- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] b1a247: Add data managers on Test
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b1a2477ec7e0867432df1c0923e5b54822a3b297 https://github.com/galaxyproject/usegalaxy-playbook/commit/b1a2477ec7e08674… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add data managers on Test

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[galaxyproject/galaxy] 884b1d: Change scratchbook close icon
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 884b1d42db8ca46dc5613e398cc22015a5384935 https://github.com/galaxyproject/galaxy/commit/884b1d42db8ca46dc5613e398cc2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map 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/ui/ui-frames.js Log Message: ----------- Change scratchbook close icon Commit: 1730c12f8d3ba9d7e32bfbd1625835ab0d7dae53 https://github.com/galaxyproject/galaxy/commit/1730c12f8d3ba9d7e32bfbd16258… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map 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/ui/ui-frames.js Log Message: ----------- Merge pull request #1425 from guerler/fix_close_icon_000 Change scratchbook close icon Compare: https://github.com/galaxyproject/galaxy/compare/099f1447a666...1730c12f8d3b

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[galaxyproject/galaxy] 62b80d: Fix onclick broken in #1407
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62b80dfcc5e00ee92c2be83bbd89911158b9f9b4 https://github.com/galaxyproject/galaxy/commit/62b80dfcc5e00ee92c2be83bbd89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/layout/menu.js Log Message: ----------- Fix onclick broken in #1407 Commit: 099f1447a66631250f61f5b61920f9b11018daa2 https://github.com/galaxyproject/galaxy/commit/099f1447a66631250f61f5b61920… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/layout/menu.js Log Message: ----------- Merge pull request #1424 from dannon/fix_onclick Fix masthead/menu.js onclick functionality Compare: https://github.com/galaxyproject/galaxy/compare/c97053a5e844...099f1447a666

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[galaxyproject/galaxy] 6cea51: Fix conda installation in debug mode
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6cea5121b1159a1966647dafb8d7930e9c5ee53c https://github.com/galaxyproject/galaxy/commit/6cea5121b1159a1966647dafb8d7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix conda installation in debug mode Commit: c97053a5e844ff19b628f65282a1392c86240b0a https://github.com/galaxyproject/galaxy/commit/c97053a5e844ff19b628f65282a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #1421 from galaxyproject/conda_install_fix Fix conda installation in debug mode Compare: https://github.com/galaxyproject/galaxy/compare/5a441044fbc1...c97053a5e844

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[galaxyproject/galaxy] 6cea51: Fix conda installation in debug mode
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/conda_install_fix Home: https://github.com/galaxyproject/galaxy Commit: 6cea5121b1159a1966647dafb8d7930e9c5ee53c https://github.com/galaxyproject/galaxy/commit/6cea5121b1159a1966647dafb8d7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix conda installation in debug mode

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[galaxyproject/usegalaxy-playbook] a4bea6: update Main mutable confs
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4bea6cd5f0c997fb4ee7cbb2090d6bb5af21a25 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4bea6cd5f0c997f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Main mutable confs

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[galaxyproject/galaxy] 8af567: Allow input collections to specify mutiple collect...
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8af5671953df12e5207a8b3e5e70c742cea9f158 https://github.com/galaxyproject/galaxy/commit/8af5671953df12e5207a8b3e5e70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-13 (Sun, 13 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Allow input collections to specify mutiple collection types. Parallelling format specifier which can take multiple formats. Commit: 5a441044fbc1b773f9a59f12050a8b7dcda11694 https://github.com/galaxyproject/galaxy/commit/5a441044fbc1b773f9a59f12050a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1308 from jmchilton/multi_collection_types Allow input collections to specify multiple collection types. Compare: https://github.com/galaxyproject/galaxy/compare/4c0bb9902ada...5a441044fbc1

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[galaxyproject/galaxy] 3924a5: Fixed indentation errors
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 3924a5a0e3d2c7d787e81fabc4e2908f30ff0168 https://github.com/galaxyproject/galaxy/commit/3924a5a0e3d2c7d787e81fabc4e2… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed indentation errors Commit: 7b45f7b4047377dc1e5c622a3dc6449e3c68f9ad https://github.com/galaxyproject/galaxy/commit/7b45f7b4047377dc1e5c622a3dc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1259 from markiskander/reporter_fixes Fixed indentation errors for Reports Compare: https://github.com/galaxyproject/galaxy/compare/5d26f589cc47...7b45f7b40473

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[galaxyproject/galaxy] d24bc3: Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to s...
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d24bc3df1e627a0586860600a89352f6bddf49b1 https://github.com/galaxyproject/galaxy/commit/d24bc3df1e627a0586860600a893… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS Commit: 1c21ba82417f2a6d3e8d024ccd3a60a3416f5340 https://github.com/galaxyproject/galaxy/commit/1c21ba82417f2a6d3e8d024ccd3a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables. Commit: 9bbe4b869e000e0b86e85e19743390c0bed77d57 https://github.com/galaxyproject/galaxy/commit/9bbe4b869e000e0b86e85e197433… Author: Lance Parsons <lparsons(a)yahoo.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Merge pull request #1 from natefoo/lparsons_galaxy_slots Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables. Commit: 4c0bb9902ada3ed2dea7f1eeeb047aa4f9228be0 https://github.com/galaxyproject/galaxy/commit/4c0bb9902ada3ed2dea7f1eeeb04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Merge pull request #1347 from lparsons/galaxy_slots Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS Compare: https://github.com/galaxyproject/galaxy/compare/28cf2822f7bb...4c0bb9902ada

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[galaxyproject/usegalaxy-playbook] 616da9: install bamtools 0.2; meme; dunovo tools on Main
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 616da97a0daa7c22aa36b369ef504bc7612c72c1 https://github.com/galaxyproject/usegalaxy-playbook/commit/616da97a0daa7c22… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- install bamtools 0.2; meme; dunovo tools on Main

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[galaxyproject/galaxy] 61f4c8: Add test case for importing a workflow with missin...
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61f4c82642c5f48057d36fb9c728b66242807879 https://github.com/galaxyproject/galaxy/commit/61f4c82642c5f48057d36fb9c728… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py Log Message: ----------- Add test case for importing a workflow with missing tool. Commit: bed79b5e6a90965c0c0ba73a3c14851319ab90d2 https://github.com/galaxyproject/galaxy/commit/bed79b5e6a90965c0c0ba73a3c14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix importing pre-16.01 workflows with missing tools. Fixes #1386 (thanks to @trevor for the bug report). Test with: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_import_missing_tool ``` Commit: 28cf2822f7bb3497cedee1951c22ca21e3aca956 https://github.com/galaxyproject/galaxy/commit/28cf2822f7bb3497cedee1951c22… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/managers/workflows.py A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py Log Message: ----------- Merge pull request #1416 from jmchilton/workflow_missing_tool_import Fix importing pre-16.01 workflows with missing tools. Compare: https://github.com/galaxyproject/galaxy/compare/607db31b0432...28cf2822f7bb

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[galaxyproject/galaxy] c9870c: Fix url formatting
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9870cb89d92f52d04d5dd163c340dd4f6cf499c https://github.com/galaxyproject/galaxy/commit/c9870cb89d92f52d04d5dd163c34… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix url formatting Commit: 607db31b0432c4bf30d84a4662aa0cc0f9cd3442 https://github.com/galaxyproject/galaxy/commit/607db31b0432c4bf30d84a4662aa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1415 from guerler/fix_url_001 Fix url formatting Compare: https://github.com/galaxyproject/galaxy/compare/34bb21c411c3...607db31b0432

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[galaxyproject/galaxy] 339ad5: Cleanup Masthead and Scratchbook
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 339ad57f3fa626fe30c1bf26f90e0647be038cc9 https://github.com/galaxyproject/galaxy/commit/339ad57f3fa626fe30c1bf26f90e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/templates/charts.mako M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/onload.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/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Cleanup Masthead and Scratchbook Cleanup Masthead and Scratchbook Commit: 4cd621dd378e3a9db0d934203a5e1cdebd817b6c https://github.com/galaxyproject/galaxy/commit/4cd621dd378e3a9db0d934203a5e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-31 (Thu, 31 Dec 2015) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js Log Message: ----------- Add test cases Commit: 34bb21c411c3ebce94e67f996e70387d33e7f8cf https://github.com/galaxyproject/galaxy/commit/34bb21c411c3ebce94e67f996e70… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/templates/charts.mako M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/onload.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/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/webapps/galaxy/galaxy.masthead.mako A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1407 from guerler/revise_masthead_000 Masthead/Scratchbook revision and test cases Compare: https://github.com/galaxyproject/galaxy/compare/905adbac3899...34bb21c411c3

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[galaxyproject/galaxy] a6cbb8: Enable tool isolation by default and fix bugs.
by GitHub 04 Jan '16

04 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6cbb88ad12288eca031c0469113abc831a42d37 https://github.com/galaxyproject/galaxy/commit/a6cbb88ad12288eca031c0469113… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Enable tool isolation by default and fix bugs. Commit: 1084f14dd0637bc47978a33122c74d86cb617241 https://github.com/galaxyproject/galaxy/commit/1084f14dd0637bc47978a33122c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M test/unit/jobs/test_command_factory.py Log Message: ----------- Unit test modifications for running tool commands in isolated scripts. Commit: 7f8e37d5a1aa96c2c839acea4511e071e81eb450 https://github.com/galaxyproject/galaxy/commit/7f8e37d5a1aa96c2c839acea4511… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py Log Message: ----------- Attempt to fix samtools resolution for metadata when tool command externalized. Commit: acab90d63c6c96a6e609f32080f5b610b33dd549 https://github.com/galaxyproject/galaxy/commit/acab90d63c6c96a6e609f32080f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix unicode-y problem with tool command externalization. Commit: 340aef2550d16bb987b36bc7b2df8e0ed4f6f56b https://github.com/galaxyproject/galaxy/commit/340aef2550d16bb987b36bc7b2df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix logging for tool script externalization. Commit: 7cbf41feb3dfd6eb12c99630692776565c72c579 https://github.com/galaxyproject/galaxy/commit/7cbf41feb3dfd6eb12c996306927… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/__init__.py Log Message: ----------- Better exception when samtools is required but not on PATH. Commit: 905adbac38992ae2fc889d23f000fa2541e87939 https://github.com/galaxyproject/galaxy/commit/905adbac38992ae2fc889d23f000… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1412 from jmchilton/isolate Isolate tool commands by default. Compare: https://github.com/galaxyproject/galaxy/compare/10677319f74f...905adbac3899

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[galaxyproject/galaxy] 308435: Fix bug in db845fa1875bcb08aa2129830f1d405d1d894cf...
by GitHub 03 Jan '16

03 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 308435b7391d349b0077375409d631eb96038889 https://github.com/galaxyproject/galaxy/commit/308435b7391d349b0077375409d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Fix bug in db845fa1875bcb08aa2129830f1d405d1d894cfb. Commit: 10677319f74f96160a4ee0b48e7d1053df242951 https://github.com/galaxyproject/galaxy/commit/10677319f74f96160a4ee0b48e7d… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #1414 from jmchilton/lib_1 Fix bug in db845fa1875bcb08aa2129830f1d405d1d894cfb. Compare: https://github.com/galaxyproject/galaxy/compare/73defd48ce70...10677319f74f

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[galaxyproject/galaxy] 0da66e: Small improvements to load_directory for downstrea...
by GitHub 03 Jan '16

03 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0da66ee8dcf5fef52b11558228c1eb95479cbce9 https://github.com/galaxyproject/galaxy/commit/0da66ee8dcf5fef52b11558228c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Small improvements to load_directory for downstream extension. Commit: a9d4783f2c3d22e7d830fc88d30b6112e2d43fc0 https://github.com/galaxyproject/galaxy/commit/a9d4783f2c3d22e7d830fc88d30b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Add CWL suppoort to tool checking and parsing. To be clear, this provides none of the infrastructure for running the tools. This is just so that planemo and future tool registry efforts can have a unified interface for accessing and reasoning about tools using the same methods Galaxy does. Commit: 2054f538be010ab6d47e0de1da646268ca6d6ff4 https://github.com/galaxyproject/galaxy/commit/2054f538be010ab6d47e0de1da64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Infrastructure for parsing CWL tools. Commit: db845fa1875bcb08aa2129830f1d405d1d894cfb https://github.com/galaxyproject/galaxy/commit/db845fa1875bcb08aa2129830f1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Refactor loader_directory to support beta formats in other ways. Commit: fcc83d4e09d4603c5fbd831e9e1933916bf00827 https://github.com/galaxyproject/galaxy/commit/fcc83d4e09d4603c5fbd831e9e19… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py Log Message: ----------- Introduce ToolBox parser. Abstract simpler ToolBox interactions to separate XML representation from handling. Doesn't cover tool shed operations since the tool shed explicitly writes XML. Commit: b68991c4caa44aefeaba752748ae62db98a446fd https://github.com/galaxyproject/galaxy/commit/b68991c4caa44aefeaba752748ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M test/unit/tools/test_toolbox.py Log Message: ----------- Allow loading tool confs written in YAML and JSON. Because lets say someone was writing a programatic way to manage elements in a tool conf, that hypothetical person probably shouldn't be writing XML. Commit: 864cc32892a1b4bf91b5d2fe70f7e64eec736393 https://github.com/galaxyproject/galaxy/commit/864cc32892a1b4bf91b5d2fe70f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M templates/admin/reload_tool.mako Log Message: ----------- Allow toolbox reloading via app, UI, and API. Introduce an app ToolCache to help ensure this operation remains speedy. Commit: 4086dd61dafe562ec01a8b1fce687a539aedbcfe https://github.com/galaxyproject/galaxy/commit/4086dd61dafe562ec01a8b1fce68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_watcher.py Log Message: ----------- Implement toolbox monitoring. - Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes. - Refactoring and test improvements for existing tool monitoring code. - Implement toolbox shutdown process to ensure different watchers don't compete with each other. - Set the default tool conf to be monitored. Commit: 8027228639a771e4c62131ab15ba4ffbb656498a https://github.com/galaxyproject/galaxy/commit/8027228639a771e4c62131ab15ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Revise tool caching for tool shed tool loading... The tool shed appears to load the same tool in the toolbox multiple times with different settings. Get around this by not using the cache when loading tools from a few tool shed components later in this process. Commit: eddfec36fdf6d19bae398d09ee16952136d2b379 https://github.com/galaxyproject/galaxy/commit/eddfec36fdf6d19bae398d09ee16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Refactor package_tool for better separation of concerns. The tool should know how to package itself, it shouldn't be the responsiblity of the toolbox. Update the code to reflect this and use more pythonic exception handling. Commit: ce24ec6821bdb87f14f3047eef186c246de2d5ed https://github.com/galaxyproject/galaxy/commit/ce24ec6821bdb87f14f3047eef18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M templates/admin/reload_tool.mako Log Message: ----------- Remove alert from toolbox reload. Commit: 523e2b40063d2abb7662a163f0144902541bed18 https://github.com/galaxyproject/galaxy/commit/523e2b40063d2abb7662a163f014… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix shutdown of tool watcher if never activated. Caused a harmless, but distracting stacktrace to be printed on toolbox reload as pointed out by @bgruening https://github.com/galaxyproject/galaxy/pull/1398#issuecomment-168499678. Commit: 73defd48ce70241d7cc163aaadfef6fcd6830231 https://github.com/galaxyproject/galaxy/commit/73defd48ce70241d7cc163aaadfe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py M templates/admin/reload_tool.mako M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge pull request #1398 from jmchilton/toolbox_overhaul ToolBox Overhaul Compare: https://github.com/galaxyproject/galaxy/compare/5ca71d6f292f...73defd48ce70

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[galaxyproject/galaxy] f597b0: Refactor ToolBox functionality.
by GitHub 03 Jan '16

03 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f597b08b878f478b9beee32c59b5e4218458c4fe https://github.com/galaxyproject/galaxy/commit/f597b08b878f478b9beee32c59b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor ToolBox functionality. This moves in two directions toward a better design. It moves some Galaxy tool specific logic out of the AbstractToolBox (which should just be worried about panels, etc... IMO) and it moves more galaxy-lib functionality (dependency resolution) into a galaxy-lib module (galaxy.tools.toolbox). It does this by creating a BaseGalaxyToolBox that can reason about which files look like tools and what dependency resoution should be - without dependening on Galaxy models, job running, etc... that is in galaxy.tools.__init__. Commit: 204aa96206a7fdaff69d22fde6387a9956c1a0bc https://github.com/galaxyproject/galaxy/commit/204aa96206a7fdaff69d22fde638… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/test_routes.py Log Message: ----------- API-ify tool dependency resolution. Commit: b167a741a444c3988447b0d63a1ba3dc5e4e62f5 https://github.com/galaxyproject/galaxy/commit/b167a741a444c3988447b0d63a1b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Include information about whether matches are dependencies are exact. Commit: 71a876840a6c9acf11bd2ac7706ec21b32d2fb88 https://github.com/galaxyproject/galaxy/commit/71a876840a6c9acf11bd2ac7706e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement concept of listable dependency resolvers. DependencyResolver classes which can enumerate the requirements then can resolve "exactly" should mix in ListableDependencyResolver and implement list_dependencies. The galaxy package resolver can easily be enumerated but its subclasses like the tool shed dependency resolver couldn't, so I have separated that class into a base class that there others can inherit and an actual resolver that implements ListableDependencyResolver. Rebase into listable. Commit: 29f20cf09c18e24e898517bf685418ec1db4cd11 https://github.com/galaxyproject/galaxy/commit/29f20cf09c18e24e898517bf6854… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement concept of installable dependency resolvers. DependencyResolver classes which can install "simple" dependences should mix in the new InstallableDependencyResolver and implement install_dependency. Currently this is only the conda dependency resolver, one can easily imagine doing the same for the brew dependency resolver and potentially doing it for some variant of the unlinked dependency resolvers. Commit: 868a7dfe0e03503adaf6646e10d8184d18b66a34 https://github.com/galaxyproject/galaxy/commit/868a7dfe0e03503adaf6646e10d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Modify unmodified conda behavior. - Add configuration option for overriding condarc location used by conda resolve commands. - Default location of condarc to be in tool_dependency_dir. - Delay updating the condarc to ensure channels until this would actually be needed (during package installation). - Add configuration flag to allow Galaxy to *NOT* check the PATH for conda. - Update unit test that verifies conda's installation to never use conda on PATH, since a precondition of this test is that certain packages haven't been installed previously. - Change default behavior to not check the PATH for conda, everything else here I feel pretty good about - this I'm ambivalent about - it will reduce error reports and problems with network filesystems, but doesn't seem to be good Unix best practice. Points 2 and 3 above should address this issue: https://github.com/galaxyproject/ansible-galaxy-extras/pull/33#issuecomment… This commit also addresses most of #1406. Commit: ef9e1876a2d4dd02718784f2b9f1045f2f9d0b59 https://github.com/galaxyproject/galaxy/commit/ef9e1876a2d4dd02718784f2b9f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Fixup dependency module and API comments. Thanks to suggestions by @bgruening. Commit: 4650d77bd988b90b6652cc108f83bf6d86cae271 https://github.com/galaxyproject/galaxy/commit/4650d77bd988b90b6652cc108f83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix listing conda requirements if conda hasn't been installed. Fix problem discovered by @bgruening. Commit: 5ca71d6f292ff122d35c25d0dfd7c0e14d5366e2 https://github.com/galaxyproject/galaxy/commit/5ca71d6f292ff122d35c25d0dfd7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/test_routes.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #1409 from jmchilton/dep_resolution_api Evolving from dependency resolution to dependency management. Compare: https://github.com/galaxyproject/galaxy/compare/0aa1c5133e02...5ca71d6f292f

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[galaxyproject/galaxy] 114808: Implement a conda dependency resolver.
by GitHub 30 Dec '15

30 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1148081435e6eb4075eb62783129299ebbd4d490 https://github.com/galaxyproject/galaxy/commit/1148081435e6eb4075eb62783129… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_job_wrapper.py A test/unit/tools/test_conda_resolution.py Log Message: ----------- Implement a conda dependency resolver. Much more information on planemo PR that I used to build a test bed for this: https://github.com/galaxyproject/planemo/pull/392 Also syncs galaxy with planemo shared library changed. Commit: 0aa1c5133e029196444ac9c0b32f43489cee3713 https://github.com/galaxyproject/galaxy/commit/0aa1c5133e029196444ac9c0b32f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_job_wrapper.py A test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #1345 from jmchilton/conda_0 Implement a conda dependency resolver. Compare: https://github.com/galaxyproject/galaxy/compare/2b2f93d393a4...0aa1c5133e02

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[galaxyproject/galaxy] d5d404: Implement special config file to dump parameters a...
by GitHub 30 Dec '15

30 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5d404c912340013aab34fe3350a2570010b0898 https://github.com/galaxyproject/galaxy/commit/d5d404c912340013aab34fe3350a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement special config file to dump parameters as json. ``` <configfiles> <inputs name="inputs" format="json" version="1" /> </configfiles> ``` Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday. Commit: de0c913b8bb3ca01fd0ab5c8286450dbef9b604d https://github.com/galaxyproject/galaxy/commit/de0c913b8bb3ca01fd0ab5c82864… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M test/functional/tools/inputs_as_json.xml Log Message: ----------- More work on converting tool inputs to json. - Drop version requirement per commends by @bgruening. - Add examples for conditionals, repeats, sections, colors, and booleans specified truevalue/falsevalue. - Various bug fixes unearthed by new test cases. Commit: cd32b91dc9f562d17349d8cc15ba1b60eba07f70 https://github.com/galaxyproject/galaxy/commit/cd32b91dc9f562d17349d8cc15ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M test/functional/tools/inputs_as_json.xml Log Message: ----------- Update inputs_as_json.xml to drop version attribute. Also add note about filename. Commit: 9a0ef0ed14893bf1dcaae67b466a8b1167571032 https://github.com/galaxyproject/galaxy/commit/9a0ef0ed14893bf1dcaae67b466a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Expose hidden parameters in inputs json. Commit: 2b2f93d393a4e66c0e466e98a945222bd54e448a https://github.com/galaxyproject/galaxy/commit/2b2f93d393a4e66c0e466e98a945… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1405 from jmchilton/json_config Implement special config file to dump parameters as json. Compare: https://github.com/galaxyproject/galaxy/compare/14a618ee3ab0...2b2f93d393a4

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[galaxyproject/galaxy] 7269f7: Remove transiently failing maxseconds.xml framewor...
by GitHub 28 Dec '15

28 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7269f76e6e8227d26c928e76cd81941498c0acd7 https://github.com/galaxyproject/galaxy/commit/7269f76e6e8227d26c928e76cd81… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Remove transiently failing maxseconds.xml framework test. Commit: 79bbc97a189bea03392bff2ab6a819aca1fad0db https://github.com/galaxyproject/galaxy/commit/79bbc97a189bea03392bff2ab6a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Attempt to fix transiently failing capsule TS test. Guess here is that a flush is not occuring on that file because it is happening as part of garbage collection and not explictly as part of an explicit close. Commit: 14a618ee3ab084e43f51f72136afd6b4c482b4cf https://github.com/galaxyproject/galaxy/commit/14a618ee3ab084e43f51f72136af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-28 (Mon, 28 Dec 2015) Changed paths: M test/functional/tools/samples_tool_conf.xml M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1401 from jmchilton/transient_tests_2 Fix and potential fix for transiently failing tests. Compare: https://github.com/galaxyproject/galaxy/compare/798c7e20c338...14a618ee3ab0

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[galaxyproject/galaxy] 47a442: Add Jupyter Interactive Environment
by GitHub 27 Dec '15

27 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47a44202673839fe1ff00408c50c533ddd823a27 https://github.com/galaxyproject/galaxy/commit/47a44202673839fe1ff00408c50c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Add Jupyter Interactive Environment Commit: 38d40e7af11525348bb54bad3a3a8496539a2a3a https://github.com/galaxyproject/galaxy/commit/38d40e7af11525348bb54bad3a3a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- move keep_alive into jupyter.js Commit: 6ac01675f3f37a6af1d498b96cad753a03a8a776 https://github.com/galaxyproject/galaxy/commit/6ac01675f3f37a6af1d498b96cad… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample Log Message: ----------- Change default image name to a versioned tagged Docker release. Commit: 798c7e20c33860ada2bb066277a3280488e25492 https://github.com/galaxyproject/galaxy/commit/798c7e20c33860ada2bb066277a3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Merge pull request #1400 from bgruening/jupyter Add Jupyter Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/4e55f7e519a0...798c7e20c338

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[galaxyproject/usegalaxy-playbook] fa5643: Dropped Barcelona slide from rotation.
by GitHub 27 Dec '15

27 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa5643bf13d5f2fb27051425aa94a55412b52074 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa5643bf13d5f2fb… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped Barcelona slide from rotation.

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[galaxyproject/galaxy] ed11f7: Offer galaxy_web_port in all scenarios, this can b...
by GitHub 27 Dec '15

27 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed11f7ab00b0ff3f414dc23736c054a655b44663 https://github.com/galaxyproject/galaxy/commit/ed11f7ab00b0ff3f414dc23736c0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Offer galaxy_web_port in all scenarios, this can be useful in some local dev settings. Commit: 7b118990d2bee4377b364373fd596b88d0275307 https://github.com/galaxyproject/galaxy/commit/7b118990d2bee4377b364373fd59… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Catch errors in some wired cases. This will prevent the proxy to crash badly if the Docker container just disappears. Commit: 1873d2c5edbb44eb0e8138612d55510b3492782b https://github.com/galaxyproject/galaxy/commit/1873d2c5edbb44eb0e8138612d55… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- update js scripts Commit: 4e55f7e519a0e03805e0f3d91ab8de47c357d040 https://github.com/galaxyproject/galaxy/commit/4e55f7e519a0e03805e0f3d91ab8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1399 from bgruening/ie Interactive Environment updates Compare: https://github.com/galaxyproject/galaxy/compare/6aa7691a637e...4e55f7e519a0

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[galaxyproject/galaxy] 355bb2: Finish swapping unencoded ids with order_index in ...
by GitHub 26 Dec '15

26 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 355bb281e21e701e05d1f671f080022de9df987b https://github.com/galaxyproject/galaxy/commit/355bb281e21e701e05d1f671f080… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Finish swapping unencoded ids with order_index in workflows API. Running a workflow or showing a workflow can both restore the previous behavior by passing legacy=True as an API parameter. By changing these two endpoints in tandem I believe backward compatiblity for most existing code should be maintained unless: - The external application saved these workflow IDs previously and re-runs workflows without refetching the workflow definition. I could imagine Refinery for instance might do this and will have to update indexed workflows or add legacy=True to workflow requests. - The external application contacted the database directly after using this API endpoint to fetch more information about the step (seems unlikely). See conversation: - http://dev.list.galaxyproject.org/workflow-API-step-order-vs-step-id-in-bio… Rebased with changes suggested by @nsoranzo. Commit: 6aa7691a637e86491a51d41a1672521f42a06bb5 https://github.com/galaxyproject/galaxy/commit/6aa7691a637e86491a51d41a1672… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Merge pull request #1137 from jmchilton/workflow_api_order_2 Finish swapping unencoded ids with order_index in workflows API. Compare: https://github.com/galaxyproject/galaxy/compare/2466b1cb6575...6aa7691a637e

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[galaxyproject/galaxy] ddaa11: Adding uuid support to directory_hash_id
by GitHub 24 Dec '15

24 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ddaa1189f75627f516926b5363398fe7e24fe992 https://github.com/galaxyproject/galaxy/commit/ddaa1189f75627f516926b536339… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Adding uuid support to directory_hash_id Commit: 8f34f2a6104ff595d411bfc5e77b488f2c86dfd9 https://github.com/galaxyproject/galaxy/commit/8f34f2a6104ff595d411bfc5e77b… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Fixing issues for PR unit testing and linting Commit: 4840a3d8b1caae9666eeebf95d4aeaebaee8260b https://github.com/galaxyproject/galaxy/commit/4840a3d8b1caae9666eeebf95d4a… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Fixing lint problem Commit: 2466b1cb65757b0157dab67a16c7bbfd7b48c710 https://github.com/galaxyproject/galaxy/commit/2466b1cb65757b0157dab67a16c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-24 (Thu, 24 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Merge pull request #1397 from kellrott/dev Adding uuid support to directory_hash_id Compare: https://github.com/galaxyproject/galaxy/compare/26d7e97ed7b4...2466b1cb6575

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