- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 14e4c8: Had to respin the TACC controller with a new IP
by GitHub 29 Apr '16

29 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 14e4c87a627333d529e965f7e62d01bdf69bb69d https://github.com/galaxyproject/infrastructure-playbook/commit/14e4c87a627… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/all.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M roles/jetstream_nfs/tasks/server.yml Log Message: ----------- Had to respin the TACC controller with a new IP

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[galaxyproject/galaxy] 0b1275: Fix problem with FTP configuration introduced in f...
by GitHub 29 Apr '16

29 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b1275ba1232cec563616403578561485d07b487 https://github.com/galaxyproject/galaxy/commit/0b1275ba1232cec5636164035785… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M lib/galaxy/managers/context.py Log Message: ----------- Fix problem with FTP configuration introduced in f95cbf8f38801f03ba1ea9c065bc1796253d6eaf Thanks for @guerler for the catch. Commit: 1282fb19838b5cd8f72541c11d9b94edaf5d02a9 https://github.com/galaxyproject/galaxy/commit/1282fb19838b5cd8f72541c11d9b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M lib/galaxy/managers/context.py Log Message: ----------- Merge pull request #2271 from jmchilton/ftp_ident_fix Fix problem with FTP configuration. Compare: https://github.com/galaxyproject/galaxy/compare/9ac50faee3ec...1282fb19838b

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[galaxyproject/usegalaxy-playbook] a9283c: adjust tool panel search config
by GitHub 29 Apr '16

29 Apr '16

Branch: refs/heads/adjust-panel-search Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a9283c31557a56bc640160f271f46708303917e9 https://github.com/galaxyproject/usegalaxy-playbook/commit/a9283c31557a56bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- adjust tool panel search config we need more results with more weight on name and section

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[galaxyproject/galaxy] 9ba510: This is a preliminary fix for displaying raw text/...
by GitHub 29 Apr '16

29 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9ba510d68675ca7bb2ea036bbffeb82cd725f0fc https://github.com/galaxyproject/galaxy/commit/9ba510d68675ca7bb2ea036bbffe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- This is a preliminary fix for displaying raw text/html unicodify'd data (html reports, etc). TODO: Push this logic up into the framework so inside the webapp it's all unicode all the time. Commit: 8b6729e8535c4221da4c979652a389e7d6258fc2 https://github.com/galaxyproject/galaxy/commit/8b6729e8535c4221da4c979652a3… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #2266 from dannon/cherrypick_display_encoding [16.04] Cherrypick of encoding fix Commit: 9ac50faee3ec2cc938f5eb279a3b62a762661101 https://github.com/galaxyproject/galaxy/commit/9ac50faee3ec2cc938f5eb279a3b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a46ee8eaef28...9ac50faee3ec

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[galaxyproject/galaxy]
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/ts_printdebug Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 573887: Add default for print debug in the sample .ini
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5738870d86fde8f1a11280fcff9e8bf7fc7ca47e https://github.com/galaxyproject/galaxy/commit/5738870d86fde8f1a11280fcff9e… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/tool_shed.ini.sample Log Message: ----------- Add default for print debug in the sample .ini Commit: be6313f426e33f38b62d301913486605da60f1de https://github.com/galaxyproject/galaxy/commit/be6313f426e33f38b62d30191348… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample Log Message: ----------- remove unused config options; turn debug off for TS; other minor changes Commit: a46ee8eaef2877ce36e987c26361f6baf30055d8 https://github.com/galaxyproject/galaxy/commit/a46ee8eaef2877ce36e987c26361… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample Log Message: ----------- Merge pull request #2267 from galaxyproject/ts_printdebug cleanup TS and Reports configs Compare: https://github.com/galaxyproject/galaxy/compare/789b86f94bea...a46ee8eaef28

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[galaxyproject/galaxy] 07fc59: Correctly use defaults specified in galaxy.ini.sam...
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07fc59147f5d8bb047153ca9298b1319c89a4912 https://github.com/galaxyproject/galaxy/commit/07fc59147f5d8bb047153ca9298b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Correctly use defaults specified in galaxy.ini.sample for statsd. Commit: 789b86f94bead9f655afce09bb6b214109a3b976 https://github.com/galaxyproject/galaxy/commit/789b86f94bead9f655afce09bb6b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2268 from dannon/statsd_defaults_fix Correctly use defaults specified in galaxy.ini.sample for statsd. Compare: https://github.com/galaxyproject/galaxy/compare/bf0491f17acb...789b86f94bea

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[galaxyproject/galaxy] be6313: remove unused config options; turn debug off for T...
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/ts_printdebug Home: https://github.com/galaxyproject/galaxy Commit: be6313f426e33f38b62d301913486605da60f1de https://github.com/galaxyproject/galaxy/commit/be6313f426e33f38b62d30191348… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample Log Message: ----------- remove unused config options; turn debug off for TS; other minor changes

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[galaxyproject/galaxy] 573887: Add default for print debug in the sample .ini
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/ts_printdebug Home: https://github.com/galaxyproject/galaxy Commit: 5738870d86fde8f1a11280fcff9e8bf7fc7ca47e https://github.com/galaxyproject/galaxy/commit/5738870d86fde8f1a11280fcff9e… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/tool_shed.ini.sample Log Message: ----------- Add default for print debug in the sample .ini

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[galaxyproject/galaxy] 9ba510: This is a preliminary fix for displaying raw text/...
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 9ba510d68675ca7bb2ea036bbffeb82cd725f0fc https://github.com/galaxyproject/galaxy/commit/9ba510d68675ca7bb2ea036bbffe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- This is a preliminary fix for displaying raw text/html unicodify'd data (html reports, etc). TODO: Push this logic up into the framework so inside the webapp it's all unicode all the time. Commit: 8b6729e8535c4221da4c979652a389e7d6258fc2 https://github.com/galaxyproject/galaxy/commit/8b6729e8535c4221da4c979652a3… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #2266 from dannon/cherrypick_display_encoding [16.04] Cherrypick of encoding fix Compare: https://github.com/galaxyproject/galaxy/compare/ce31431f2949...8b6729e8535c

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[galaxyproject/galaxy] 5175ef: This is a preliminary fix for displaying raw text/...
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5175efd47dcaa229f2d6ae03d240fb5430ce1dea https://github.com/galaxyproject/galaxy/commit/5175efd47dcaa229f2d6ae03d240… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- This is a preliminary fix for displaying raw text/html unicodify'd data (html reports, etc). TODO: Push this logic up into the framework so inside the webapp it's all unicode all the time. Commit: bf0491f17acb5149b21799702e45d044cfb7e89f https://github.com/galaxyproject/galaxy/commit/bf0491f17acb5149b21799702e45… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #2263 from dannon/encode_raw_html_output Preliminary fix for displaying raw text/html Compare: https://github.com/galaxyproject/galaxy/compare/f7d748395252...bf0491f17acb

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[galaxyproject/galaxy] 1d7ddc: fixed ui bugs in tours
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d7ddc3c2ba9dcb17a523f87169e66f510078009 https://github.com/galaxyproject/galaxy/commit/1d7ddc3c2ba9dcb17a523f87169e… Author: Thomas Wollmann <thomas.wollmann(a)bioquant.uni-heidelberg.de> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- fixed ui bugs in tours Commit: f7d748395252dbfcb128a5fdbe986ce4b3084616 https://github.com/galaxyproject/galaxy/commit/f7d748395252dbfcb128a5fdbe98… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Merge pull request #2262 from ThomasWollmann/dev fixed ui bugs in tours Compare: https://github.com/galaxyproject/galaxy/compare/9242847a4f5d...f7d748395252

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[galaxyproject/galaxy] 65a3a6: Cleanup of the install and test framework.
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 65a3a6dcf650a74a74d8de04e4ea2ca418960e7f https://github.com/galaxyproject/galaxy/commit/65a3a6dcf650a74a74d8de04e4ea… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako R test/shed_functional/functional/test_0450_skip_tool_tests.py Log Message: ----------- Cleanup of the install and test framework. The system to install and test repositories has been deprecated, and this commit removes the parts that would display the results. Commit: cb1ca652f0fd3f3d9297a22474dfd7edb9b4c3b0 https://github.com/galaxyproject/galaxy/commit/cb1ca652f0fd3f3d9297a22474df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py Log Message: ----------- Remove imports that became unused. Commit: 9242847a4f5d3d63a6ed44f68ec0e48b2a256ab1 https://github.com/galaxyproject/galaxy/commit/9242847a4f5d3d63a6ed44f68ec0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako R test/shed_functional/functional/test_0450_skip_tool_tests.py Log Message: ----------- Merge pull request #2249 from davebx/remove_ttr Cleanup of the install and test framework. Compare: https://github.com/galaxyproject/galaxy/compare/898588a4d571...9242847a4f5d

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[galaxyproject/galaxy] 0187b7: Use standard model.orm.now for toolshed's password...
by GitHub 28 Apr '16

28 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0187b7f5e09566fde582997ab142627adfc9ebfc https://github.com/galaxyproject/galaxy/commit/0187b7f5e09566fde582997ab142… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Use standard model.orm.now for toolshed's password reset token datetime math Commit: 898588a4d5718e6f711659b2f6a226bb77bc03dd https://github.com/galaxyproject/galaxy/commit/898588a4d5718e6f711659b2f6a2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #2261 from dannon/prt_now Use standard model.orm.now for toolshed's password reset token dateti… Compare: https://github.com/galaxyproject/galaxy/compare/881c149f5a61...898588a4d571

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[galaxyproject/galaxy] 1f8834: Sort contributors by surname ASC.
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f8834bce2ff26f1ca11f95444351a66246b7461 https://github.com/galaxyproject/galaxy/commit/1f8834bce2ff26f1ca11f9544435… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Sort contributors by surname ASC. Commit: fa739eb1e6b7552bf9de8e0fe1e4bf0db4f1bc5c https://github.com/galaxyproject/galaxy/commit/fa739eb1e6b7552bf9de8e0fe1e4… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Update spelling. Commit: 881c149f5a618eca8d766f6b0f7397e2474c7359 https://github.com/galaxyproject/galaxy/commit/881c149f5a618eca8d766f6b0f73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #2258 from davebx/sort_contributors Sort contributors by surname ASC. Compare: https://github.com/galaxyproject/galaxy/compare/feb7fb92b70d...881c149f5a61

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[galaxyproject/galaxy] 846395: add Saskia to contributors
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84639571a188f4692f475ea79378e0566b5dcb57 https://github.com/galaxyproject/galaxy/commit/84639571a188f4692f475ea79378… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- add Saskia to contributors Commit: feb7fb92b70ddcb6660bcc2b80582a054e649cea https://github.com/galaxyproject/galaxy/commit/feb7fb92b70ddcb6660bcc2b8058… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #2256 from martenson/add-sas add Saskia to contributors Compare: https://github.com/galaxyproject/galaxy/compare/b51a1860cb20...feb7fb92b70d

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[galaxyproject/galaxy] c93f19: Cast everything to a string
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c93f1964933fb1a8596a958511b93908b3746f23 https://github.com/galaxyproject/galaxy/commit/c93f1964933fb1a8596a958511b9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-26 (Tue, 26 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Cast everything to a string cgi.escape doesn't work on non-strings Commit: a0db81e5a47e976aa9af0257a44cc5c958f67d9e https://github.com/galaxyproject/galaxy/commit/a0db81e5a47e976aa9af0257a44c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Address review comments Commit: b51a1860cb20f15f1dedc1c9f2237d14b88f64b0 https://github.com/galaxyproject/galaxy/commit/b51a1860cb20f15f1dedc1c9f223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #2252 from erasche/fix-2251 Cast everything to a string Compare: https://github.com/galaxyproject/galaxy/compare/c72381c528a9...b51a1860cb20

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[galaxyproject/usegalaxy-playbook] 759033: Swap test over to use galaxy-repl for sanitize_whi...
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 759033bc9364e73c4cab1e6950cc7812620031c9 https://github.com/galaxyproject/usegalaxy-playbook/commit/759033bc9364e73c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Swap test over to use galaxy-repl for sanitize_whitelist as well

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[galaxyproject/galaxy] 3e5505: initial files by IyadKandalaft
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e5505fa4de90cdb23f9fb1e00dcb4af6289521c https://github.com/galaxyproject/galaxy/commit/3e5505fa4de90cdb23f9fb1e00dc… Author: Iyad Kandalaft <ik(a)iyadk.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml A lib/galaxy/datatypes/mothur.py Log Message: ----------- initial files by IyadKandalaft Commit: f8a2dbd05a87782f5f0c30540ef463330d040589 https://github.com/galaxyproject/galaxy/commit/f8a2dbd05a87782f5f0c30540ef4… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml Log Message: ----------- add mothur prefix Commit: 8961d8bd3d52cdd1abeba6060a226192277dbc2d https://github.com/galaxyproject/galaxy/commit/8961d8bd3d52cdd1abeba6060a22… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- use 'with open' throughout Commit: 4311a4fbf84c073fbe01806ce7968c10cabfd00b https://github.com/galaxyproject/galaxy/commit/4311a4fbf84c073fbe01806ce796… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- minor changes to list creations Commit: 65dde43041b94fd7f04f47369cb3302514a3e997 https://github.com/galaxyproject/galaxy/commit/65dde43041b94fd7f04f47369cb3… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-03-26 (Sat, 26 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- remove sniffers for datatypes that were subclassed Commit: 45bf09dad0c8b3db9c0f9973d9347932d108e172 https://github.com/galaxyproject/galaxy/commit/45bf09dad0c8b3db9c0f9973d934… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/mothur.py Log Message: ----------- add mothur prefix to extension, update sniffers and sniffer order, subclass taxonomy datatypes Commit: ef32ee15fd9ee7a61c018a7e22a3cae0cc498b87 https://github.com/galaxyproject/galaxy/commit/ef32ee15fd9ee7a61c018a7e22a3… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/mothur.py Log Message: ----------- remove phylip datatype (not specific to mothur) Commit: 6ac7ec56032e25e9f883421d5aba6d1e6165e2cc https://github.com/galaxyproject/galaxy/commit/6ac7ec56032e25e9f883421d5aba… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- make sniffers for otu and distmatrices stricter Commit: c43235011bf211da96b4507b986850ccc59567f8 https://github.com/galaxyproject/galaxy/commit/c43235011bf211da96b4507b9868… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- remove two unused classes Commit: b833d385056f23dfb314e4c8162982374766e73d https://github.com/galaxyproject/galaxy/commit/b833d385056f23dfb314e4c81629… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml Log Message: ----------- stop using deprecated 'interpreter' Commit: f3820538d186a1143443e47e764ad8ddc001d27f https://github.com/galaxyproject/galaxy/commit/f3820538d186a1143443e47e764a… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- stylefixes Commit: 31129e9d18b52eb9842a0ebbfe1eabbaedc73334 https://github.com/galaxyproject/galaxy/commit/31129e9d18b52eb9842a0ebbfe1e… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- subclass mothur.align Commit: 43f7564365ac101bfd43c55b741b1543eed6457d https://github.com/galaxyproject/galaxy/commit/43f7564365ac101bfd43c55b741b… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist Log Message: ----------- update sniffers and add doctests Commit: a82a5b20ddd71e1a5180a15220e9aa000f307dbe https://github.com/galaxyproject/galaxy/commit/a82a5b20ddd71e1a5180a15220e9… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/mothur.py Log Message: ----------- stylefixes and updates set_metas Commit: 3a74c774095c2d3967bba869e74cceaf94479f66 https://github.com/galaxyproject/galaxy/commit/3a74c774095c2d3967bba869e74c… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/mothur.py Log Message: ----------- add python optimisations Commit: f56e81a996511869f4a068418ffcd104c1b0ccdc https://github.com/galaxyproject/galaxy/commit/f56e81a996511869f4a068418ffc… Author: shiltemann <zazkia(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- allow for comment lines in Otu files Commit: d47f8f577e358b4e7a71b15a905040e5d3b079d4 https://github.com/galaxyproject/galaxy/commit/d47f8f577e358b4e7a71b15a9050… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fixup exception handling in mothur datatypes. Commit: d73a86d3658ed2ff7815ba5bd57ae63e527d4381 https://github.com/galaxyproject/galaxy/commit/d73a86d3658ed2ff7815ba5bd57a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Add a sample sniff test for new Mothur datatype. The existing sniffer tests with the mothur stuff tests the sniffers in isolation - this is more of an integration test that tests the sample datatype configuration for the newly added mothur stuff. Commit: 04476160aa19f3ce5cbd345cd8b3073575ed327b https://github.com/galaxyproject/galaxy/commit/04476160aa19f3ce5cbd345cd8b3… Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #1 from jmchilton/mothur_datatypes Small tweaks to mothur dataytpes. Commit: c72381c528a9ab0afc231f1d109c8f4e66860b2e https://github.com/galaxyproject/galaxy/commit/c72381c528a9ab0afc231f1d109c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist Log Message: ----------- Merge pull request #2038 from shiltemann/mothur_datatypes Import mothur datatypes Compare: https://github.com/galaxyproject/galaxy/compare/a7bcd69f9e6b...c72381c528a9

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[galaxyproject/usegalaxy-playbook] c620ad: Swap main to use a location we can actually write ...
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c620ad87abb00056ee20c8140761c041e7bb8995 https://github.com/galaxyproject/usegalaxy-playbook/commit/c620ad87abb00056… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Swap main to use a location we can actually write to for sanitize_whitelist_file

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[galaxyproject/galaxy] aaf09d: Generate metadata in separate conda environment
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aaf09dc99b0dc2896cbba5d21c132e998f5126e7 https://github.com/galaxyproject/galaxy/commit/aaf09dc99b0dc2896cbba5d21c13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 5dd9d1bafcc4532fdb48b312a47e2f90b7178d80 https://github.com/galaxyproject/galaxy/commit/5dd9d1bafcc4532fdb48b312a47e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: a7bcd69f9e6b72279772cc9ca003408df830e881 https://github.com/galaxyproject/galaxy/commit/a7bcd69f9e6b72279772cc9ca003… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2253 from mvdbeek/conda-metadata-env Generate metadata in separate conda environment Compare: https://github.com/galaxyproject/galaxy/compare/8a3b5d3d3e36...a7bcd69f9e6b

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[galaxyproject/galaxy] 4630c6: Tool execution dependency resolution already conta...
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4630c6417d4e2c0ec747df02d28578f9576bb2a4 https://github.com/galaxyproject/galaxy/commit/4630c6417d4e2c0ec747df02d285… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Tool execution dependency resolution already contains the relevant information for viewing dependency resolution attempts and warns when the dependency isn't found (Null resolver). Pretty sure this was just a stray extra debugging statement that got unintentionally left in, and it's pretty chatty. Commit: 8a3b5d3d3e36946f240b55de071b75e4c0fa2e07 https://github.com/galaxyproject/galaxy/commit/8a3b5d3d3e36946f240b55de071b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2254 from dannon/remove_dep_debugging Tool execution dependency resolution already contains the relevant Compare: https://github.com/galaxyproject/galaxy/compare/e2287e2c9dd6...8a3b5d3d3e36

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[galaxyproject/galaxy] bf5568: Quote some parameters in Trim tool command
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf5568d86ae2e111ab90b9658192ee70faf11fc7 https://github.com/galaxyproject/galaxy/commit/bf5568d86ae2e111ab90b9658192… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M tools/filters/trimmer.xml Log Message: ----------- Quote some parameters in Trim tool command Make the tool more robust, see issue #2245. Also: - use format_source instead of deprecated format='input'; - explicitly call python in command instead of using the depredated interpreter attribute; - use CDATA in command. Commit: e2287e2c9dd6cf394dbb30b1e77123a25a29d8f5 https://github.com/galaxyproject/galaxy/commit/e2287e2c9dd6cf394dbb30b1e771… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M tools/filters/trimmer.xml Log Message: ----------- Merge pull request #2248 from nsoranzo/fix_trimmer_tool Quote some parameters in Trim tool command Compare: https://github.com/galaxyproject/galaxy/compare/d7031d982219...e2287e2c9dd6

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[galaxyproject/galaxy] 7718ac: Rename Utils.validate() to Utils.isEmpty()
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7718ac511b87078c48a2c6d1f396990e6dbb7f1a https://github.com/galaxyproject/galaxy/commit/7718ac511b87078c48a2c6d1f396… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.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/mvc/form/form-parameters.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js Log Message: ----------- Rename Utils.validate() to Utils.isEmpty() Commit: faa2e69ec72e51b10e8a8d96a3a92b2868192c6e https://github.com/galaxyproject/galaxy/commit/faa2e69ec72e51b10e8a8d96a3a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js Log Message: ----------- Add test cases Commit: d7031d982219c1530a83d645cf897dc609fb6431 https://github.com/galaxyproject/galaxy/commit/d7031d982219c1530a83d645cf89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.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/mvc/form/form-parameters.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js Log Message: ----------- Merge pull request #2239 from guerler/rename_jsvalidate_000 Rename/refactor Utils.validate() to Utils.isEmpty() Compare: https://github.com/galaxyproject/galaxy/compare/01472fdc0188...d7031d982219

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[galaxyproject/usegalaxy-playbook] f019c1: Update main version
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f019c1a2e581a5ae5e2f75fe26ea265d9f8c4514 https://github.com/galaxyproject/usegalaxy-playbook/commit/f019c1a2e581a5ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-26 (Tue, 26 Apr 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update main version

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