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

[galaxyproject/galaxy] 74afe4: fix old jobparam hack for importing files to libra...
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74afe4127a2e5d1b2e3b36fcc220866a6db02e7f https://github.com/galaxyproject/galaxy/commit/74afe4127a2e5d1b2e3b36fcc220… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- fix old jobparam hack for importing files to library Commit: f41550f69f05df63e762b771a22c0b677357db85 https://github.com/galaxyproject/galaxy/commit/f41550f69f05df63e762b771a22c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #1488 from martenson/fix-jobparam-hack fix old jobparam hack for importing files to library Compare: https://github.com/galaxyproject/galaxy/compare/84fd89d67a5a...f41550f69f05

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[galaxyproject/galaxy] 0bcfa7: Set mime type when previewing tabular data that ha...
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 0bcfa74ea1e0eb57927bd1850feb9331489af6bc https://github.com/galaxyproject/galaxy/commit/0bcfa74ea1e0eb57927bd1850feb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Fixes the issue of losing newlines and actual spacing (i.e. do not treat as html). Commit: eb3fc642fc1bddaeb5aaec3d4dbba8efd0ab398d https://github.com/galaxyproject/galaxy/commit/eb3fc642fc1bddaeb5aaec3d4dbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1498 from blankenberg/tab_mime [16.01] Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Compare: https://github.com/galaxyproject/galaxy/compare/0902c23f3491...eb3fc642fc1b

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[galaxyproject/galaxy] 4b5b97: Fix disabled css
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4b5b970d7898a33faca5557b4382ddc9d3923ae6 https://github.com/galaxyproject/galaxy/commit/4b5b970d7898a33faca5557b4382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 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 M test/qunit/tests/masthead_tests.js Log Message: ----------- Fix disabled css Commit: 0902c23f3491b4840b649a203315939d0c7caa8c https://github.com/galaxyproject/galaxy/commit/0902c23f3491b4840b649a203315… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 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 M test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1501 from guerler/fix_disabled_000 [16.01] Fix disabled css Compare: https://github.com/galaxyproject/galaxy/compare/2e62388b2f34...0902c23f3491

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[galaxyproject/galaxy] 55677f: Fix to ensure integrity of tool_script.sh also.
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 55677f2d3db723c023540b8d640563a9f3ca04c5 https://github.com/galaxyproject/galaxy/commit/55677f2d3db723c023540b8d6405… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix to ensure integrity of tool_script.sh also. Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected. Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable. Commit: 2e62388b2f34ad83f215bb3eff4c6ae5b1efd7b7 https://github.com/galaxyproject/galaxy/commit/2e62388b2f34ad83f215bb3eff4c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1494 from jmchilton/tool_command_integrity [16.01] Fix to ensure integrity of tool_script.sh also. Compare: https://github.com/galaxyproject/galaxy/compare/9d52a4a31dd9...2e62388b2f34

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[galaxyproject/usegalaxy-playbook] 30e451: disable user activation on Main since sending mail...
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 30e4519b6ca894b55ea76ce944b8274709089578 https://github.com/galaxyproject/usegalaxy-playbook/commit/30e4519b6ca894b5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- disable user activation on Main since sending mails is broken and will get probably fixed tomorrow

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[galaxyproject/usegalaxy-playbook] 6f4f8d: fix welcomepage tiny things
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f4f8d4fa8691bc8f3d4d03ac048667f2b638859 https://github.com/galaxyproject/usegalaxy-playbook/commit/6f4f8d4fa8691bc8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- fix welcomepage tiny things Commit: 2b597fcde4856fe7021d63a87488cc7a6cf81309 https://github.com/galaxyproject/usegalaxy-playbook/commit/2b597fcde4856fe7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- add alt text for images Commit: a04eab98b994cb9d06ef383642efc47341a8dc9c https://github.com/galaxyproject/usegalaxy-playbook/commit/a04eab98b994cb9d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Merge pull request #16 from galaxyproject/fix-welcome-tinies fix welcomepage tiny things Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d10cbd5443f3...…

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[galaxyproject/galaxy] 37f803: Undo user icon in masthead
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 37f8038d63f8243151e817e9d564f90c58772c1f https://github.com/galaxyproject/galaxy/commit/37f8038d63f8243151e817e9d564… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 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: ----------- Undo user icon in masthead Commit: 9d52a4a31dd9e660855bf1e12bd07d3c49b73fd9 https://github.com/galaxyproject/galaxy/commit/9d52a4a31dd9e660855bf1e12bd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 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 #1493 from guerler/undo_user_000 [16.01] Undo user icon in masthead Compare: https://github.com/galaxyproject/galaxy/compare/becffe93a3f7...9d52a4a31dd9

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[galaxyproject/galaxy] e14449: Revise label handling in form
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e14449e62dbf89e2c4f8a41448582f332aaefdcf https://github.com/galaxyproject/galaxy/commit/e14449e62dbf89e2c4f8a4144858… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-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.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Revise label handling in form Commit: 84fd89d67a5a9cca9647cdf6dedd86fe7786cb44 https://github.com/galaxyproject/galaxy/commit/84fd89d67a5a9cca9647cdf6dedd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-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.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #1496 from guerler/labels_000 Revise label handling in form Compare: https://github.com/galaxyproject/galaxy/compare/91fe9d09aab5...84fd89d67a5a

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[galaxyproject/galaxy] 9dc9dd: Add --replace-pip option to common_startup.sh.
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9dc9ddf8cdede7c62d4ba5f00283675b872891e4 https://github.com/galaxyproject/galaxy/commit/9dc9ddf8cdede7c62d4ba5f00283… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Add --replace-pip option to common_startup.sh. Needed to restore correct functionality to planemo. Commit: 8fd83df6652a40882bcc3ca8a1db917887b71c11 https://github.com/galaxyproject/galaxy/commit/8fd83df6652a40882bcc3ca8a1db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Allow override of location of virtual env Galaxy manages. Commit: b559cf303c1b14aa862ba394d7bc868bc517db5a https://github.com/galaxyproject/galaxy/commit/b559cf303c1b14aa862ba394d7bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M setup.cfg Log Message: ----------- Drop E731 from flake8 enforcement (though we should revisit this and see if we *do* want to follow this or not) Commit: 2f1dbeee68ddd75a561fe0f463d5b9968278ef13 https://github.com/galaxyproject/galaxy/commit/2f1dbeee68ddd75a561fe0f463d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M test/casperjs/casperjs_runner.py Log Message: ----------- Address W503 and E721 errors now enforced by pep8 1.7. Commit: 86158cbc7fb601d0f3563fa2bea67e23b464db93 https://github.com/galaxyproject/galaxy/commit/86158cbc7fb601d0f3563fa2bea6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1487 from dannon/release_16.01 [16.01] Cherrypick of pep8 fixes. Commit: becffe93a3f78ca74b5d093974844a3634e1ed6b https://github.com/galaxyproject/galaxy/commit/becffe93a3f78ca74b5d09397484… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #1485 from jmchilton/common_startup_fixes [16.01] Fix common_startup options for planemo. Commit: e13fb12569a84c78b23b71e0f90bcea13439bc53 https://github.com/galaxyproject/galaxy/commit/e13fb12569a84c78b23b71e0f90b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0 Commit: 91fe9d09aab5e78115ba87c42406b709796119dc https://github.com/galaxyproject/galaxy/commit/91fe9d09aab5e78115ba87c42406… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #1497 from jmchilton/dev_merge_0 Merge 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/790953e6e786...91fe9d09aab5

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[galaxyproject/usegalaxy-playbook] 2b597f: add alt text for images
by GitHub 13 Jan '16

13 Jan '16

Branch: refs/heads/fix-welcome-tinies Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2b597fcde4856fe7021d63a87488cc7a6cf81309 https://github.com/galaxyproject/usegalaxy-playbook/commit/2b597fcde4856fe7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- add alt text for images

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