January 2016 - galaxy-commits - lists.galaxyproject.org

[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 03 Jan '16

03 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 03 Jan '16

03 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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