.. to_doc ------------------------------- 15.07 ------------------------------- Enhancements ------------------------------- .. enhancements * Interactive environment (IE) framework updates including a new IE for RStudio. (Thanks to a team effort spearheaded by `@hexylena `__.) `Pull Request 229`_, `Pull Request 230`_ * Rework workflow editor to use newer tool form components and allow construction of workflows with tools explicitly producing output collections. `Pull Request 286`_, `Pull Request 328`_, `Pull Request 311`_, `Pull Request 397`_, `Pull Request 233`_, `Pull Request 625`_, `Pull Request 602`_ * Implement policies for committers and pull requests. `Pull Request 295`_, `Pull Request 314`_ * Allow exporting a library folder to a history. (Thanks to `@ericenns `__.) `Pull Request 426`_ * Fix and update documentation available on the ReadTheDocs with particular focus on the API documentation. (Thanks to `@nsoranzo `__.) `Pull Request 399`_, `Pull Request 405`_ * Add EDAM IDs to Galaxy datatypes. (Thanks to a team effort initiated by `@hexylena `__.) `Pull Request 80`_, `Pull Request 342`_ * Improved reports app sorting and bug fixes thanks to Daniel Bouchard (`@Airistotal `__). Even more reports enhancements will be included in the next release of Galaxy including new landing page, pagination, and sparkline graphs. `Pull Request 303`_, `Pull Request 330`_, `Pull Request 338`_ * Significant speedup of tool panel/homepage loading. (Thanks to `@abretaud `__.) `Pull Request 159`_ * Allow parameterization of tool XML macros. `Pull Request 362`_ * Allow use of tool-style XML macros in ``job_conf.xml``. `Pull Request 362`_ * Update and clarify admin menu. `Pull Request 302`_ * Add usage information to python cleanup scripts. (Thanks to `@dpryan79 `__.) `Pull Request 274`_ * Added default indexing for bcf files. `Pull Request 163`_ * Implement merging of BAM files for the parallelism framework. (Thanks to `@roalva1 `__.) `Pull Request 149`_ * Send signal to reload data tables when adding an entry (Thanks to `@abretaud `__.) `Pull Request 250`_ * Add display for Interval files at IGV via bedstrict. `Pull Request 259`_ * Include more information in default ``welcome.html`` file. `Pull Request 190`_ * Implement a command line script for collecting stats on job runtimes. `Pull Request 151`_ * Implement an authentication provider for PAM (Pluggable Authentication Modules) (Thanks to `@pvanheus `__.) `Pull Request 458`_ * Re-implement library data and FTP file parameters for new tool form. `Pull Request 132`_, `Pull Request 546`_ * Adding tool error tracking. (Thanks to `@kellrott `__.) `Pull Request 322`_ * Implement ```` tag for output collections. `Pull Request 455`_ * Allow environment variable definitions in tool XML. `Pull Request 395`_ * Add new ``exclude_min`` and ``exclude_max`` attributes to ``InRangeValidator`` for numeric tool parameters. (Thanks to `@gregvonkuster `__.) `Pull Request 339`_ * Added unlinked Tool Shed dependency resolver. (Thanks to `@Christian-B `__.) `Pull Request 441`_ * Add emboss datatypes (previously migrated to Tool Shed). (Thanks to `@bgruening `__.) `Pull Request 148`_ * Add new Hmmer & Stockholm datatypes. (Thanks to `@hexylena `__.) `Pull Request 218`_ * Add an RData datatype. (Thanks to `@hexylena `__.) `Pull Request 239`_ * Add mauve XMFA datatype (Thanks to `@hexylena `__.) `Pull Request 270`_ * Add ConnectivityTable (\*.ct) (RNA 2D structure format) datatype. (Thanks to `@yhoogstrate `__.) `Pull Request 439`_ * Add Illumina methylation datatype (IDAT). `Pull Request 335`_ * Add Dot-Bracket notation (dbn) datatype. (Thanks to `@yhoogstrate `__.) `Pull Request 366`_ * Add proteomics datatypes. (Thanks to `@iracooke `__.) `Pull Request 389`_ * Add new MzSQlite datatype for aggregating MS-based protein identification information. (Thanks to `@jj-umn `__.) `Pull Request 427`_ * Allow ``display_in_upload`` by default for h5 files. `Pull Request 470`_ * Accept history id in tool state construction API. `Pull Request 268`_ * Adding dataset uuid information to job and workflow invocation calls. (Thanks to `@kellrott `__.) `Pull Request 181`_ * Allow workflows executed via the API to optionally run with tool upgrades. `Pull Request 402`_ * Various PEP-8 fixes, more to come next release. (Thanks to efforts lead by `@nsoranzo `__, `@remimarenco `__, and `@bgruening `__.) `Pull Request 421`_, `Pull Request 422`_, `Pull Request 424`_, `Pull Request 433`_, `Pull Request 449`_, `Pull Request 350`_, `Pull Request 453`_, `Pull Request 394`_, `Pull Request 204`_ * Nose update with ``--debug`` option added to ``run_tests.sh``. `Pull Request 172`_ * Mention ``-installed`` option in ``run_tests.sh`` help. `Pull Request 323`_ * Allow config of shed tool configuration file used with ``run_tests.sh -installed``. `Pull Request 267`_ * Allow running tests from outer directories (Thanks to `@yhoogstrate `__.) `Pull Request 137`_ * Enhancement allowing use of DRMAA when Galaxy instance isn't on a shared volume with compute nodes. (Thanks to `@vavrusa `__.) `Pull Request 160`_ * Enhancements for Condor. (Thanks to `@dpryan79 `__.) `Pull Request 289`_ * Update ``gsummary`` dependencies. (Thanks to `@bgruening `__.) `Pull Request 182`_ * Refactor visualization plugins to promote implementation to a class. `Pull Request 186`_ * Switch visualizations registry to entry_point config definition for built-in visualizations. `Pull Request 243`_ * Set default value for IE sig proxy (Thanks to `@hexylena `__.) `Pull Request 197`_ * Other smaller interactive environment updates. (Thanks to `@hexylena `__.) `Pull Request 412`_ * Refuse to load interactive debugging middleware under uwsgi. `Pull Request 200`_ * Move stylesheet source files from ``static/style/src`` to ``client/galaxy/style``. `Pull Request 208`_ * Fix sprite paths by using hardcoded path in task. `Pull Request 279`_ * Improve various focus handling behavior in the UI. `Pull Request 280`_ * Fixes and updates to various JavaScript-based unit tests. `Pull Request 219`_ * Update various client libs (e.g. jQuery, Raven, d3, requirejs). `Pull Request 221`_, `Pull Request 241`_ * Ignore sample files from toolshed installed tools. (Thanks to `@Unode `__.) `Pull Request 248`_ * Add test option for disabling truncation of test diffs. `Pull Request 249`_ * Various documentation and wording improvements for various files. (Thanks to `@nsoranzo `__.) `Pull Request 277`_ * Allow external display applications optional access to files within a dataset's ``extra_files_path``. `Pull Request 284`_ * Improve the data manager JSON datatype's class to be more specific. `Pull Request 285`_ * Allow setting connection options for LDAP authentication. (Thanks to `@Unode `__.) `Pull Request 287`_ * Fix for gzip being imported twice. (Thanks to `@bgruening `__.) `Pull Request 296`_ * Export environment variables from all dependent repositories. (Thanks to `@bgruening `__.) `Pull Request 297`_ * Improve ``auth_conf.xml.sample`` documentation. (Thanks to `@nsoranzo `__.) `Pull Request 299`_ * Preserve unix permissions, if any, when extracting .zip files during tool shed installations. `Pull Request 308`_ * Update mailing lists to use lists.galaxyproject.org addresses. `Pull Request 316`_ * Add new argument to inject volumes in ``docker_cmd()`` and ``launch()``. (Thanks to `@bgruening `__.) `Pull Request 318`_ * Create a separate application entry point to be used by uWSGI without ``--ini- paste`` and PasteDeploy. `Pull Request 325`_ * Implement groups in Tool Shed models and UI. `Pull Request 326`_, `Pull Request 374`_ * Improved datatype registry debugging. `Pull Request 329`_ * Add app option to client process to allow building Tool Shed scripts. `Pull Request 332`_ * Add grunt command ``grunt decompress`` to copy decompressed artifacts. `Pull Request 173`_ * Improvements to Tool Shed search API. `Pull Request 334`_, `Pull Request 376`_, `Pull Request 420`_, `Pull Request 563`_ * Restore link to mercurial browsing of repositories. `Pull Request 340`_ * Enhance tool testing to only cleanup successful jobs. `Pull Request 341`_ * Implement metadata size limiting. `Pull Request 345`_, `Pull Request 416`_ * Add tool parameter argument to parameter help. `Pull Request 346`_, `Pull Request 351`_ * Refactor Tool Shed JavaScript files to be separated from Galaxy Java Script `Pull Request 347`_ * Fixed object store path - ``job_work``. (Thanks to `@charz `__.) `Pull Request 354`_ * Make debugging output nicer for IE's (Thanks to `@bgruening `__.) `Pull Request 355`_ * Add configurable Docker hostname (Thanks to `@bgruening `__.) `Pull Request 356`_ * Improve XML styling of display applications. (Thanks to `@hexylena `__.) `Pull Request 364`_ * README improvements including - adding shields for Biostar, IRC, and Travis. `Pull Request 368`_, `Pull Request 369`_ * Use passed in URL for getbuilds method of parse_builds.py (Thanks to `@dctrud `__.) `Pull Request 384`_ * Add error message for bad dependency declaration (Thanks to `@kaktus42 `__.) `Pull Request 419`_ * Refactor JavaScript set up code for tagging toward reuse. `Pull Request 429`_ * Improved md5sum/sha256 in Tool Shed actions. (Thanks to `@yhoogstrate `__.) `Pull Request 444`_ * Include owner annotations of HDAs in published history display. `Pull Request 490`_ * Added log error for config file not found. (Thanks to `@Christian-B `__.) `Pull Request 443`_ * Fix for installing dependencies from source when download of precompiled binaries has failed. `Pull Request 531`_ * Use a password field for deprecated cloudlaunch's secret key field. `Pull Request 551`_ * Normalize ``datatypes_by_ext`` upon entry. `Pull Request 567`_ * Stop creating unneeded ``database/message.mako.py``. `Pull Request 575`_ Fixes ------------------------------- .. fixes * During the 15.07 development cycle dozens of fixes were pushed to the ``release_15.05`` branch of Galaxy. These are all included in 15.07 and summarized `here `__ (with special thanks to `@bgruening `__, `@mvdbeek `__, `@nsoranzo `__, and `@abretaud `__). * Stop Trackster location wrapping in Chrome. (Thanks to `@dctrud `__.) `Pull Request 440`_ * Fix return integer values when 'round to nearest integer' is selected in Group tool. `Pull Request 452`_ * Fix external set_meta under sqlalchemy 1.0.0. `Pull Request 150`_ * Fix ``base.util`` to get the changeset from git. `Pull Request 161`_ * Remove ``biomart_test`` tool, http://test.biomart.org/ is down. (Thanks to `@nsoranzo `__.) `Pull Request 183`_ * Fix broken browser tests. `Pull Request 202`_ * Fix assertions in ``test_VisualizationsRegistry.py``. `Pull Request 223`_ * Fix ``run_tests.sh`` exit code. `Pull Request 225`_ * Use ``unittest2`` to allow Python 2.7 assertions under Python 2.6. `Pull Request 246`_ * Have ``trans.user_ftp_dir`` return ``None`` instead of error if upload dir unset. `Pull Request 257`_ * Allow IGV external displays to use a name with a comma in it. `Pull Request 261`_ * Fix bug in history sharing. (Thanks to `@bgruening `__.) `Pull Request 263`_ * Convert tools directory to only use unix newline characters. (Thanks to `@nsoranzo `__.) `Pull Request 264`_ * Remove spurious numpy requirement on ``maf_stats.xml`` tool. (Thanks to `@nsoranzo `__.) `Pull Request 264`_ * Use more actionable ``package`` requirement type on some tools. (Thanks to `@nsoranzo `__.) `Pull Request 264`_ * Small doc fix for ``config/plugins/visualizations/README.txt``. (Thanks to `@nsoranzo `__.) `Pull Request 264`_ * Fix function names for dynamic tool test functions. `Pull Request 266`_ * Fixes to dataset chooser. `Pull Request 272`_ * Fix Trackster load order of require and d3. `Pull Request 291`_ * Remove bad HTML tags from login template. (Thanks to `@Unode `__.) `Pull Request 294`_ * Exclude curly braces from API-key to fix toolshed bootstrapping. (Thanks to `@mvdbeek `__.) `Pull Request 301`_ * Fix repeated error messages with identical text. `Pull Request 306`_ * Fix shared mako templates that would not work properly with the Tool Shed. `Pull Request 307`_ * Fix json sniffer for large files. `Pull Request 309`_ * Fix a typo error in ``visualization/plugins/resource_parser.py``. (Thanks to `@remimarenco `__.) `Pull Request 312`_ * Fix for generating metadata on toolshed tools tests, under certain conditions. `Pull Request 319`_ * Fix Tool Shed metadata generation bug. (Thanks to `@bgruening `__.) `Pull Request 333`_ * Fixing string appending error in library dictification. (Thanks to `@kellrott `__.) `Pull Request 336`_ * Hide constantly broken Tool Shed test results. `Pull Request 337`_ * Fix for fix for handling of unix permissions in .zip files. `Pull Request 344`_ * Fix common API scripts so they don't fail when response has no URL param. `Pull Request 352`_ * Fix for dynamic test data fetching. `Pull Request 371`_ * Fix bug in ``Text.split()`` method. (Thanks to `@nsoranzo `__.) `Pull Request 373`_ * Fix and update serializer call to non-``trans`` form for histories. `Pull Request 390`_ * Fix getting admin key when bootstrapping toolshed. (Thanks to `@galaxyproject `__.) `Pull Request 392`_ * Fix error when displaying job params for tools containing a section. (Thanks to `@abretaud `__.) `Pull Request 398`_ * Fix for setting environment variable paths for installed tools. (Thanks to `@gregvonkuster `__.) `Pull Request 403`_ * Quota calculation fixes for managers. `Pull Request 406`_ * Fix paging issue with whoosh due to missing ``str`` to ``int`` conversion. `Pull Request 407`_ * Use ``web.url_for( '/', qualified=True )`` instead of ``'/'`` to generate URLs (for correctness). (Thanks to `@mvdbeek `__.) `Pull Request 414`_ * Fix for async datasources. `Pull Request 423`_ * Fix UI bug related to ID collisions for display of certain collections. `Pull Request 431`_ * Fix ``run_tests.sh`` example API test command. `Pull Request 432`_ * Fixed typo in Tool Shed docstring. (Thanks to `@peterjc `__.) `Pull Request 438`_ * Various Trackster fixes. `Pull Request 446`_ * Fix job query to allow admins to view other histories. `Pull Request 465`_ * Fix ``dbkey`` filtering of multiple input targets. `Pull Request 534`_ * Fixes for ``DeleteIntermediatesAction``. `Pull Request 547`_ * Fix overriding the name variable in Tool Shed index code. `Pull Request 566`_ * Fix batch mode input in new tool form UI. (Thanks to `@ericenns `__.) `Pull Request 568`_ * CSV/SAM sniff order fix. `Pull Request 571`_ * Show field for entering remote/home url when managing a Tool Shed repository. `Pull Request 580`_ * Fix regenerating repository metadata when coming from batch interface. `Pull Request 600`_ .. github_links .. _Pull Request 80: https://github.com/galaxyproject/galaxy/pull/80 .. _Pull Request 132: https://github.com/galaxyproject/galaxy/pull/132 .. _Pull Request 137: https://github.com/galaxyproject/galaxy/pull/137 .. _Pull Request 148: https://github.com/galaxyproject/galaxy/pull/148 .. _Pull Request 149: https://github.com/galaxyproject/galaxy/pull/149 .. _Pull Request 150: https://github.com/galaxyproject/galaxy/pull/150 .. _Pull Request 151: https://github.com/galaxyproject/galaxy/pull/151 .. _Pull Request 159: https://github.com/galaxyproject/galaxy/pull/159 .. _Pull Request 160: https://github.com/galaxyproject/galaxy/pull/160 .. _Pull Request 161: https://github.com/galaxyproject/galaxy/pull/161 .. _Pull Request 163: https://github.com/galaxyproject/galaxy/pull/163 .. _Pull Request 172: https://github.com/galaxyproject/galaxy/pull/172 .. _Pull Request 173: https://github.com/galaxyproject/galaxy/pull/173 .. _Pull Request 181: https://github.com/galaxyproject/galaxy/pull/181 .. _Pull Request 182: https://github.com/galaxyproject/galaxy/pull/182 .. _Pull Request 183: https://github.com/galaxyproject/galaxy/pull/183 .. _Pull Request 186: https://github.com/galaxyproject/galaxy/pull/186 .. _Pull Request 190: https://github.com/galaxyproject/galaxy/pull/190 .. _Pull Request 191: https://github.com/galaxyproject/galaxy/pull/191 .. _Pull Request 197: https://github.com/galaxyproject/galaxy/pull/197 .. _Pull Request 200: https://github.com/galaxyproject/galaxy/pull/200 .. _Pull Request 202: https://github.com/galaxyproject/galaxy/pull/202 .. _Pull Request 204: https://github.com/galaxyproject/galaxy/pull/204 .. _Pull Request 208: https://github.com/galaxyproject/galaxy/pull/208 .. _Pull Request 218: https://github.com/galaxyproject/galaxy/pull/218 .. _Pull Request 219: https://github.com/galaxyproject/galaxy/pull/219 .. _Pull Request 221: https://github.com/galaxyproject/galaxy/pull/221 .. _Pull Request 223: https://github.com/galaxyproject/galaxy/pull/223 .. _Pull Request 225: https://github.com/galaxyproject/galaxy/pull/225 .. _Pull Request 229: https://github.com/galaxyproject/galaxy/pull/229 .. _Pull Request 230: https://github.com/galaxyproject/galaxy/pull/230 .. _Pull Request 233: https://github.com/galaxyproject/galaxy/pull/233 .. _Pull Request 239: https://github.com/galaxyproject/galaxy/pull/239 .. _Pull Request 240: https://github.com/galaxyproject/galaxy/pull/240 .. _Pull Request 241: https://github.com/galaxyproject/galaxy/pull/241 .. _Pull Request 243: https://github.com/galaxyproject/galaxy/pull/243 .. _Pull Request 246: https://github.com/galaxyproject/galaxy/pull/246 .. _Pull Request 248: https://github.com/galaxyproject/galaxy/pull/248 .. _Pull Request 249: https://github.com/galaxyproject/galaxy/pull/249 .. _Pull Request 250: https://github.com/galaxyproject/galaxy/pull/250 .. _Pull Request 257: https://github.com/galaxyproject/galaxy/pull/257 .. _Pull Request 259: https://github.com/galaxyproject/galaxy/pull/259 .. _Pull Request 261: https://github.com/galaxyproject/galaxy/pull/261 .. _Pull Request 263: https://github.com/galaxyproject/galaxy/pull/263 .. _Pull Request 264: https://github.com/galaxyproject/galaxy/pull/264 .. _Pull Request 266: https://github.com/galaxyproject/galaxy/pull/266 .. _Pull Request 267: https://github.com/galaxyproject/galaxy/pull/267 .. _Pull Request 268: https://github.com/galaxyproject/galaxy/pull/268 .. _Pull Request 269: https://github.com/galaxyproject/galaxy/pull/269 .. _Pull Request 270: https://github.com/galaxyproject/galaxy/pull/270 .. _Pull Request 272: https://github.com/galaxyproject/galaxy/pull/272 .. _Pull Request 274: https://github.com/galaxyproject/galaxy/pull/274 .. _Pull Request 277: https://github.com/galaxyproject/galaxy/pull/277 .. _Pull Request 279: https://github.com/galaxyproject/galaxy/pull/279 .. _Pull Request 280: https://github.com/galaxyproject/galaxy/pull/280 .. _Pull Request 284: https://github.com/galaxyproject/galaxy/pull/284 .. _Pull Request 285: https://github.com/galaxyproject/galaxy/pull/285 .. _Pull Request 286: https://github.com/galaxyproject/galaxy/pull/286 .. _Pull Request 287: https://github.com/galaxyproject/galaxy/pull/287 .. _Pull Request 289: https://github.com/galaxyproject/galaxy/pull/289 .. _Pull Request 290: https://github.com/galaxyproject/galaxy/pull/290 .. _Pull Request 291: https://github.com/galaxyproject/galaxy/pull/291 .. _Pull Request 294: https://github.com/galaxyproject/galaxy/pull/294 .. _Pull Request 295: https://github.com/galaxyproject/galaxy/pull/295 .. _Pull Request 296: https://github.com/galaxyproject/galaxy/pull/296 .. _Pull Request 297: https://github.com/galaxyproject/galaxy/pull/297 .. _Pull Request 299: https://github.com/galaxyproject/galaxy/pull/299 .. _Pull Request 301: https://github.com/galaxyproject/galaxy/pull/301 .. _Pull Request 302: https://github.com/galaxyproject/galaxy/pull/302 .. _Pull Request 303: https://github.com/galaxyproject/galaxy/pull/303 .. _Pull Request 306: https://github.com/galaxyproject/galaxy/pull/306 .. _Pull Request 307: https://github.com/galaxyproject/galaxy/pull/307 .. _Pull Request 308: https://github.com/galaxyproject/galaxy/pull/308 .. _Pull Request 309: https://github.com/galaxyproject/galaxy/pull/309 .. _Pull Request 311: https://github.com/galaxyproject/galaxy/pull/311 .. _Pull Request 312: https://github.com/galaxyproject/galaxy/pull/312 .. _Pull Request 314: https://github.com/galaxyproject/galaxy/pull/314 .. _Pull Request 316: https://github.com/galaxyproject/galaxy/pull/316 .. _Pull Request 318: https://github.com/galaxyproject/galaxy/pull/318 .. _Pull Request 319: https://github.com/galaxyproject/galaxy/pull/319 .. _Pull Request 322: https://github.com/galaxyproject/galaxy/pull/322 .. _Pull Request 323: https://github.com/galaxyproject/galaxy/pull/323 .. _Pull Request 325: https://github.com/galaxyproject/galaxy/pull/325 .. _Pull Request 326: https://github.com/galaxyproject/galaxy/pull/326 .. _Pull Request 328: https://github.com/galaxyproject/galaxy/pull/328 .. _Pull Request 329: https://github.com/galaxyproject/galaxy/pull/329 .. _Pull Request 330: https://github.com/galaxyproject/galaxy/pull/330 .. _Pull Request 332: https://github.com/galaxyproject/galaxy/pull/332 .. _Pull Request 333: https://github.com/galaxyproject/galaxy/pull/333 .. _Pull Request 334: https://github.com/galaxyproject/galaxy/pull/334 .. _Pull Request 335: https://github.com/galaxyproject/galaxy/pull/335 .. _Pull Request 336: https://github.com/galaxyproject/galaxy/pull/336 .. _Pull Request 337: https://github.com/galaxyproject/galaxy/pull/337 .. _Pull Request 338: https://github.com/galaxyproject/galaxy/pull/338 .. _Pull Request 339: https://github.com/galaxyproject/galaxy/pull/339 .. _Pull Request 340: https://github.com/galaxyproject/galaxy/pull/340 .. _Pull Request 341: https://github.com/galaxyproject/galaxy/pull/341 .. _Pull Request 342: https://github.com/galaxyproject/galaxy/pull/342 .. _Pull Request 344: https://github.com/galaxyproject/galaxy/pull/344 .. _Pull Request 345: https://github.com/galaxyproject/galaxy/pull/345 .. _Pull Request 346: https://github.com/galaxyproject/galaxy/pull/346 .. _Pull Request 347: https://github.com/galaxyproject/galaxy/pull/347 .. _Pull Request 349: https://github.com/galaxyproject/galaxy/pull/349 .. _Pull Request 350: https://github.com/galaxyproject/galaxy/pull/350 .. _Pull Request 351: https://github.com/galaxyproject/galaxy/pull/351 .. _Pull Request 352: https://github.com/galaxyproject/galaxy/pull/352 .. _Pull Request 354: https://github.com/galaxyproject/galaxy/pull/354 .. _Pull Request 355: https://github.com/galaxyproject/galaxy/pull/355 .. _Pull Request 356: https://github.com/galaxyproject/galaxy/pull/356 .. _Pull Request 362: https://github.com/galaxyproject/galaxy/pull/362 .. _Pull Request 364: https://github.com/galaxyproject/galaxy/pull/364 .. _Pull Request 366: https://github.com/galaxyproject/galaxy/pull/366 .. _Pull Request 368: https://github.com/galaxyproject/galaxy/pull/368 .. _Pull Request 369: https://github.com/galaxyproject/galaxy/pull/369 .. _Pull Request 370: https://github.com/galaxyproject/galaxy/pull/370 .. _Pull Request 371: https://github.com/galaxyproject/galaxy/pull/371 .. _Pull Request 373: https://github.com/galaxyproject/galaxy/pull/373 .. _Pull Request 374: https://github.com/galaxyproject/galaxy/pull/374 .. _Pull Request 376: https://github.com/galaxyproject/galaxy/pull/376 .. _Pull Request 381: https://github.com/galaxyproject/galaxy/pull/381 .. _Pull Request 383: https://github.com/galaxyproject/galaxy/pull/383 .. _Pull Request 384: https://github.com/galaxyproject/galaxy/pull/384 .. _Pull Request 386: https://github.com/galaxyproject/galaxy/pull/386 .. _Pull Request 389: https://github.com/galaxyproject/galaxy/pull/389 .. _Pull Request 390: https://github.com/galaxyproject/galaxy/pull/390 .. _Pull Request 392: https://github.com/galaxyproject/galaxy/pull/392 .. _Pull Request 394: https://github.com/galaxyproject/galaxy/pull/394 .. _Pull Request 395: https://github.com/galaxyproject/galaxy/pull/395 .. _Pull Request 397: https://github.com/galaxyproject/galaxy/pull/397 .. _Pull Request 398: https://github.com/galaxyproject/galaxy/pull/398 .. _Pull Request 399: https://github.com/galaxyproject/galaxy/pull/399 .. _Pull Request 402: https://github.com/galaxyproject/galaxy/pull/402 .. _Pull Request 403: https://github.com/galaxyproject/galaxy/pull/403 .. _Pull Request 405: https://github.com/galaxyproject/galaxy/pull/405 .. _Pull Request 406: https://github.com/galaxyproject/galaxy/pull/406 .. _Pull Request 407: https://github.com/galaxyproject/galaxy/pull/407 .. _Pull Request 410: https://github.com/galaxyproject/galaxy/pull/410 .. _Pull Request 412: https://github.com/galaxyproject/galaxy/pull/412 .. _Pull Request 414: https://github.com/galaxyproject/galaxy/pull/414 .. _Pull Request 416: https://github.com/galaxyproject/galaxy/pull/416 .. _Pull Request 419: https://github.com/galaxyproject/galaxy/pull/419 .. _Pull Request 420: https://github.com/galaxyproject/galaxy/pull/420 .. _Pull Request 421: https://github.com/galaxyproject/galaxy/pull/421 .. _Pull Request 422: https://github.com/galaxyproject/galaxy/pull/422 .. _Pull Request 423: https://github.com/galaxyproject/galaxy/pull/423 .. _Pull Request 424: https://github.com/galaxyproject/galaxy/pull/424 .. _Pull Request 426: https://github.com/galaxyproject/galaxy/pull/426 .. _Pull Request 427: https://github.com/galaxyproject/galaxy/pull/427 .. _Pull Request 429: https://github.com/galaxyproject/galaxy/pull/429 .. _Pull Request 431: https://github.com/galaxyproject/galaxy/pull/431 .. _Pull Request 432: https://github.com/galaxyproject/galaxy/pull/432 .. _Pull Request 433: https://github.com/galaxyproject/galaxy/pull/433 .. _Pull Request 438: https://github.com/galaxyproject/galaxy/pull/438 .. _Pull Request 439: https://github.com/galaxyproject/galaxy/pull/439 .. _Pull Request 440: https://github.com/galaxyproject/galaxy/pull/440 .. _Pull Request 441: https://github.com/galaxyproject/galaxy/pull/441 .. _Pull Request 443: https://github.com/galaxyproject/galaxy/pull/443 .. _Pull Request 444: https://github.com/galaxyproject/galaxy/pull/444 .. _Pull Request 446: https://github.com/galaxyproject/galaxy/pull/446 .. _Pull Request 449: https://github.com/galaxyproject/galaxy/pull/449 .. _Pull Request 452: https://github.com/galaxyproject/galaxy/pull/452 .. _Pull Request 453: https://github.com/galaxyproject/galaxy/pull/453 .. _Pull Request 454: https://github.com/galaxyproject/galaxy/pull/454 .. _Pull Request 455: https://github.com/galaxyproject/galaxy/pull/455 .. _Pull Request 458: https://github.com/galaxyproject/galaxy/pull/458 .. _Pull Request 459: https://github.com/galaxyproject/galaxy/pull/459 .. _Pull Request 462: https://github.com/galaxyproject/galaxy/pull/462 .. _Pull Request 463: https://github.com/galaxyproject/galaxy/pull/463 .. _Pull Request 465: https://github.com/galaxyproject/galaxy/pull/465 .. _Pull Request 470: https://github.com/galaxyproject/galaxy/pull/470 .. _Pull Request 472: https://github.com/galaxyproject/galaxy/pull/472 .. _Pull Request 473: https://github.com/galaxyproject/galaxy/pull/473 .. _Pull Request 478: https://github.com/galaxyproject/galaxy/pull/478 .. _Pull Request 479: https://github.com/galaxyproject/galaxy/pull/479 .. _Pull Request 480: https://github.com/galaxyproject/galaxy/pull/480 .. _Pull Request 481: https://github.com/galaxyproject/galaxy/pull/481 .. _Pull Request 482: https://github.com/galaxyproject/galaxy/pull/482 .. _Pull Request 484: https://github.com/galaxyproject/galaxy/pull/484 .. _Pull Request 485: https://github.com/galaxyproject/galaxy/pull/485 .. _Pull Request 486: https://github.com/galaxyproject/galaxy/pull/486 .. _Pull Request 487: https://github.com/galaxyproject/galaxy/pull/487 .. _Pull Request 488: https://github.com/galaxyproject/galaxy/pull/488 .. _Pull Request 490: https://github.com/galaxyproject/galaxy/pull/490 .. _Pull Request 491: https://github.com/galaxyproject/galaxy/pull/491 .. _Pull Request 492: https://github.com/galaxyproject/galaxy/pull/492 .. _Pull Request 493: https://github.com/galaxyproject/galaxy/pull/493 .. _Pull Request 494: https://github.com/galaxyproject/galaxy/pull/494 .. _Pull Request 495: https://github.com/galaxyproject/galaxy/pull/495 .. _Pull Request 496: https://github.com/galaxyproject/galaxy/pull/496 .. _Pull Request 499: https://github.com/galaxyproject/galaxy/pull/499 .. _Pull Request 500: https://github.com/galaxyproject/galaxy/pull/500 .. _Pull Request 509: https://github.com/galaxyproject/galaxy/pull/509 .. _Pull Request 510: https://github.com/galaxyproject/galaxy/pull/510 .. _Pull Request 511: https://github.com/galaxyproject/galaxy/pull/511 .. _Pull Request 512: https://github.com/galaxyproject/galaxy/pull/512 .. _Pull Request 514: https://github.com/galaxyproject/galaxy/pull/514 .. _Pull Request 515: https://github.com/galaxyproject/galaxy/pull/515 .. _Pull Request 516: https://github.com/galaxyproject/galaxy/pull/516 .. _Pull Request 517: https://github.com/galaxyproject/galaxy/pull/517 .. _Pull Request 526: https://github.com/galaxyproject/galaxy/pull/526 .. _Pull Request 527: https://github.com/galaxyproject/galaxy/pull/527 .. _Pull Request 529: https://github.com/galaxyproject/galaxy/pull/529 .. _Pull Request 530: https://github.com/galaxyproject/galaxy/pull/530 .. _Pull Request 531: https://github.com/galaxyproject/galaxy/pull/531 .. _Pull Request 532: https://github.com/galaxyproject/galaxy/pull/532 .. _Pull Request 533: https://github.com/galaxyproject/galaxy/pull/533 .. _Pull Request 534: https://github.com/galaxyproject/galaxy/pull/534 .. _Pull Request 536: https://github.com/galaxyproject/galaxy/pull/536 .. _Pull Request 537: https://github.com/galaxyproject/galaxy/pull/537 .. _Pull Request 538: https://github.com/galaxyproject/galaxy/pull/538 .. _Pull Request 539: https://github.com/galaxyproject/galaxy/pull/539 .. _Pull Request 540: https://github.com/galaxyproject/galaxy/pull/540 .. _Pull Request 543: https://github.com/galaxyproject/galaxy/pull/543 .. _Pull Request 544: https://github.com/galaxyproject/galaxy/pull/544 .. _Pull Request 545: https://github.com/galaxyproject/galaxy/pull/545 .. _Pull Request 546: https://github.com/galaxyproject/galaxy/pull/546 .. _Pull Request 547: https://github.com/galaxyproject/galaxy/pull/547 .. _Pull Request 550: https://github.com/galaxyproject/galaxy/pull/550 .. _Pull Request 551: https://github.com/galaxyproject/galaxy/pull/551 .. _Pull Request 553: https://github.com/galaxyproject/galaxy/pull/553 .. _Pull Request 561: https://github.com/galaxyproject/galaxy/pull/561 .. _Pull Request 563: https://github.com/galaxyproject/galaxy/pull/563 .. _Pull Request 565: https://github.com/galaxyproject/galaxy/pull/565 .. _Pull Request 566: https://github.com/galaxyproject/galaxy/pull/566 .. _Pull Request 567: https://github.com/galaxyproject/galaxy/pull/567 .. _Pull Request 568: https://github.com/galaxyproject/galaxy/pull/568 .. _Pull Request 569: https://github.com/galaxyproject/galaxy/pull/569 .. _Pull Request 571: https://github.com/galaxyproject/galaxy/pull/571 .. _Pull Request 575: https://github.com/galaxyproject/galaxy/pull/575 .. _Pull Request 577: https://github.com/galaxyproject/galaxy/pull/577 .. _Pull Request 580: https://github.com/galaxyproject/galaxy/pull/580 .. _Pull Request 581: https://github.com/galaxyproject/galaxy/pull/581 .. _Pull Request 583: https://github.com/galaxyproject/galaxy/pull/583 .. _Pull Request 584: https://github.com/galaxyproject/galaxy/pull/584 .. _Pull Request 585: https://github.com/galaxyproject/galaxy/pull/585 .. _Pull Request 587: https://github.com/galaxyproject/galaxy/pull/587 .. _Pull Request 589: https://github.com/galaxyproject/galaxy/pull/589 .. _Pull Request 591: https://github.com/galaxyproject/galaxy/pull/591 .. _Pull Request 592: https://github.com/galaxyproject/galaxy/pull/592 .. _Pull Request 594: https://github.com/galaxyproject/galaxy/pull/594 .. _Pull Request 600: https://github.com/galaxyproject/galaxy/pull/600 .. _Pull Request 602: https://github.com/galaxyproject/galaxy/pull/602 .. _Pull Request 625: https://github.com/galaxyproject/galaxy/pull/625