- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e87569: add TS API to check current user
by GitHub 25 Apr '16

25 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8756907039de8fa9f3a2c571c987982d716bc54 https://github.com/galaxyproject/galaxy/commit/e8756907039de8fa9f3a2c571c98… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py Log Message: ----------- add TS API to check current user Commit: 01472fdc018823527968d6e78fb2255cdfbed271 https://github.com/galaxyproject/galaxy/commit/01472fdc018823527968d6e78fb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py Log Message: ----------- Merge pull request #2243 from martenson/check-curr-ts-user add TS API to check current user Compare: https://github.com/galaxyproject/galaxy/compare/af4ebccebbc6...01472fdc0188

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[galaxyproject/galaxy] 5749e3: Encode collection reduce in serializable fashion
by GitHub 25 Apr '16

25 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5749e3484bffdc0b066f281d0708ffe3228d5415 https://github.com/galaxyproject/galaxy/commit/5749e3484bffdc0b066f281d0708… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Encode collection reduce in serializable fashion Commit: ce31431f2949344d72c949d0ba5b495b0c90a1be https://github.com/galaxyproject/galaxy/commit/ce31431f2949344d72c949d0ba5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-23 (Sat, 23 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2238 from guerler/fix_collection_reduce_000 [16.04] Encode collection reduce in serializable fashion Commit: af4ebccebbc66551e1ab71400fa6e7ac4b6dae33 https://github.com/galaxyproject/galaxy/commit/af4ebccebbc66551e1ab71400fa6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-25 (Mon, 25 Apr 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2c56b5f995e3...af4ebccebbc6

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[galaxyproject/galaxy] 18556b: Encode collection reduce in serializable fashion
by GitHub 25 Apr '16

25 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18556be6fcbd53bcec88e233e8cd856309e404ae https://github.com/galaxyproject/galaxy/commit/18556be6fcbd53bcec88e233e8cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-24 (Sun, 24 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Encode collection reduce in serializable fashion Commit: 2c56b5f995e356de0bb446577ac96ff4f1ee0f4c https://github.com/galaxyproject/galaxy/commit/2c56b5f995e356de0bb446577ac9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2241 from guerler/fix_test_000 Encode collection reduce in serializable fashion Compare: https://github.com/galaxyproject/galaxy/compare/18a6393010d1...2c56b5f995e3

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[galaxyproject/galaxy] c2b091: Tests demonstrating multi-data params in repeats a...
by GitHub 23 Apr '16

23 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2b091d207197759e9693b6d5bf3581a678043ee https://github.com/galaxyproject/galaxy/commit/c2b091d207197759e9693b6d5bf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M test/api/test_tools.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Tests demonstrating multi-data params in repeats are broken. A test cases and a tool that can be tested directory. Commit: 18a6393010d17d0477ecafeb98c29595f0b9ec34 https://github.com/galaxyproject/galaxy/commit/18a6393010d17d0477ecafeb98c2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-23 (Sat, 23 Apr 2016) Changed paths: M test/api/test_tools.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2233 from jmchilton/repeat_multidata [16.04] Multi-data collection reductions in repeat blocks are broken. Compare: https://github.com/galaxyproject/galaxy/compare/581e5ccdcb21...18a6393010d1

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[galaxyproject/galaxy] 5749e3: Encode collection reduce in serializable fashion
by GitHub 23 Apr '16

23 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 5749e3484bffdc0b066f281d0708ffe3228d5415 https://github.com/galaxyproject/galaxy/commit/5749e3484bffdc0b066f281d0708… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Encode collection reduce in serializable fashion Commit: ce31431f2949344d72c949d0ba5b495b0c90a1be https://github.com/galaxyproject/galaxy/commit/ce31431f2949344d72c949d0ba5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-23 (Sat, 23 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2238 from guerler/fix_collection_reduce_000 [16.04] Encode collection reduce in serializable fashion Compare: https://github.com/galaxyproject/galaxy/compare/62bc415ae6ed...ce31431f2949

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[galaxyproject/usegalaxy-playbook] ae79ac: Add HISAT2 indexes to Main, enable remote metadata...
by GitHub 23 Apr '16

23 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ae79ac819ffb86a927e0a15c30f65acb08f6d3fc https://github.com/galaxyproject/usegalaxy-playbook/commit/ae79ac819ffb86a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Add HISAT2 indexes to Main, enable remote metadata for Jetstream destinations

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[galaxyproject/usegalaxy-playbook] b9a5e8: Add tacc-protected nginx stuff
by GitHub 23 Apr '16

23 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b9a5e8ead04ef2b888283f9682ef52549ce0b5be https://github.com/galaxyproject/usegalaxy-playbook/commit/b9a5e8ead04ef2b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M stage/secret_vars/galaxyservers.yml A templates/nginx/tacc_protected.j2 Log Message: ----------- Add tacc-protected nginx stuff

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[galaxyproject/galaxy] 83628d: Add conditional statsd requirement. Wheel is live...
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83628d5ecda9d353594e97e5ee329dd1a80d3e30 https://github.com/galaxyproject/galaxy/commit/83628d5ecda9d353594e97e5ee32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. Commit: 581e5ccdcb21f92d108021bf8fbc8e834999a157 https://github.com/galaxyproject/galaxy/commit/581e5ccdcb21f92d108021bf8fbc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Log Message: ----------- Merge pull request #2227 from dannon/stats_req_backport [16.04] Add conditional statsd requirement Compare: https://github.com/galaxyproject/galaxy/compare/f23c3ae662b7...581e5ccdcb21

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[galaxyproject/galaxy] 6460b1: Correctly check set_environment declarations when ...
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6460b19045a951ac2594ee2d606f923b9fdedc25 https://github.com/galaxyproject/galaxy/commit/6460b19045a951ac2594ee2d606f… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correctly check set_environment declarations when updating repository. Commit: f23c3ae662b72b56175be5d8daf01dcfec43d814 https://github.com/galaxyproject/galaxy/commit/f23c3ae662b72b56175be5d8daf0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2116 from davebx/update_environment Correctly check set_environment declarations when updating repository. Compare: https://github.com/galaxyproject/galaxy/compare/bbf5722f27ef...f23c3ae662b7

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[galaxyproject/galaxy] e5b3c9: Fix js value validator
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5b3c94c5e03a963059a58243858b7244508fb63 https://github.com/galaxyproject/galaxy/commit/e5b3c94c5e03a963059a58243858… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Fix js value validator Commit: 62bc415ae6ed331d0dacaafb2e62a79055972500 https://github.com/galaxyproject/galaxy/commit/62bc415ae6ed331d0dacaafb2e62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2234 from guerler/fix_validator_000 [16.04] Fix js value validator Commit: bbf5722f27efe4a477ed21e876f14d300f03cff0 https://github.com/galaxyproject/galaxy/commit/bbf5722f27efe4a477ed21e876f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1243bd5eb200...bbf5722f27ef

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[galaxyproject/galaxy] e5b3c9: Fix js value validator
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e5b3c94c5e03a963059a58243858b7244508fb63 https://github.com/galaxyproject/galaxy/commit/e5b3c94c5e03a963059a58243858… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Fix js value validator Commit: 62bc415ae6ed331d0dacaafb2e62a79055972500 https://github.com/galaxyproject/galaxy/commit/62bc415ae6ed331d0dacaafb2e62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2234 from guerler/fix_validator_000 [16.04] Fix js value validator Compare: https://github.com/galaxyproject/galaxy/compare/0b9ed993d6eb...62bc415ae6ed

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[galaxyproject/galaxy] 7dcc7a: Fixes #2230
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7dcc7a5af007483dc18a139ded42474d1f690d39 https://github.com/galaxyproject/galaxy/commit/7dcc7a5af007483dc18a139ded42… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fixes #2230 This sanitizes some instances where tool parameters were included directly into the DOM. workflow/run.mako displayed the parameter as a value in a hidden input. This was base64 encoded as there was no better solution apparent at the time. I'm not sure where this parameter is POSTed to but we should figure that out and b64decode it, or remove the hidden parameter. client/... added the parameter value into the DOM. This was easily sanitized using a standard method. workflow/display.mako included the parameter value directly into the HTML. This was cgi.esacped Commit: 1243bd5eb20083c9832d0bb6dbe1c5830c480ff7 https://github.com/galaxyproject/galaxy/commit/1243bd5eb20083c9832d0bb6dbe1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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-input.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2231 from erasche/fix-2230 Fixes #2230 Compare: https://github.com/galaxyproject/galaxy/compare/46585014c09b...1243bd5eb200

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[galaxyproject/infrastructure-playbook] 42df2d: More IU JS nodes
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 42df2d8517e76d1525b9ff55573cf92bfc37f12f https://github.com/galaxyproject/infrastructure-playbook/commit/42df2d8517e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- More IU JS nodes

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[galaxyproject/usegalaxy-playbook] 3eec59: Test and Main updates, Jetstream config changes an...
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3eec599a7c17e57f3d1d85ce5d740fb98e162af0 https://github.com/galaxyproject/usegalaxy-playbook/commit/3eec599a7c17e57f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: A files/galaxy/common/config/pulsar_jetstream_actions.yml M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml A files/galaxy/test.galaxyproject.org/config/pulsar_jetstream.yml M files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_actions.yml R files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_iu.yml R files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_tacc.yml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml A files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml A files/galaxy/usegalaxy.org/config/pulsar_jetstream_actions.yml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Test and Main updates, Jetstream config changes and fixes for Test, enable Jetstream destinations for Main

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[galaxyproject/galaxy] e65cfe: Add pyparsing dependency of svgwrite. Unpin mercur...
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e65cfe57487566760de82b2ed1992744d9820f59 https://github.com/galaxyproject/galaxy/commit/e65cfe57487566760de82b2ed199… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add pyparsing dependency of svgwrite. Unpin mercurial. Also sync missing dependencies of dependencies and move some Galaxy dependencies to the correct section. Commit: 46585014c09baffc42eb9627303eabd880f81247 https://github.com/galaxyproject/galaxy/commit/46585014c09baffc42eb9627303e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #2223 from nsoranzo/fix_requirements Add pyparsing dependency of svgwrite. Unpin mercurial. Compare: https://github.com/galaxyproject/galaxy/compare/5cda797832c8...46585014c09b

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[galaxyproject/galaxy] ebb49d: Make client, somehow this got out of sync.
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Commit: ef12ae303577b2cc1967a08b341962f0ef1ffc5a https://github.com/galaxyproject/galaxy/commit/ef12ae303577b2cc1967a08b3419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako Log Message: ----------- Test fix for christ-h's french language date abbreviations breaking the old library display Commit: 7e93d462392952d27d414ba87d2dd406c9a60be1 https://github.com/galaxyproject/galaxy/commit/7e93d462392952d27d414ba87d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Another location where the non-ascii month was breaking display. Commit: 3907d83abe98a77dc6ecfb4abe818ea1bf31e9eb https://github.com/galaxyproject/galaxy/commit/3907d83abe98a77dc6ecfb4abe81… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations Commit: 912e6ea30ffc8c67033c7815d7adee0cc9db5f90 https://github.com/galaxyproject/galaxy/commit/912e6ea30ffc8c67033c7815d7ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- port TS test fix so we can rely on jenkins Commit: 9e980862c8b763cf3dd0209be49f0d2d75a90614 https://github.com/galaxyproject/galaxy/commit/9e980862c8b763cf3dd0209be49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins Commit: 0b9ed993d6eb054dc6c68fcd20d0873fd837b32f https://github.com/galaxyproject/galaxy/commit/0b9ed993d6eb054dc6c68fcd20d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 5cda797832c8823695eca6b82ad25a195e3f194c https://github.com/galaxyproject/galaxy/commit/5cda797832c8823695eca6b82ad2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d0028bde0fee...5cda797832c8

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[galaxyproject/galaxy] ebb49d: Make client, somehow this got out of sync.
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Commit: ef12ae303577b2cc1967a08b341962f0ef1ffc5a https://github.com/galaxyproject/galaxy/commit/ef12ae303577b2cc1967a08b3419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako Log Message: ----------- Test fix for christ-h's french language date abbreviations breaking the old library display Commit: 7e93d462392952d27d414ba87d2dd406c9a60be1 https://github.com/galaxyproject/galaxy/commit/7e93d462392952d27d414ba87d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Another location where the non-ascii month was breaking display. Commit: 3907d83abe98a77dc6ecfb4abe818ea1bf31e9eb https://github.com/galaxyproject/galaxy/commit/3907d83abe98a77dc6ecfb4abe81… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations Commit: 912e6ea30ffc8c67033c7815d7adee0cc9db5f90 https://github.com/galaxyproject/galaxy/commit/912e6ea30ffc8c67033c7815d7ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- port TS test fix so we can rely on jenkins Commit: 9e980862c8b763cf3dd0209be49f0d2d75a90614 https://github.com/galaxyproject/galaxy/commit/9e980862c8b763cf3dd0209be49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins Commit: 0b9ed993d6eb054dc6c68fcd20d0873fd837b32f https://github.com/galaxyproject/galaxy/commit/0b9ed993d6eb054dc6c68fcd20d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/2734c2c4835a...0b9ed993d6eb

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[galaxyproject/galaxy] 912e6e: port TS test fix so we can rely on jenkins
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 912e6ea30ffc8c67033c7815d7adee0cc9db5f90 https://github.com/galaxyproject/galaxy/commit/912e6ea30ffc8c67033c7815d7ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- port TS test fix so we can rely on jenkins Commit: 9e980862c8b763cf3dd0209be49f0d2d75a90614 https://github.com/galaxyproject/galaxy/commit/9e980862c8b763cf3dd0209be49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins Compare: https://github.com/galaxyproject/galaxy/compare/3907d83abe98...9e980862c8b7

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[galaxyproject/infrastructure-playbook] 482643: Additional TACC JS nodes
by GitHub 22 Apr '16

22 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 482643cabff22b5cff626a499b6cacb20963e8d8 https://github.com/galaxyproject/infrastructure-playbook/commit/482643cabff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Additional TACC JS nodes

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[galaxyproject/galaxy] 9681de: Improve handling of a missing R environment.
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9681ded30b087904005774435b2acc201a618a0a https://github.com/galaxyproject/galaxy/commit/9681ded30b087904005774435b2a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Improve handling of a missing R environment. Previously, the error message 'Missing R environment. Please check your specified R installation exists.' would be displayed in an obscure location in the log. With this change, galaxy will set the tool dependency to Error and display the error message in the admin panel. Commit: d0028bde0fee5a6158473a56ad357e942a92b7cb https://github.com/galaxyproject/galaxy/commit/d0028bde0fee5a6158473a56ad35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #2215 from davebx/td_fix Improve handling of a missing R environment. Compare: https://github.com/galaxyproject/galaxy/compare/c563d37bfd8d...d0028bde0fee

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[galaxyproject/infrastructure-playbook] d4f94a: Jetstream GO!
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d4f94ab28a7c4dac8a11ac06b3b44530baf52f3f https://github.com/galaxyproject/infrastructure-playbook/commit/d4f94ab28a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Jetstream GO!

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[galaxyproject/galaxy] ca5f60: Fix tool action redirects for non-default tools di...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca5f6053c7b13fa8f631f0a96f78a8aac544175c https://github.com/galaxyproject/galaxy/commit/ca5f6053c7b13fa8f631f0a96f78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Fix tool action redirects for non-default tools displaying tool forms Commit: f70a2b024237dcc797665134e311e7ada7602b1c https://github.com/galaxyproject/galaxy/commit/f70a2b024237dcc797665134e311… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Merge pull request #2211 from guerler/fix_nondefault_000 [16.04] Fix tool action redirect url for non-default tools Commit: 971613404c68a3c3e8ee1ca8bc34693714c4ae17 https://github.com/galaxyproject/galaxy/commit/971613404c68a3c3e8ee1ca8bc34… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) 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: ----------- Avoid reset of cursor position for input fields during manual entry Commit: 2734c2c4835ae725440c25314034f3dd296b00f1 https://github.com/galaxyproject/galaxy/commit/2734c2c4835ae725440c25314034… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) 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 #2218 from guerler/fix_cursor_001 [16.04] Avoid reset of cursor position for input fields during manual entry Commit: c563d37bfd8da83fcd090067b32e3421b35802fb https://github.com/galaxyproject/galaxy/commit/c563d37bfd8da83fcd090067b32e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/266a45ad7100...c563d37bfd8d

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[galaxyproject/galaxy] 971613: Avoid reset of cursor position for input fields du...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 971613404c68a3c3e8ee1ca8bc34693714c4ae17 https://github.com/galaxyproject/galaxy/commit/971613404c68a3c3e8ee1ca8bc34… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) 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: ----------- Avoid reset of cursor position for input fields during manual entry Commit: 2734c2c4835ae725440c25314034f3dd296b00f1 https://github.com/galaxyproject/galaxy/commit/2734c2c4835ae725440c25314034… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) 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 #2218 from guerler/fix_cursor_001 [16.04] Avoid reset of cursor position for input fields during manual entry Compare: https://github.com/galaxyproject/galaxy/compare/f70a2b024237...2734c2c4835a

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[galaxyproject/galaxy] ef12ae: Test fix for christ-h's french language date abbre...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ef12ae303577b2cc1967a08b341962f0ef1ffc5a https://github.com/galaxyproject/galaxy/commit/ef12ae303577b2cc1967a08b3419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako Log Message: ----------- Test fix for christ-h's french language date abbreviations breaking the old library display Commit: 7e93d462392952d27d414ba87d2dd406c9a60be1 https://github.com/galaxyproject/galaxy/commit/7e93d462392952d27d414ba87d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Another location where the non-ascii month was breaking display. Commit: 3907d83abe98a77dc6ecfb4abe818ea1bf31e9eb https://github.com/galaxyproject/galaxy/commit/3907d83abe98a77dc6ecfb4abe81… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations Compare: https://github.com/galaxyproject/galaxy/compare/5aefe1b193d8...3907d83abe98

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[galaxyproject/galaxy] c04fcc: Fix bug when determining locale
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c04fcc86b48ce7bfeed793e45d1b5418d9c11a55 https://github.com/galaxyproject/galaxy/commit/c04fcc86b48ce7bfeed793e45d1b… Author: yangyuanjie <jayyoung(a)yangyuanjiedeMacBook-Pro.local> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/utils/localization.js Log Message: ----------- Fix bug when determining locale Commit: 9cd168bbabf1347a02a435cc1186fdf4aac183bb https://github.com/galaxyproject/galaxy/commit/9cd168bbabf1347a02a435cc1186… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M static/maps/utils/localization.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/localization.js Log Message: ----------- make client Commit: 18dcf10aca7b65f2be2661886ddee86c6bb2c6c7 https://github.com/galaxyproject/galaxy/commit/18dcf10aca7b65f2be2661886dde… Author: xiaojay <xiaojay(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M static/maps/utils/localization.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/localization.js Log Message: ----------- Merge pull request #1 from dannon/xiaojay_dev Building the client Commit: 266a45ad71002e391b646da24aa40eccda0f21cc https://github.com/galaxyproject/galaxy/commit/266a45ad71002e391b646da24aa4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/utils/localization.js M static/maps/utils/localization.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/localization.js Log Message: ----------- Merge pull request #2213 from xiaojay/dev Fix bug when determining locale Compare: https://github.com/galaxyproject/galaxy/compare/be588228869a...266a45ad7100

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