to allow key combinations ``Ctrl-A`` and ``Ctrl-X``. e8564d7_, `Trello `__ * New, consistent button for displaying citation BibTeX. `Pull Request 19`_ * Improved ``README`` reflecting move to Github - thanks in part to Eric Rasche. `PR #2 (old repo) `__, 226e826_, 2650d09_, 7d5dde8_ * Update application to use new logo. 2748f9d_, `Pull Request 187`_, `Pull Request 206`_ * Update many documentation links to use https sites - thanks to Nicola Soranzo. 8254cab_ * Sync report options config with ``galaxy.ini`` - thanks to Björn Grüning. `Pull Request 12`_ * Eliminate need to use API key to list tools via API. cd7abe8_ * Restore function necessary for splitting sequence datatypes - thanks to Roberto Alonso. `Pull Request 5`_ * Suppress filenames in SAM merge using ``egrep`` - thanks to Peter Cock and Roberto Alonso. `Pull Request 4`_ * Option to sort counts in ``Count1`` tool (``tools/filters/uniq.xml``) - thanks to Peter Cock. `Pull Request 16`_ * Preserve spaces in ``Count1`` tool (``tools/filters/uniq.xml``) - thanks to Peter Cock. `Pull Request 13`_ * `Interactive Environments`_ improvements and fixes from multiple developers including Eric Rasche and Björn Grüning. `Pull Request 69`_, `Pull Request 73`_, `Pull Request 131`_, `Pull Request 135`_, `Pull Request 152`_, `Pull Request 197`_ * Enable multi-part upload for exporting files with the GenomeSpace export tool. `Pull Request 74`_, `Trello `__ * Large refactoring, expansion, and increase in test coverage for "managers". `Pull Request 76`_ * Improved display of headers in tool help. 157eba6_, `Biostar `__ * Uniform configuration of "From" field for sent emails - thanks to Nicola Soranzo. `Pull Request 23`_ * Allow setting ``job_conf.xml`` params via environment variables & ``galaxy.ini``. dde2fc9_ * Allow a tool data table to declare that duplicate entries are not allowed. `Pull Request 245`_ * Add verbose test error flag option in run_tests.sh. 62f0495_ * Update ``.gitignore`` to include ``run_api_tests.html``. b52cc98_ * Add experimental options to run tests in Docker. e99adb5_ * Improve ``run_test.sh --help`` documentation to detail running specific tests. `Pull Request 86`_ * Remove older, redundant history tests. `Pull Request 120`_, `Trello `__ * Add test tool demonstrating citing a Github repository. 65def71_ * Add option to track all automated changes to the integrated tool panel. 10bb492_ * Make tool version explicit in all distribution tool - thanks to Peter Cock. `Pull Request 14`_. * Relocate the external metadata setting script. `Pull Request 7`_ * Parameterize script used to pull new builds from the UCSC Browser. e4e5df0_ * Enhance jobs and workflow logging to report timings. 06346a4_ * Add debug message for dynamic options exceptions. `Pull Request 91`_ * Remove demo sequencer app. 3af3bf5_ * Tweaks to the Pulsar's handling of async messages. `Pull Request 109`_ * Return more specific API authentication errors. 71a64ca_ * Upgrade Python dependency sqlalchemy to 1.0.0. d725aab_, `Pull Request 129`_ * Upgrade Python dependency amqp to 1.4.6. `Pull Request 128`_ * Upgrade Python dependency kombu to 3.0.24. `Pull Request 128`_ * Upgrade JavaScript dependency raven.js to 1.1.17. bcd1701_ .. fixes Fixes ------------------------------- * During the 15.05 development cycle dozens of fixes were pushed to the ``release_15.03`` branch of Galaxy. These are all included in 15.05 and summarized `here `__ (with special thanks to Björn Grüning and Marius van den Beek). * Fix race condition that would occasionally prevent Galaxy from starting properly. `Pull Request 198`_, `Trello `__ * Fix scatter plot API communications for certain proxied Galaxy instances - thanks to @yhoogstrate. `Pull Request 89`_ * Fix bug in collectl_ job metrics plugin - thanks to Carrie Ganote. `Pull Request 231`_ * Fix late validation of tool parameters. `Pull Request 115`_ * Fix ``fasta_to_tabular_converter.py`` (for implicit conversion) - thanks to Peter Cock. `Pull Request 11`_ * Fix to eliminate race condition by collecting extra files before declaring dataset's OK. `Pull Request 48`_ * Fix setting current history for certain proxied Galaxy instances - thanks to @wezen. 6946e46_. * Fix typo in tool failure testing example - thanks to Peter Cock. `Pull Request 18`_. * Fix Galaxy to default to using SSL for communicating with Tool Sheds. 0b037a2_ * Fix data source tools to open in ``_top`` window. `Pull Request 17`_ * Fix to fallback to name for tool parameters without labels. `Pull Request 189`_, `Trello `__ * Fix to remove redundant version ids in tool version selector. `Pull Request 244`_ * Fix for downloading metadata files. `Pull Request 234`_ * Fix for history failing to render if it contains more exotic dataset collection types. `Pull Request 196`_ * Fixes for BaseURLToolParameter. `Pull Request 247`_ * Fix to suppress pysam binary incompatibility warning when using datatypes in ``binary.py``. `Pull Request 252`_ * Fix for library UI duplication bug. `Pull Request 179`_ * Fix for `Backbone.js`_ loading as AMD_. 4e5218f_ * Other small Tool Shed fixes. 815f86f_, 76e0915_ * Fix file closing in ``lped_to_pbed_converter``. 182b67f_ * Fix undefined variables in Tool Shed ``add_repository_entry`` API script. 47e6f08_ * Fix user registration to respect use_panels when in the Galaxy app. 7ac8631_, `Trello `__ * Fix bug in scramble exception, incorrect reference to source_path 79d50d8_ * Fix error handling in ``pbed_to_lped``. 7aecd7a_ * Fix error handling in Tool Shed step handler for ``chmod`` action. 1454396_ * Fix ``__safe_string_wrapper`` in tool evaluation object_wrapper. ab6f13e_ * Fixes for data types and data providers. c1d2d1f_, 8da70bb_, 0b83b1e_ * Fixes for Tool Shed commit and mercurial handling modules. 6102edf_, b639bc0_, debea9d_ * Fix to clean working directory during job re-submission. `Pull Request 236`_ * Fix bug when task splitting jobs fail. `Pull Request 214`_ * Fix some minor typos in comment docs in ``config/galaxy.ini.sample``. `Pull Request 210`_ * Fix admin disk usage message. `Pull Request 205`_, `Trello `__ * Fix to sessionStorage Model to suppress QUOTA DOMExceptions when Safari users are in private browsing mode. 0c94f04_ .. _IGV: https://www.broadinstitute.org/igv/ .. _External Display Application: https://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial .. _Interactive Environments: https://galaxyproject.org/Admin/IEs .. _TravisCI: https://travis-ci.org/ .. _Tox: https://testrun.org/tox/latest/ .. _Source Maps: https://developer.chrome.com/devtools/docs/javascript-debugging#source-maps .. _uglify: https://developer.chrome.com/devtools/docs/javascript-debugging#source-maps .. _collectl: http://collectl.sourceforge.net/ .. _Backbone.js: http://backbonejs.org/ .. _AMD: http://requirejs.org/docs/whyamd.html .. github_links .. _Pull Request 129: https://github.com/galaxyproject/galaxy/pull/129 .. _Pull Request 128: https://github.com/galaxyproject/galaxy/pull/128 .. _Pull Request 2: https://github.com/galaxyproject/galaxy/pull/2 .. _Pull Request 247: https://github.com/galaxyproject/galaxy/pull/247 .. _Pull Request 252: https://github.com/galaxyproject/galaxy/pull/252 .. _Pull Request 245: https://github.com/galaxyproject/galaxy/pull/245 .. _Pull Request 244: https://github.com/galaxyproject/galaxy/pull/244 .. _Pull Request 236: https://github.com/galaxyproject/galaxy/pull/236 .. _Pull Request 235: https://github.com/galaxyproject/galaxy/pull/235 .. _Pull Request 222: https://github.com/galaxyproject/galaxy/pull/222 .. _Pull Request 234: https://github.com/galaxyproject/galaxy/pull/234 .. _Pull Request 231: https://github.com/galaxyproject/galaxy/pull/231 .. _Pull Request 226: https://github.com/galaxyproject/galaxy/pull/226 .. _Pull Request 216: https://github.com/galaxyproject/galaxy/pull/216 .. _Pull Request 215: https://github.com/galaxyproject/galaxy/pull/215 .. _Pull Request 214: https://github.com/galaxyproject/galaxy/pull/214 .. _Pull Request 198: https://github.com/galaxyproject/galaxy/pull/198 .. _Pull Request 210: https://github.com/galaxyproject/galaxy/pull/210 .. _Pull Request 206: https://github.com/galaxyproject/galaxy/pull/206 .. _Pull Request 205: https://github.com/galaxyproject/galaxy/pull/205 .. _Pull Request 197: https://github.com/galaxyproject/galaxy/pull/197 .. _Pull Request 196: https://github.com/galaxyproject/galaxy/pull/196 .. _Pull Request 189: https://github.com/galaxyproject/galaxy/pull/189 .. _Pull Request 187: https://github.com/galaxyproject/galaxy/pull/187 .. _Pull Request 179: https://github.com/galaxyproject/galaxy/pull/179 .. _Pull Request 153: https://github.com/galaxyproject/galaxy/pull/153 .. _Pull Request 152: https://github.com/galaxyproject/galaxy/pull/152 .. _5abb8ad: https://github.com/galaxyproject/galaxy/commit/5abb8ad .. _Pull Request 130: https://github.com/galaxyproject/galaxy/pull/130 .. _Pull Request 146: https://github.com/galaxyproject/galaxy/pull/146 .. _Pull Request 135: https://github.com/galaxyproject/galaxy/pull/135 .. _Pull Request 143: https://github.com/galaxyproject/galaxy/pull/143 .. _Pull Request 142: https://github.com/galaxyproject/galaxy/pull/142 .. _Pull Request 131: https://github.com/galaxyproject/galaxy/pull/131 .. _d725aab: https://github.com/galaxyproject/galaxy/commit/d725aab .. _Pull Request 126: https://github.com/galaxyproject/galaxy/pull/126 .. _e09761e: https://github.com/galaxyproject/galaxy/commit/e09761e .. _8d3c531: https://github.com/galaxyproject/galaxy/commit/8d3c531 .. _Pull Request 125: https://github.com/galaxyproject/galaxy/pull/125 .. _Pull Request 123: https://github.com/galaxyproject/galaxy/pull/123 .. _Pull Request 121: https://github.com/galaxyproject/galaxy/pull/121 .. _Pull Request 120: https://github.com/galaxyproject/galaxy/pull/120 .. _Pull Request 119: https://github.com/galaxyproject/galaxy/pull/119 .. _Pull Request 117: https://github.com/galaxyproject/galaxy/pull/117 .. _Pull Request 118: https://github.com/galaxyproject/galaxy/pull/118 .. _Pull Request 134: https://github.com/galaxyproject/galaxy/pull/134 .. _Pull Request 116: https://github.com/galaxyproject/galaxy/pull/116 .. _Pull Request 109: https://github.com/galaxyproject/galaxy/pull/109 .. _647cf55: https://github.com/galaxyproject/galaxy/commit/647cf55 .. _Pull Request 108: https://github.com/galaxyproject/galaxy/pull/108 .. _Pull Request 107: https://github.com/galaxyproject/galaxy/pull/107 .. _8254cab: https://github.com/galaxyproject/galaxy/commit/8254cab .. _Pull Request 99: https://github.com/galaxyproject/galaxy/pull/99 .. _Pull Request 98: https://github.com/galaxyproject/galaxy/pull/98 .. _Pull Request 115: https://github.com/galaxyproject/galaxy/pull/115 .. _Pull Request 97: https://github.com/galaxyproject/galaxy/pull/97 .. _Pull Request 91: https://github.com/galaxyproject/galaxy/pull/91 .. _Pull Request 89: https://github.com/galaxyproject/galaxy/pull/89 .. _Pull Request 86: https://github.com/galaxyproject/galaxy/pull/86 .. _Pull Request 87: https://github.com/galaxyproject/galaxy/pull/87 .. _Pull Request 73: https://github.com/galaxyproject/galaxy/pull/73 .. _Pull Request 74: https://github.com/galaxyproject/galaxy/pull/74 .. _Pull Request 75: https://github.com/galaxyproject/galaxy/pull/75 .. _Pull Request 70: https://github.com/galaxyproject/galaxy/pull/70 .. _Pull Request 69: https://github.com/galaxyproject/galaxy/pull/69 .. _Pull Request 62: https://github.com/galaxyproject/galaxy/pull/62 .. _Pull Request 51: https://github.com/galaxyproject/galaxy/pull/51 .. _Pull Request 76: https://github.com/galaxyproject/galaxy/pull/76 .. _2650d09: https://github.com/galaxyproject/galaxy/commit/2650d09 .. _7d5dde8: https://github.com/galaxyproject/galaxy/commit/7d5dde8 .. _2748f9d: https://github.com/galaxyproject/galaxy/commit/2748f9d .. _d6d61bc: https://github.com/galaxyproject/galaxy/commit/d6d61bc .. _815f86f: https://github.com/galaxyproject/galaxy/commit/815f86f .. _76e0915: https://github.com/galaxyproject/galaxy/commit/76e0915 .. _bce8171: https://github.com/galaxyproject/galaxy/commit/bce8171 .. _06346a4: https://github.com/galaxyproject/galaxy/commit/06346a4 .. _b4cf49a: https://github.com/galaxyproject/galaxy/commit/b4cf49a .. _Pull Request 40: https://github.com/galaxyproject/galaxy/pull/40 .. _Pull Request 38: https://github.com/galaxyproject/galaxy/pull/38 .. _a24e206: https://github.com/galaxyproject/galaxy/commit/a24e206 .. _Pull Request 35: https://github.com/galaxyproject/galaxy/pull/35 .. _e36e51e: https://github.com/galaxyproject/galaxy/commit/e36e51e .. _1e55206: https://github.com/galaxyproject/galaxy/commit/1e55206 .. _0c79680: https://github.com/galaxyproject/galaxy/commit/0c79680 .. _Pull Request 1: https://github.com/galaxyproject/galaxy/pull/1 .. _Pull Request 33: https://github.com/galaxyproject/galaxy/pull/33 .. _Pull Request 48: https://github.com/galaxyproject/galaxy/pull/48 .. _21d1d6b: https://github.com/galaxyproject/galaxy/commit/21d1d6b .. _Pull Request 30: https://github.com/galaxyproject/galaxy/pull/30 .. _Pull Request 29: https://github.com/galaxyproject/galaxy/pull/29 .. _c0e5509: https://github.com/galaxyproject/galaxy/commit/c0e5509 .. _157eba6: https://github.com/galaxyproject/galaxy/commit/157eba6 .. _72c876c: https://github.com/galaxyproject/galaxy/commit/72c876c .. _9a7f5fc: https://github.com/galaxyproject/galaxy/commit/9a7f5fc .. _648a623: https://github.com/galaxyproject/galaxy/commit/648a623 .. _59028c0: https://github.com/galaxyproject/galaxy/commit/59028c0 .. _bcd1701: https://github.com/galaxyproject/galaxy/commit/bcd1701 .. _22f280f: https://github.com/galaxyproject/galaxy/commit/22f280f .. _6946e46: https://github.com/galaxyproject/galaxy/commit/6946e46 .. _65def71: https://github.com/galaxyproject/galaxy/commit/65def71 .. _4e5218f: https://github.com/galaxyproject/galaxy/commit/4e5218f .. _Pull Request 16: https://github.com/galaxyproject/galaxy/pull/16 .. _Pull Request 13: https://github.com/galaxyproject/galaxy/pull/13 .. _e8564d7: https://github.com/galaxyproject/galaxy/commit/e8564d7 .. _Pull Request 23: https://github.com/galaxyproject/galaxy/pull/23 .. _Pull Request 22: https://github.com/galaxyproject/galaxy/pull/22 .. _10bb492: https://github.com/galaxyproject/galaxy/commit/10bb492 .. _Pull Request 19: https://github.com/galaxyproject/galaxy/pull/19 .. _Pull Request 18: https://github.com/galaxyproject/galaxy/pull/18 .. _0b037a2: https://github.com/galaxyproject/galaxy/commit/0b037a2 .. _Pull Request 17: https://github.com/galaxyproject/galaxy/pull/17 .. _b29a5e9: https://github.com/galaxyproject/galaxy/commit/b29a5e9 .. _Pull Request 14: https://github.com/galaxyproject/galaxy/pull/14 .. _7aecd7a: https://github.com/galaxyproject/galaxy/commit/7aecd7a .. _Pull Request 12: https://github.com/galaxyproject/galaxy/pull/12 .. _cd7abe8: https://github.com/galaxyproject/galaxy/commit/cd7abe8 .. _62f0495: https://github.com/galaxyproject/galaxy/commit/62f0495 .. _Pull Request 11: https://github.com/galaxyproject/galaxy/pull/11 .. _Pull Request 9: https://github.com/galaxyproject/galaxy/pull/9 .. _632ec4e: https://github.com/galaxyproject/galaxy/commit/632ec4e .. _Pull Request 8: https://github.com/galaxyproject/galaxy/pull/8 .. _Pull Request 7: https://github.com/galaxyproject/galaxy/pull/7 .. _b52cc98: https://github.com/galaxyproject/galaxy/commit/b52cc98 .. _1454396: https://github.com/galaxyproject/galaxy/commit/1454396 .. _8da70bb: https://github.com/galaxyproject/galaxy/commit/8da70bb .. _b639bc0: https://github.com/galaxyproject/galaxy/commit/b639bc0 .. _ab6f13e: https://github.com/galaxyproject/galaxy/commit/ab6f13e .. _debea9d: https://github.com/galaxyproject/galaxy/commit/debea9d .. _6102edf: https://github.com/galaxyproject/galaxy/commit/6102edf .. _c1d2d1f: https://github.com/galaxyproject/galaxy/commit/c1d2d1f .. _0b83b1e: https://github.com/galaxyproject/galaxy/commit/0b83b1e .. _216fb95: https://github.com/galaxyproject/galaxy/commit/216fb95 .. _182b67f: https://github.com/galaxyproject/galaxy/commit/182b67f .. _47e6f08: https://github.com/galaxyproject/galaxy/commit/47e6f08 .. _7ac8631: https://github.com/galaxyproject/galaxy/commit/7ac8631 .. _2bf52fe: https://github.com/galaxyproject/galaxy/commit/2bf52fe .. _e4e5df0: https://github.com/galaxyproject/galaxy/commit/e4e5df0 .. _6e17bf4: https://github.com/galaxyproject/galaxy/commit/6e17bf4 .. _0c94f04: https://github.com/galaxyproject/galaxy/commit/0c94f04 .. _Pull Request 1: https://github.com/galaxyproject/galaxy/pull/1 .. _ec549db: https://github.com/galaxyproject/galaxy/commit/ec549db .. _226e826: https://github.com/galaxyproject/galaxy/commit/226e826 .. _79d50d8: https://github.com/galaxyproject/galaxy/commit/79d50d8 .. _964e081: https://github.com/galaxyproject/galaxy/commit/964e081 .. _Pull Request 5: https://github.com/galaxyproject/galaxy/pull/5 .. _1f1bb29: https://github.com/galaxyproject/galaxy/commit/1f1bb29 .. _Pull Request 4: https://github.com/galaxyproject/galaxy/pull/4 .. _dde2fc9: https://github.com/galaxyproject/galaxy/commit/dde2fc9 .. _c2eb74c: https://github.com/galaxyproject/galaxy/commit/c2eb74c .. _71a64ca: https://github.com/galaxyproject/galaxy/commit/71a64ca .. _3af3bf5: https://github.com/galaxyproject/galaxy/commit/3af3bf5 .. _e99adb5: https://github.com/galaxyproject/galaxy/commit/e99adb5