- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0ba54e: Treat the value of `message_box_visible` in galaxy...
by GitHub 08 Nov '16

08 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ba54e922046733e582b7c5b4066525edc3957aa https://github.com/galaxyproject/galaxy/commit/0ba54e922046733e582b7c5b4066… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Treat the value of `message_box_visible` in galaxy.ini as a boolean Commit: 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 https://github.com/galaxyproject/galaxy/commit/7bee2651aa8f08ea0495d167e33d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- string_as_bool for message_box_visible on webapps Commit: 3d69a2d1a5f7ee5606834c45e34e341fa4822721 https://github.com/galaxyproject/galaxy/commit/3d69a2d1a5f7ee5606834c45e34e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #3139 from natefoo/message-box-bool Treat the value of `message_box_visible` in galaxy.ini as a boolean Compare: https://github.com/galaxyproject/galaxy/compare/6a8ca92dd70b...3d69a2d1a5f7

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[galaxyproject/galaxy] 7c030e: Use sed instead of pandoc to insert TOC in schema ...
by GitHub 08 Nov '16

08 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c030ebf2f51c6800966a2fc2d1b0048f0930f1d https://github.com/galaxyproject/galaxy/commit/7c030ebf2f51c6800966a2fc2d1b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Use sed instead of pandoc to insert TOC in schema doc pandoc < 1.14 adds the TOC depth as a float, which is not recognised by Sphinx. Also, move the TOC after the introduction, which looks nicer. Commit: 6a8ca92dd70bc88bee962cd079460118f998c351 https://github.com/galaxyproject/galaxy/commit/6a8ca92dd70bc88bee962cd07946… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Merge pull request #3135 from nsoranzo/followup_on_3086 Use sed instead of pandoc to insert TOC in schema doc Compare: https://github.com/galaxyproject/galaxy/compare/3b8f543ebdd1...6a8ca92dd70b

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[galaxyproject/galaxy] 192f66: Update galaxy.xsd
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 192f66a714f3c7dd320550def43d7cd283dfa6af https://github.com/galaxyproject/galaxy/commit/192f66a714f3c7dd320550def43d… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Update galaxy.xsd Add `hidden_data` in `ParamType` The context [cufflinks](https://github.com/galaxyproject/tools-devteam/blob/master/tool_… `planemo lint .` ``` Applying linter tool_xsd... FAIL .. ERROR: Invalid tmpw5U2MV found. Errors [/tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_ENUMERATION_VALID: Element 'param', attribute 'type': [facet 'enumeration'] The value 'hidden_data' is not an element of the set {'text', 'integer', 'float', 'color', 'boolean', 'genomebuild', 'library_data', 'select', 'data_column', 'hidden', 'baseurl', 'file', 'data', 'drill_down', 'data_collection'}. /tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_DATATYPE_VALID_1_2_1: Element 'param', attribute 'type': 'hidden_data' is not a valid value of the atomic type 'ParamType'. ``` I don’t know so much this tag `hidden_data`, but it seems that it’s still in the [Galaxy doc](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-p… Commit: 3b8f543ebdd1307c91c3ae719bbb7072476d7b9a https://github.com/galaxyproject/galaxy/commit/3b8f543ebdd1307c91c3ae719bbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3132 from lecorguille/patch-2 Update galaxy.xsd Compare: https://github.com/galaxyproject/galaxy/compare/78dfb95f0264...3b8f543ebdd1

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[galaxyproject/galaxy] e06581: Extended the linter rules to accept a help attribu...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e06581c587cdfe24822fba2f79ddaf60619858d2 https://github.com/galaxyproject/galaxy/commit/e06581c587cdfe24822fba2f79dd… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Extended the linter rules to accept a help attribute for sections Commit: b169299b5efbd144d5ab43f28e079a3fa5cf45a8 https://github.com/galaxyproject/galaxy/commit/b169299b5efbd144d5ab43f28e07… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Extended linter rule for help attribute in section Commit: 78dfb95f0264e349ee03b5c1a7c1cde9c6e38ba4 https://github.com/galaxyproject/galaxy/commit/78dfb95f0264e349ee03b5c1a7c1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3131 from joachimwolff/dev Extended the linter rules to accept a help attribute for sections Compare: https://github.com/galaxyproject/galaxy/compare/04935ce94b86...78dfb95f0264

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[galaxyproject/galaxy] 05fbef: Add doc for conda_copy_dependencies option
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05fbef510c7497911a2abea83c5bdc26bf338460 https://github.com/galaxyproject/galaxy/commit/05fbef510c7497911a2abea83c5b… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add doc for conda_copy_dependencies option Discussed on IUC gitter, related to https://github.com/galaxyproject/galaxy/issues/3008 Commit: 16866b5e8075d648bd17ac3786f76356e23c43a2 https://github.com/galaxyproject/galaxy/commit/16866b5e8075d648bd17ac3786f7… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- add extra time problem Commit: 69cda7ee10d78a61830f90f957500ba41821640b https://github.com/galaxyproject/galaxy/commit/69cda7ee10d78a61830f90f95750… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- clarify links Commit: 8a972cc325fd39b71d89f28d9eec62630d9859ac https://github.com/galaxyproject/galaxy/commit/8a972cc325fd39b71d89f28d9eec… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- be stronger Commit: 04935ce94b864a7898dc62895a11023dec805580 https://github.com/galaxyproject/galaxy/commit/04935ce94b864a7898dc62895a11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3105 from abretaud/patch-2 Add doc for conda_copy_dependencies option Compare: https://github.com/galaxyproject/galaxy/compare/3200fa343b12...04935ce94b86

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Commit: 53a66c9d46780a4910a8a03de565eb3fb53f5bdc https://github.com/galaxyproject/galaxy/commit/53a66c9d46780a4910a8a03de565… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 3200fa343b12b2c40ad6b3e29b77c6628d66b7a0 https://github.com/galaxyproject/galaxy/commit/3200fa343b12b2c40ad6b3e29b77… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/util/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/202f96c73114...3200fa343b12

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Commit: 53a66c9d46780a4910a8a03de565eb3fb53f5bdc https://github.com/galaxyproject/galaxy/commit/53a66c9d46780a4910a8a03de565… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/d72cc77bebd4...53a66c9d4678

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/65338b3adb92...788dc1ebef51

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[galaxyproject/galaxy] 51c586: Fix tools placed outside of panel section
by GitHub 06 Nov '16

06 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51c586c264f2acd912060297804d61c2539f2483 https://github.com/galaxyproject/galaxy/commit/51c586c264f2acd912060297804d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix tools placed outside of panel section Occasionally tools were being installed outside of the selected too panel section. In the log one would find contradicting messages such as ``` tool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'. galaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools 172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e…" " Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.71 Safari/537.36 nvalid tool_panel_section_key "ncbi_sra_tools" specified. Tools will be loaded outside of sections in the tool panel. ``` The intermittent POST is picked up by a different thread, that didn't have its toolbox updated with the new section. To circumvent this, we send the `create_panel_section` task to all threads. Commit: 4365b907293e366d4ad48396bb5c9dc00f134611 https://github.com/galaxyproject/galaxy/commit/4365b907293e366d4ad48396bb5c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Fix toolbox unittests Commit: 202f96c73114fe9f05ed295505243ba17716b0e2 https://github.com/galaxyproject/galaxy/commit/202f96c73114fe9f05ed29550524… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3125 from mvdbeek/fix_invalid_section_key Fix tools placed outside of panel section Compare: https://github.com/galaxyproject/galaxy/compare/58b7b6cf15c5...202f96c73114

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[galaxyproject/ansible-galaxy] ac29aa: Drop support for "Galaxy pip"
by GitHub 05 Nov '16

05 Nov '16

Branch: refs/tags/0.6.4 Home: https://github.com/galaxyproject/ansible-galaxy Commit: ac29aad5e27b546c51a4ce584b78056cb0a4631f https://github.com/galaxyproject/ansible-galaxy/commit/ac29aad5e27b546c51a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Drop support for "Galaxy pip"

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 05 Nov '16

05 Nov '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Compare: https://github.com/galaxyproject/galaxy/compare/f7c3e25e5db1...a274e635a6f7

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[galaxyproject/galaxy] 2956f9: BLAST database *.loc.sample files
by GitHub 05 Nov '16

05 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2956f94aa06f62fc0adde93d5aacc69e693a62d8 https://github.com/galaxyproject/galaxy/commit/2956f94aa06f62fc0adde93d5aac… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample Log Message: ----------- BLAST database *.loc.sample files Commit: 2e36fdb0bd0fff246eeff6322542c31150804eb2 https://github.com/galaxyproject/galaxy/commit/2e36fdb0bd0fff246eeff6322542… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Include all three BLAST .loc files in data table conf Commit: f060795335e564f79ed3f28b5390db4ac8e7d735 https://github.com/galaxyproject/galaxy/commit/f060795335e564f79ed3f28b5390… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A lib/galaxy/datatypes/blast.py Log Message: ----------- BLAST datatypes as of standalone blast_datatypes v0.0.21 Copied from separate BLAST+ Galaxy repository, https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatyp… Currently available from the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Primary contributors to the BLAST datatypes for Galaxy: * Peter Cock (The James Hutton Institute, UK) * Edward Kirton * Nicola Soranzo * Bjoern Gruening This work and the associated BLAST+ wrappers can be cited as: NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo *GigaScience* 2015, 4:39 DOI: http://dx.doi.org/10.1186/s13742-015-0080-7 Commit: a53e9fa9dbd635ee6359fb6b68371a3d0e5159c6 https://github.com/galaxyproject/galaxy/commit/a53e9fa9dbd635ee6359fb6b6837… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Remove unused imports Commit: bdd046a2e86c935e1c932421a25e7ed480aacdf8 https://github.com/galaxyproject/galaxy/commit/bdd046a2e86c935e1c932421a25e… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Missing import required for use as doctest Commit: 193651c88d325a5c1710def37386524e956ac147 https://github.com/galaxyproject/galaxy/commit/193651c88d325a5c1710def37386… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml Log Message: ----------- Sample blastxml file for sniff doctest Commit: ea717dd0013c9ef69d5ea0cd8edb72f44546e5d8 https://github.com/galaxyproject/galaxy/commit/ea717dd0013c9ef69d5ea0cd8edb… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add BLAST datatypes to datatypes_conf.xml.sample Commit: 8b73de6f50572ea2fb815fa75460f5850b877f12 https://github.com/galaxyproject/galaxy/commit/8b73de6f50572ea2fb815fa75460… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Adjust import order as per Galaxy tox flake8 checks Commit: f9eff95613cdf27f5300ea393418f017da8e8012 https://github.com/galaxyproject/galaxy/commit/f9eff95613cdf27f5300ea393418… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- More accurate module docstring Commit: 0152254a6f455bae538c96f3ce85baee1ae1c9f8 https://github.com/galaxyproject/galaxy/commit/0152254a6f455bae538c96f3ce85… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- megablast_xml_parser_test1.blastxml should now sniff as blastxml Commit: 48664fa2fe7f43ee667e9fa4ece51852632570e7 https://github.com/galaxyproject/galaxy/commit/48664fa2fe7f43ee667e9fa4ece5… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Ensure all BLAST datatype contributors in CONTRIBUTORS.md Commit: ce5ceeb29b134a84cf577f0bf2244011ac0cdfe4 https://github.com/galaxyproject/galaxy/commit/ce5ceeb29b134a84cf577f0bf224… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Give my work email address as well. My Galaxy work to date has been while employed at The James Hutton Institute (UK). Commit: 17783cec36f4bf0d3b79137842dad52a64f80da2 https://github.com/galaxyproject/galaxy/commit/17783cec36f4bf0d3b79137842da… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py Log Message: ----------- Tweak testing installing BLAST datatypes from Tool Shed This is a short term pragmatic solution for the planned return of the BLAST datatypes to the main Galaxy distribution. Long term an additional test using an alternative Tool Shed defined datatype may be needed. Commit: 7fe47735209e43501e6116453a2fd961e5934429 https://github.com/galaxyproject/galaxy/commit/7fe47735209e43501e6116453a2f… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Clearer error message if BLAST XML header too long Commit: 4159770ed9d173a2a3b45f7615aa764be9e99188 https://github.com/galaxyproject/galaxy/commit/4159770ed9d173a2a3b45f7615aa… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Explicitly label blast.py as MIT licensed. Edward Kirton's contributions were made under the MIT license while this code was developed outside of the main Galaxy Project and distributed via the Galaxy Tool Shed). We have not been able to contact him to authorise re-licensing under the main Galaxy Project's license instead. Commit: b5ba9605e56b8a8c8a827c6bd83208314ab8ccf0 https://github.com/galaxyproject/galaxy/commit/b5ba9605e56b8a8c8a827c6bd832… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Mark BLAST XML with EDAM ontology terms. As per Herve Menager, EDAM format should be 3331 and data 0857 (sequence search results). Commit: 58b7b6cf15c57a9a42340baeb2131e42cc76d02d https://github.com/galaxyproject/galaxy/commit/58b7b6cf15c57a9a42340baeb213… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M CONTRIBUTORS.md M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample Log Message: ----------- Merge pull request #2696 from peterjc/blast_datatypes Returning Blast datatypes to Galaxy core (work-in-progress) Compare: https://github.com/galaxyproject/galaxy/compare/b1892b7e30f9...58b7b6cf15c5

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[galaxyproject/galaxy] 66dec1: Add download_to_file function to galaxy.util
by GitHub 04 Nov '16

04 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66dec1d580b426ad955db03608ec7da7eb5c5018 https://github.com/galaxyproject/galaxy/commit/66dec1d580b426ad955db03608ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/base/driver_util.py Log Message: ----------- Add download_to_file function to galaxy.util Use it in 2 places: - test/base/driver_util.py (thus adding timeout and chunking) - lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py where the total download timeout is substituted with the usual urllib timeout Commit: b1892b7e30f9e2a9be94bd8ee064c0f548525bfe https://github.com/galaxyproject/galaxy/commit/b1892b7e30f9e2a9be94bd8ee064… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/base/driver_util.py Log Message: ----------- Merge pull request #3100 from nsoranzo/followup_on_3013 Add download_to_file function to galaxy.util Compare: https://github.com/galaxyproject/galaxy/compare/37399049552d...b1892b7e30f9

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[galaxyproject/galaxy] d5132a: Log invalid xml filename
by GitHub 04 Nov '16

04 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5132a374c25d17e63a19379bcec1d42b99f8547 https://github.com/galaxyproject/galaxy/commit/d5132a374c25d17e63a19379bcec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: 37399049552dd1f2f4492e4eb9f168ac8a9abd5f https://github.com/galaxyproject/galaxy/commit/37399049552dd1f2f4492e4eb9f1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3124 from mvdbeek/escape_sections Log invalid xml filename Compare: https://github.com/galaxyproject/galaxy/compare/4866e72ad22b...37399049552d

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[galaxyproject/galaxy] 5e19d6: Escape section id and name when writing integrated...
by GitHub 04 Nov '16

04 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e19d6c57465ce79d4ee96e3206542ac655d137d https://github.com/galaxyproject/galaxy/commit/5e19d6c57465ce79d4ee96e32065… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: 4866e72ad22b1772f93c8973e51f32086896277f https://github.com/galaxyproject/galaxy/commit/4866e72ad22b1772f93c8973e51f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #3122 from mvdbeek/escape_sections Escape section name when writing to xml, Compare: https://github.com/galaxyproject/galaxy/compare/1d8f31c4f488...4866e72ad22b

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[galaxyproject/usegalaxy-playbook] 4150f1: Increase flanking_features_1 to 16GB
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4150f10af479199882735a039af2769edb4e9a9d https://github.com/galaxyproject/usegalaxy-playbook/commit/4150f10af4791998… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase flanking_features_1 to 16GB

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[galaxyproject/galaxy] 6082f7: Fix path
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Commit: d72cc77bebd46b0e60d09e19cee2496777503f11 https://github.com/galaxyproject/galaxy/commit/d72cc77bebd46b0e60d09e19cee2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 1d8f31c4f488dc380ffe657e5fa4a9d9cdd697ae https://github.com/galaxyproject/galaxy/commit/1d8f31c4f488dc380ffe657e5fa4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/94fd3a51a2a3...1d8f31c4f488

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[galaxyproject/galaxy] 6082f7: Fix path
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Commit: d72cc77bebd46b0e60d09e19cee2496777503f11 https://github.com/galaxyproject/galaxy/commit/d72cc77bebd46b0e60d09e19cee2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/5963a2fa22e6...d72cc77bebd4

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[galaxyproject/galaxy] 6082f7: Fix path
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Compare: https://github.com/galaxyproject/galaxy/compare/2adb98e58cc0...65338b3adb92

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[galaxyproject/galaxy] 8f89a0: Fix job_working_directory commented default
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8f89a04eae27e615434e268f93d492b6c0cd54be https://github.com/galaxyproject/galaxy/commit/8f89a04eae27e615434e268f93d4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix job_working_directory commented default Follow-up to commit 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726. Commit: 83760e6a01cd3fa16a17158bb1182ffebb00c5d7 https://github.com/galaxyproject/galaxy/commit/83760e6a01cd3fa16a17158bb118… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M doc/source/conf.py Log Message: ----------- Don't skip __init__() methods when generating docs Commit: 402f2815c23d695f0673d0af9acb9cf0e3527afa https://github.com/galaxyproject/galaxy/commit/402f2815c23d695f0673d0af9acb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Drop code which is never executed After commit 59583f26ea11b44cb17f260230be820b304cd918, self.object_store_config_file is always set. Commit: ad515397388056b8587c80350b755444602a49d0 https://github.com/galaxyproject/galaxy/commit/ad515397388056b8587c80350b75… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix typo Commit: 0c28a64269048ea21701e6c5b358d783bdde8eed https://github.com/galaxyproject/galaxy/commit/0c28a64269048ea21701e6c5b358… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/objectstore/rods.py Log Message: ----------- Remove redundant ObjectStore superclass Commit: 1c68e0af3e9a02250d0d12c2149dcdbb1caf2da2 https://github.com/galaxyproject/galaxy/commit/1c68e0af3e9a02250d0d12c2149d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Fix object stores' __init__() methods doc Also: - remove unused parameters when calling the parent constructors - Python3 compatibility Commit: 94fd3a51a2a3a46aa4a834ed6d7d0bb50e6154a5 https://github.com/galaxyproject/galaxy/commit/94fd3a51a2a3a46aa4a834ed6d7d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M config/galaxy.ini.sample M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py Log Message: ----------- Merge pull request #3119 from nsoranzo/misc_fixes Object store and other misc fixes Compare: https://github.com/galaxyproject/galaxy/compare/aa72f4a0b62a...94fd3a51a2a3

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[galaxyproject/galaxy]
by GitHub 02 Nov '16

02 Nov '16

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

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[galaxyproject/galaxy] 892237: Fix linting broken in #3080
by GitHub 02 Nov '16

02 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 892237bf0042e458db7c7220eb4faf022b5a7650 https://github.com/galaxyproject/galaxy/commit/892237bf0042e458db7c7220eb4f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix linting broken in #3080 Also fix import order and Python3 compatibility. Commit: aa72f4a0b62a7795bc726dd75bdb7635d29afef5 https://github.com/galaxyproject/galaxy/commit/aa72f4a0b62a7795bc726dd75bdb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #3116 from nsoranzo/fix_for_3080 Fix linting broken in #3080 Compare: https://github.com/galaxyproject/galaxy/compare/ef3e63e6d732...aa72f4a0b62a

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[galaxyproject/galaxy] 600112: remove the communication server check
by GitHub 02 Nov '16

02 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Commit: 096a7bf94d799f905013f7052c1bdf87062a45a7 https://github.com/galaxyproject/galaxy/commit/096a7bf94d799f905013f7052c1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the incorrect handling of root when prefix is in play Commit: 65dc4f22aa7b717109aca6fac7947a84d2bd587a https://github.com/galaxyproject/galaxy/commit/65dc4f22aa7b717109aca6fac794… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #3074 from martenson/fix-libraries-prefix [16.07] Fix libraries prefix Commit: 9abe863f26ba742c9f362b3a8177af5c8efa5741 https://github.com/galaxyproject/galaxy/commit/9abe863f26ba742c9f362b3a8177… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix loading of collection operations If MODEL_TOOLS_PATH is not absolute, it will be joined with tool_path (i.e. './tools' ) inside _load_tool_tag_set(), so Galaxy will try to load e.g. './tools/lib/galaxy/tools/unzip_collection.xml' Commit: 5963a2fa22e64b5494a1aa00931808a11d792cbd https://github.com/galaxyproject/galaxy/commit/5963a2fa22e64b5494a1aa009318… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3115 from nsoranzo/release_16.07_fix_collection_ops_loading [16.07] Fix loading of collection operations Commit: ef3e63e6d7327719a4581bb939dff8fd1ac1fcd9 https://github.com/galaxyproject/galaxy/commit/ef3e63e6d7327719a4581bb939df… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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 M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/user/index.mako Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/38dd9ca509ed...ef3e63e6d732

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[galaxyproject/galaxy] 9abe86: Fix loading of collection operations
by GitHub 02 Nov '16

02 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 9abe863f26ba742c9f362b3a8177af5c8efa5741 https://github.com/galaxyproject/galaxy/commit/9abe863f26ba742c9f362b3a8177… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix loading of collection operations If MODEL_TOOLS_PATH is not absolute, it will be joined with tool_path (i.e. './tools' ) inside _load_tool_tag_set(), so Galaxy will try to load e.g. './tools/lib/galaxy/tools/unzip_collection.xml' Commit: 5963a2fa22e64b5494a1aa00931808a11d792cbd https://github.com/galaxyproject/galaxy/commit/5963a2fa22e64b5494a1aa009318… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3115 from nsoranzo/release_16.07_fix_collection_ops_loading [16.07] Fix loading of collection operations Compare: https://github.com/galaxyproject/galaxy/compare/65dc4f22aa7b...5963a2fa22e6

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[galaxyproject/galaxy] ce1c7e: Restore XML formatting for schema document.
by GitHub 01 Nov '16

01 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce1c7e41c6d90e1ca7d00c68afbd4fca8f55115e https://github.com/galaxyproject/galaxy/commit/ce1c7e41c6d90e1ca7d00c68afbd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Restore XML formatting for schema document. Commit: 38dd9ca509ed50b3cf48689522ee884226cc1219 https://github.com/galaxyproject/galaxy/commit/38dd9ca509ed50b3cf48689522ee… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M doc/Makefile Log Message: ----------- Merge pull request #3113 from jmchilton/schema_build Restore XML formatting for tool schema document. Compare: https://github.com/galaxyproject/galaxy/compare/aaf5b4d0f8a8...38dd9ca509ed

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