January 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 9373b6: Fix bug with job re-submission introduced in 34f0b...
by GitHub 18 Jan '17

18 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9373b69f8b6dd93f747d5b12bea7e4f75aef3add https://github.com/galaxyproject/galaxy/commit/9373b69f8b6dd93f747d5b12bea7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix bug with job re-submission introduced in 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c. Commit: 29cdd6007fa333e8e9caa85a1fc58ae389405cf2 https://github.com/galaxyproject/galaxy/commit/29cdd6007fa333e8e9caa85a1fc5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3439 from jmchilton/fix_resubmissions Fix bug with job re-submission introduced in 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c Compare: https://github.com/galaxyproject/galaxy/compare/d2e019844471...29cdd6007fa3

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[galaxyproject/galaxy] bf3a48: Fix import order and Python3 compatibility for lib...
by GitHub 17 Jan '17

17 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf3a487f2017d248317e9ea70e567f57a70d9cc9 https://github.com/galaxyproject/galaxy/commit/bf3a487f2017d248317e9ea70e56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/tools/ xref. #1715 Commit: d2e019844471ee29f9b2433e0f90f53ea54a7b7f https://github.com/galaxyproject/galaxy/commit/d2e019844471ee29f9b2433e0f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #3431 from nsoranzo/python3 Fix import order and Python3 compatibility for lib/galaxy/tools/ Compare: https://github.com/galaxyproject/galaxy/compare/910bbdfc54fe...d2e019844471

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[galaxyproject/galaxy] 9f4add: Bug fix in mulled.py
by GitHub 17 Jan '17

17 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f4add70d0967ccb6ddf1bd2d1393685ef639e97 https://github.com/galaxyproject/galaxy/commit/9f4add70d0967ccb6ddf1bd2d139… Author: Abdulrahman Azab <eng.azab(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Bug fix in mulled.py This bug was causing running docker with sudo while it should not Commit: 910bbdfc54fe4a84e16ebe9ed9bc7fe0eed28dc6 https://github.com/galaxyproject/galaxy/commit/910bbdfc54fe4a84e16ebe9ed9bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Merge pull request #3434 from abdulrahmanazab/patch-4 Bug fix in mulled.py Compare: https://github.com/galaxyproject/galaxy/compare/dd2ab483c095...910bbdfc54fe

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[galaxyproject/galaxy] cdaa20: Add whoami API
by GitHub 16 Jan '17

16 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cdaa20858a4b20f0080a851c6380c41e610f1346 https://github.com/galaxyproject/galaxy/commit/cdaa20858a4b20f0080a851c6380… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add whoami API Commit: b242dc3ab18c003bd3c8219305730be22d0729e9 https://github.com/galaxyproject/galaxy/commit/b242dc3ab18c003bd3c821930573… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Fix docs concerns Commit: 8c46cd5afcb63ece8d37b5051be723a359c1cc71 https://github.com/galaxyproject/galaxy/commit/8c46cd5afcb63ece8d37b5051be7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Correct API path Commit: dd2ab483c095848a372a57de3ce4f08677c402fb https://github.com/galaxyproject/galaxy/commit/dd2ab483c095848a372a57de3ce4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3423 from erasche/whoami Add whoami API Compare: https://github.com/galaxyproject/galaxy/compare/8cb61626811d...dd2ab483c095

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[galaxyproject/galaxy] 68f5bc: Reapply ui-misc.Message changes post-reversion. F...
by GitHub 16 Jan '17

16 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2 https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component. Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2 https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap form-view to use the new UnescapedMessage Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8 https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Name function appropriately for Javascript instead of being stuck in Python. Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24 https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3416 from dannon/ui_misc_message_fixes [16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html Commit: 8cb61626811d51afef0f7e27e9713fa98e6b664a https://github.com/galaxyproject/galaxy/commit/8cb61626811d51afef0f7e27e971… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/maps/mvc/ui/ui-misc.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-misc.js Compare: https://github.com/galaxyproject/galaxy/compare/ebf18440ac09...8cb61626811d

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[galaxyproject/galaxy] 68f5bc: Reapply ui-misc.Message changes post-reversion. F...
by GitHub 15 Jan '17

15 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2 https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component. Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2 https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap form-view to use the new UnescapedMessage Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8 https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Name function appropriately for Javascript instead of being stuck in Python. Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24 https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3416 from dannon/ui_misc_message_fixes [16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html Compare: https://github.com/galaxyproject/galaxy/compare/c94ccb3f28cd...02a8a7da0a0f

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[galaxyproject/galaxy] 537d6e: Fix "exact" property for merged conda dependencies...
by GitHub 15 Jan '17

15 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 537d6e645ae142962cdf59e6365299b8c99706bf https://github.com/galaxyproject/galaxy/commit/537d6e645ae142962cdf59e63652… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix "exact" property for merged conda dependencies. This was broken with there initial commit as part of #3391. Commit: 2ed131d206dbf73a141b7baf76c5ffcce6fef206 https://github.com/galaxyproject/galaxy/commit/2ed131d206dbf73a141b7baf76c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix display of repository dependency status that broke with the introduction of the all-at-once dependency resolution in #3391 and addresses in part #3398. I have only restored the (collapsed) display of dependencies for all requirements in a repository, so breaking the information out on a per tool basis remains on the TODO list. Commit: ebf18440ac09c364fa1fb6b1cdd1640808ffd593 https://github.com/galaxyproject/galaxy/commit/ebf18440ac09c364fa1fb6b1cdd1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #3427 from mvdbeek/fix_dependency_display_and_api Fix dependency display and api Compare: https://github.com/galaxyproject/galaxy/compare/b2cf773befd6...ebf18440ac09

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[galaxyproject/galaxy] a5c445: Swap the client's ui-misc.Message to escape by def...
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js A static/maps/libs/showdown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/showdown.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap the client's ui-misc.Message to escape by default. Commit: e1083132b89f854e2ec824f97f187e925ba0abe6 https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Fix RStudio login Thanks @shiltemann for reporting this Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233 https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Export UnescapedMessage from ui-misc. Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting cleanup. Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reversion of ui-misc messagebox changes. Commit: 2d69909218b287f8085a599e0a2a1214480330c9 https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50 https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login Commit: b2cf773befd655ccae204c358703c9061916a32f https://github.com/galaxyproject/galaxy/commit/b2cf773befd655ccae204c358703… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A static/maps/libs/showdown.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map A static/scripts/libs/showdown.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1f9812b5d522...b2cf773befd6

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[galaxyproject/galaxy] 422cf1: Switch to Miniconda3.
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 422cf1917e97b612e972b3824fcf831c510dc535 https://github.com/galaxyproject/galaxy/commit/422cf1917e97b612e972b3824fcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Switch to Miniconda3. It is the platformed used by bioconda for testing and will be supported longer than the older Python 2 variant. This shouldn't require Python 3 be installed on the host running Galaxy. Commit: d66d3a1a308a94dd548f29448b479c9d9b66a239 https://github.com/galaxyproject/galaxy/commit/d66d3a1a308a94dd548f29448b47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Add a log message to explain long pause during startup. When conda_auto_init is used. Commit: 1f9812b5d522118f79a304e3c4f5f69e28661b05 https://github.com/galaxyproject/galaxy/commit/1f9812b5d522118f79a304e3c4f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3419 from jmchilton/conda_tweaks Target Miniconda3 when installing Conda. Compare: https://github.com/galaxyproject/galaxy/compare/e573826e02e8...1f9812b5d522

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[galaxyproject/galaxy] 07806e: Another fix for Selenium testing on Jenkins.
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07806e628adf164e95543393a9f37a187acb9a0e https://github.com/galaxyproject/galaxy/commit/07806e628adf164e95543393a9f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Another fix for Selenium testing on Jenkins. Turns out that random sleep for 30 seconds was every bit as brittle as it seemed. This is a bit better. Commit: e573826e02e822abd63fe452b065efd690e277da https://github.com/galaxyproject/galaxy/commit/e573826e02e822abd63fe452b065… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Merge pull request #3422 from jmchilton/selenium_fixes_0 Another fix for Selenium testing on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/ec425007b11f...e573826e02e8

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