Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 268ee7f1b7e65dde514098e0779b80b7589d26b5
https://github.com/galaxyproject/galaxy/commit/268ee7f1b7e65dde514098e0779b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-21 (Wed, 21 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js
Log Message:
-----------
Improve resilience of tool url building
Commit: 69e76f98fa90782c37a2697de0204e4ff7945f09
https://github.com/galaxyproject/galaxy/commit/69e76f98fa90782c37a2697de020…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-21 (Wed, 21 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Remove redundancy of tool_id parameter
Commit: a498390bef74301816945551a9832f38747fd4fc
https://github.com/galaxyproject/galaxy/commit/a498390bef74301816945551a983…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-21 (Wed, 21 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix basic version changes for reloaded tools
Commit: 9dca211e2fe59eaad1f7b95c8d51608b2afa05af
https://github.com/galaxyproject/galaxy/commit/9dca211e2fe59eaad1f7b95c8d51…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js
Log Message:
-----------
Merge pull request #4214 from guerler/revise_tool_url
[17.05] Improve resilience of tool url building
Compare: https://github.com/galaxyproject/galaxy/compare/f7ba7295102c...9dca211e2fe5
Branch: refs/heads/reorg
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: c06cee0e218843b77ca86bab23007f16cfaa106a
https://github.com/galaxyproject/usegalaxy-playbook/commit/c06cee0e218843b7…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-06-22 (Thu, 22 Jun 2017)
Changed paths:
M env/common/files/galaxy/dynamic_rules/bridges_select.py
A env/test/files/galaxy/config/pulsar_bridges_actions.yml
M env/test/group_vars/galaxyservers/vars.yml
M env/test/templates/galaxy/config/job_conf.xml.j2
Log Message:
-----------
Run RNA Star on Bridges on Test, configure data path rewrites.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 490d738ba4efea392297941ceb266fa428ca2323
https://github.com/galaxyproject/galaxy/commit/490d738ba4efea392297941ceb26…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Fix left/right panel hiding
Commit: ecdaa04dfd14c1497f3db85409b4c0add8c91022
https://github.com/galaxyproject/galaxy/commit/ecdaa04dfd14c1497f3db85409b4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-06-21 (Wed, 21 Jun 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Merge pull request #4210 from guerler/fix_panel_hiding
Fix left/right panel hiding
Compare: https://github.com/galaxyproject/galaxy/compare/9b9e2aa22742...ecdaa04dfd14
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a407a99ae3b8a83879b5f4629c8c07d7cfa3945b
https://github.com/galaxyproject/galaxy/commit/a407a99ae3b8a83879b5f4629c8c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-29 (Mon, 29 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/workflow/workflow.js
R templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Removing run mako from workflows
Commit: 094dbe92c3e33d0184cc3691f3d9f66cb7e2b697
https://github.com/galaxyproject/galaxy/commit/094dbe92c3e33d0184cc3691f3d9…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-30 (Tue, 30 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow.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/workflow/workflow.js
Log Message:
-----------
Adding basic elements for import workflow
Commit: 6dba0c74f266483ef0a67d5d8f25f5ced1bbed37
https://github.com/galaxyproject/galaxy/commit/6dba0c74f266483ef0a67d5d8f25…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-05-30 (Tue, 30 May 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/style/less/base.less
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
A static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/maps/mvc/workflow/workflow.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
A static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow.js
M static/style/blue/base.css
R templates/webapps/galaxy/workflow/configure_menu.mako
Log Message:
-----------
Merging with dev
Commit: 764933bf3417c734ee2f5554ae122ddca1f3655a
https://github.com/galaxyproject/galaxy/commit/764933bf3417c734ee2f5554ae12…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-01 (Thu, 01 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow.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/workflow/workflow.js
Log Message:
-----------
Adding import functionality
Commit: 62bd742808e5c45a00cb64ac7ef962f936e57351
https://github.com/galaxyproject/galaxy/commit/62bd742808e5c45a00cb64ac7ef9…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-01 (Thu, 01 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow.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/workflow/workflow.js
Log Message:
-----------
Moving common functions out of view and adding messages for client actions for importing workflow
Commit: 07ea4c04347956fd5e177b052c86a63568aa28a7
https://github.com/galaxyproject/galaxy/commit/07ea4c04347956fd5e177b052c86…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-06 (Tue, 06 Jun 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/style/less/base.less
M client/webpack.config.js
M config/job_conf.xml.sample_advanced
M contrib/galaxy.debian-init
M contrib/galaxy_supervisor.conf
M doc/Makefile
R doc/patch.py
M doc/source/admin/authentication.md
M doc/source/admin/special_topics/mulled_containers.rst
R doc/source/api/api.rst
R doc/source/api/ts_api.rst
M doc/source/dev/build_a_job_runner.rst
M doc/source/lib/galaxy.actions.rst
M doc/source/lib/galaxy.auth.providers.rst
M doc/source/lib/galaxy.auth.rst
A doc/source/lib/galaxy.containers.rst
M doc/source/lib/galaxy.dataset_collections.rst
M doc/source/lib/galaxy.dataset_collections.types.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.datatypes.dataproviders.rst
M doc/source/lib/galaxy.datatypes.display_applications.rst
M doc/source/lib/galaxy.datatypes.rst
M doc/source/lib/galaxy.datatypes.util.rst
M doc/source/lib/galaxy.dependencies.rst
M doc/source/lib/galaxy.eggs.rst
M doc/source/lib/galaxy.exceptions.rst
M doc/source/lib/galaxy.external_services.result_handlers.rst
M doc/source/lib/galaxy.external_services.rst
M doc/source/lib/galaxy.forms.rst
M doc/source/lib/galaxy.jobs.actions.rst
M doc/source/lib/galaxy.jobs.deferred.rst
M doc/source/lib/galaxy.jobs.metrics.collectl.rst
M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
M doc/source/lib/galaxy.jobs.metrics.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.jobs.runners.rst
M doc/source/lib/galaxy.jobs.runners.state_handlers.rst
M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
M doc/source/lib/galaxy.jobs.runners.util.cli.rst
M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
M doc/source/lib/galaxy.jobs.runners.util.condor.rst
A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst
M doc/source/lib/galaxy.jobs.runners.util.job_script.rst
M doc/source/lib/galaxy.jobs.runners.util.rst
M doc/source/lib/galaxy.jobs.splitters.rst
M doc/source/lib/galaxy.managers.rst
M doc/source/lib/galaxy.model.migrate.rst
M doc/source/lib/galaxy.model.orm.rst
M doc/source/lib/galaxy.model.rst
M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
M doc/source/lib/galaxy.model.tool_shed_install.rst
M doc/source/lib/galaxy.objectstore.rst
M doc/source/lib/galaxy.openid.rst
M doc/source/lib/galaxy.quota.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.sample_tracking.rst
M doc/source/lib/galaxy.security.rst
R doc/source/lib/galaxy.tags.rst
M doc/source/lib/galaxy.tools.actions.rst
A doc/source/lib/galaxy.tools.cwl.rst
M doc/source/lib/galaxy.tools.data.rst
M doc/source/lib/galaxy.tools.data_manager.rst
A doc/source/lib/galaxy.tools.deps.container_resolvers.rst
A doc/source/lib/galaxy.tools.deps.mulled.rst
M doc/source/lib/galaxy.tools.deps.resolvers.rst
M doc/source/lib/galaxy.tools.deps.rst
M doc/source/lib/galaxy.tools.filters.rst
M doc/source/lib/galaxy.tools.imp_exp.rst
M doc/source/lib/galaxy.tools.linters.rst
A doc/source/lib/galaxy.tools.locations.rst
M doc/source/lib/galaxy.tools.parameters.rst
M doc/source/lib/galaxy.tools.parser.rst
M doc/source/lib/galaxy.tools.rst
M doc/source/lib/galaxy.tools.search.rst
M doc/source/lib/galaxy.tools.toolbox.filters.rst
M doc/source/lib/galaxy.tools.toolbox.lineages.rst
M doc/source/lib/galaxy.tools.toolbox.rst
M doc/source/lib/galaxy.tools.util.galaxyops.rst
M doc/source/lib/galaxy.tools.util.rst
A doc/source/lib/galaxy.tools.verify.asserts.rst
A doc/source/lib/galaxy.tools.verify.rst
A doc/source/lib/galaxy.tours.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.log.rst
M doc/source/lib/galaxy.util.pastescript.rst
M doc/source/lib/galaxy.util.rst
M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
M doc/source/lib/galaxy.visualization.data_providers.rst
M doc/source/lib/galaxy.visualization.genome.rst
M doc/source/lib/galaxy.visualization.plugins.rst
M doc/source/lib/galaxy.visualization.rst
M doc/source/lib/galaxy.visualization.tracks.rst
M doc/source/lib/galaxy.web.base.controllers.rst
M doc/source/lib/galaxy.web.base.rst
M doc/source/lib/galaxy.web.framework.helpers.rst
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/lib/galaxy.web.framework.rst
M doc/source/lib/galaxy.web.proxy.rst
M doc/source/lib/galaxy.web.rst
M doc/source/lib/galaxy.web.security.rst
A doc/source/lib/galaxy.web.stack.rst
A doc/source/lib/galaxy.webapps.galaxy.api.rst
M doc/source/lib/galaxy.webapps.galaxy.controllers.rst
M doc/source/lib/galaxy.webapps.galaxy.rst
M doc/source/lib/galaxy.webapps.reports.controllers.rst
M doc/source/lib/galaxy.webapps.reports.rst
M doc/source/lib/galaxy.webapps.rst
A doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst
M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst
M doc/source/lib/galaxy.webapps.tool_shed.framework.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.rst
M doc/source/lib/galaxy.webapps.tool_shed.rst
M doc/source/lib/galaxy.webapps.tool_shed.search.rst
M doc/source/lib/galaxy.webapps.tool_shed.security.rst
M doc/source/lib/galaxy.webapps.tool_shed.util.rst
A doc/source/lib/galaxy.webhooks.rst
M doc/source/lib/galaxy.work.rst
M doc/source/lib/galaxy.workflow.rst
M doc/source/lib/galaxy.workflow.schedulers.rst
M doc/source/lib/galaxy_ext.metadata.rst
M doc/source/lib/galaxy_ext.rst
M doc/source/lib/log_tempfile.rst
M doc/source/lib/psyco_full.rst
M doc/source/lib/tool_shed.capsule.rst
M doc/source/lib/tool_shed.dependencies.repository.rst
M doc/source/lib/tool_shed.dependencies.rst
M doc/source/lib/tool_shed.dependencies.tool.rst
M doc/source/lib/tool_shed.galaxy_install.datatypes.rst
M doc/source/lib/tool_shed.galaxy_install.grids.rst
M doc/source/lib/tool_shed.galaxy_install.metadata.rst
M doc/source/lib/tool_shed.galaxy_install.migrate.rst
M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst
M doc/source/lib/tool_shed.galaxy_install.rst
M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst
M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
M doc/source/lib/tool_shed.galaxy_install.tools.rst
M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst
M doc/source/lib/tool_shed.grids.rst
M doc/source/lib/tool_shed.managers.rst
M doc/source/lib/tool_shed.metadata.rst
M doc/source/lib/tool_shed.repository_types.rst
M doc/source/lib/tool_shed.rst
M doc/source/lib/tool_shed.tools.rst
M doc/source/lib/tool_shed.util.rst
M doc/source/lib/tool_shed.utility_containers.rst
M doc/source/releases/13.01_announce.rst
M doc/source/releases/13.02_announce.rst
M doc/source/releases/13.04_announce.rst
M doc/source/releases/13.06_announce.rst
M doc/source/releases/13.08_announce.rst
M doc/source/releases/13.11_announce.rst
M doc/source/releases/14.02_announce.rst
M doc/source/releases/14.04_announce.rst
M doc/source/releases/14.06_announce.rst
M doc/source/releases/14.08_announce.rst
M doc/source/releases/14.10_announce.rst
M doc/source/releases/15.01_announce.rst
M doc/source/releases/15.03_announce.rst
M doc/source/releases/15.05.rst
M doc/source/releases/15.05_announce.rst
M doc/source/releases/15.07_announce.rst
M doc/source/releases/15.10_announce.rst
M doc/source/releases/16.01_announce.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07_announce.rst
M doc/source/releases/16.10_announce.rst
M doc/source/releases/17.01_announce.rst
M doc/source/slideshow/architecture/galaxy_architecture.md
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/xsd/README.md
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/compression_utils.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M scripts/bootstrap_history.py
M static/maps/layout/menu.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/workflow/workflow.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/menu.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/workflow/workflow.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/grid_base.mako
R templates/webapps/galaxy/page/list_published.mako
M test/api/test_dataset_collections.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
M test/qunit/test-data/bootstrapped.js
M test/qunit/tests/galaxy-app-base.js
Log Message:
-----------
Resolving conflicts and merging with dev
Commit: 207249a4665470288fe77ae9d532e3cb07d4ce32
https://github.com/galaxyproject/galaxy/commit/207249a4665470288fe77ae9d532…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-06 (Tue, 06 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/maps/mvc/workflow/workflow.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/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow.js
Log Message:
-----------
Moving configure menu call to user preferences
Commit: 77327d27b5f526f0b1ddd4375d32e57e83453169
https://github.com/galaxyproject/galaxy/commit/77327d27b5f526f0b1ddd4375d32…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
R templates/webapps/galaxy/workflow/import.mako
Log Message:
-----------
Removing import.mako file
Commit: f2efc6e5f77c4116a3ae28f8d83c3a9962d42f19
https://github.com/galaxyproject/galaxy/commit/f2efc6e5f77c4116a3ae28f8d83c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/style/less/ui.less
M config/job_conf.xml.sample_advanced
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M lib/galaxy/app.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
A lib/galaxy/tools/cache.py
R lib/galaxy/tools/toolbox/cache.py
M static/maps/mvc/ui/ui-slider.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/ui/ui-slider.js
M static/style/blue/base.css
M test/api/test_dataset_collections.py
M test/functional/webhooks/trans_object/config/trans_object.yaml
M test/qunit/tests/ui_tests.html
M test/qunit/tests/ui_tests.js
A test/unit/jobs/conditional_runners_job_conf.xml
M test/unit/jobs/test_job_configuration.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merging with dev
Commit: 1caf29d7591ff3787de330de58003fd9f0c0b6e1
https://github.com/galaxyproject/galaxy/commit/1caf29d7591ff3787de330de5800…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Removing extra link for custom_builds in analysis.js
Commit: 3573f4d59f3d177a0b91b06ce192e1711aaf4a0d
https://github.com/galaxyproject/galaxy/commit/3573f4d59f3d177a0b91b06ce192…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M static/maps/mvc/workflow/workflow.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/workflow/workflow.js
Log Message:
-----------
Removing usused imports in workflow.js
Commit: 785e3e557aeee7071905f1aa3d88c1ae1653ec9b
https://github.com/galaxyproject/galaxy/commit/785e3e557aeee7071905f1aa3d88…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-09 (Fri, 09 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/utils/utils.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow.js
M static/scripts/utils/utils.js
Log Message:
-----------
Fixing PR review comments
Commit: b52042ef8ebe250a1124071a98f4de486e5dc737
https://github.com/galaxyproject/galaxy/commit/b52042ef8ebe250a1124071a98f4…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-09 (Fri, 09 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/mvc/page/page-list.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/datatypes/data.py
A lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M static/maps/layout/menu.js.map
M static/maps/mvc/grid/grid-view.js.map
A static/maps/mvc/page/page-list.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/menu.js
M static/scripts/mvc/grid/grid-view.js
A static/scripts/mvc/page/page-list.js
M templates/sharing_base.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
Log Message:
-----------
Merging with dev
Commit: 5cc46a95c9c9a54ae390496b52c7efc8ac25cf0d
https://github.com/galaxyproject/galaxy/commit/5cc46a95c9c9a54ae390496b52c7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-10 (Sat, 10 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fixing PR review comments
Commit: 6d9a911ea9200d3339635c0f4370f18001271f8b
https://github.com/galaxyproject/galaxy/commit/6d9a911ea9200d3339635c0f4370…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-10 (Sat, 10 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Removing usused imports in workflow controller
Commit: 050ff3b159b7309609423c37cbf5d47a261c2944
https://github.com/galaxyproject/galaxy/commit/050ff3b159b7309609423c37cbf5…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-12 (Mon, 12 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M config/job_conf.xml.sample_advanced
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_search.py
M lib/galaxy/tools/deps/mulled/util.py
A lib/galaxy/tools/deps/singularity_util.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M static/maps/layout/menu.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/menu.js
R templates/webapps/galaxy/dataset/grid.mako
A test/functional/tools/mulled_example_multi_versionless.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merging with dev
Commit: 659c039601a474eba86156a6957dd48560630fa1
https://github.com/galaxyproject/galaxy/commit/659c039601a474eba86156a6957d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/style/less/base.less
M static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/tool/tool-form-base.js
M static/style/blue/base.css
Log Message:
-----------
Revise panel/iframe handling, align naming, rely on empty to trigger removal of previous view
Repack
Move inline styles, use consistent naming
Commit: 2c4c7147e075f036ee703a89eb6de7f39c4e10dd
https://github.com/galaxyproject/galaxy/commit/2c4c7147e075f036ee703a89eb6d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js
Log Message:
-----------
Revise and fix resize handler
Commit: 21312138a47cb0c3f958c318500937b11df31d49
https://github.com/galaxyproject/galaxy/commit/21312138a47cb0c3f958c3185009…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Fix deferred form destructor
Commit: 71498cabfdb9e988e3035915a8be647b88db1ef8
https://github.com/galaxyproject/galaxy/commit/71498cabfdb9e988e3035915a8be…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Fix log statement
Commit: d031758d7323c39ed3176c158355f9d697266ef1
https://github.com/galaxyproject/galaxy/commit/d031758d7323c39ed3176c158355…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Pack scripts
Commit: f4e4c08bab6b8ecf39a69844a904e2fa1c3e4459
https://github.com/galaxyproject/galaxy/commit/f4e4c08bab6b8ecf39a69844a904…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/style/less/base.less
M static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #36 from guerler/fix_cleanup
Fixes deferred removal of previous views, augments center panel handling
Commit: 837a5c85fcf9c6906843fe413aaf10f27ef21af4
https://github.com/galaxyproject/galaxy/commit/837a5c85fcf9c6906843fe413aaf…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
Log Message:
-----------
Merging changes with static files
Commit: 8a09836ba79e7f7b08f51a8d7db7c416b03bd44f
https://github.com/galaxyproject/galaxy/commit/8a09836ba79e7f7b08f51a8d7db7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M .gitignore
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
A config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/static/script.js
A config/plugins/webhooks/demo/tour_generator/static/styles.css
M cron/updateucsc.sh.sample
M lib/galaxy/config.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M scripts/api/library_upload_dir.py
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.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/menu.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/webhooks.js
M static/scripts/onload.js
M templates/js-app.mako
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/functional/webhooks/trans_object/helper/__init__.py
Log Message:
-----------
Merging with dev
Commit: 9b9e2aa2274202c9afe336724c78142408c94a77
https://github.com/galaxyproject/galaxy/commit/9b9e2aa2274202c9afe336724c78…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/base.less
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Merge remote-tracking branch 'bgruening/convertworkflowmako' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/6a0401e08ebc...9b9e2aa22742
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3258635c159acfa3cd4ab33e1484b20b9bced9c1
https://github.com/galaxyproject/galaxy/commit/3258635c159acfa3cd4ab33e1484…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
Log Message:
-----------
Add histories route to analaysis app
Commit: 0fa6f144d013ecac7bcd268f100b07c2c7811ffe
https://github.com/galaxyproject/galaxy/commit/0fa6f144d013ecac7bcd268f100b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Redirect masthead link
Commit: 15206d1dec8547b0ee23a5f8412478f79a6689e0
https://github.com/galaxyproject/galaxy/commit/15206d1dec8547b0ee23a5f84124…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add client route to backend app
Commit: 6af0126e60fcffc8afa3d57c8a1d9490822bdfa4
https://github.com/galaxyproject/galaxy/commit/6af0126e60fcffc8afa3d57c8a1d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Change controller response from mako to json
Commit: 658483ba5e50516d3bbef8f22411534a483a1aa6
https://github.com/galaxyproject/galaxy/commit/658483ba5e50516d3bbef8f22411…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Fix refresh handler
Commit: 23d086a9894d6ea67bf19ca0f74147f62e76c801
https://github.com/galaxyproject/galaxy/commit/23d086a9894d6ea67bf19ca0f741…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Fix sharing operation
Commit: d7d33323952d81352259bc745d749b8583a3cd16
https://github.com/galaxyproject/galaxy/commit/d7d33323952d81352259bc745d74…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Remove custom mako name from definition
Commit: 9ed0326b150e71b781994c4d2def42f71fdb48d0
https://github.com/galaxyproject/galaxy/commit/9ed0326b150e71b781994c4d2def…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Fix rename operation
Commit: c987e5fa375ce66f383482a7b30c23e71610d2a2
https://github.com/galaxyproject/galaxy/commit/c987e5fa375ce66f383482a7b30c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Revise view operation
Commit: 843ed9e6a9d2f7545919b71b057068ffb52f4d01
https://github.com/galaxyproject/galaxy/commit/843ed9e6a9d2f7545919b71b0570…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Pack
Commit: 49ae97d3a368d1352f591a8d5a6bde96307af27d
https://github.com/galaxyproject/galaxy/commit/49ae97d3a368d1352f591a8d5a6b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Remove uncommented copy statement
Commit: 0fb1059bf74bbd4ba7f12cdd0f1104141242290b
https://github.com/galaxyproject/galaxy/commit/0fb1059bf74bbd4ba7f12cdd0f11…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
Log Message:
-----------
Insert custom history-list view to accomodate copy dialog hack
Commit: 01cab673e7dcca0e7d463e3aa4982e49fa632e27
https://github.com/galaxyproject/galaxy/commit/01cab673e7dcca0e7d463e3aa498…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
A static/maps/mvc/history/history-list.js.map
A static/scripts/mvc/history/history-list.js
Log Message:
-----------
Add packed files
Commit: e3a4bf5d9ed02fe22a6732637511490d0a086f8d
https://github.com/galaxyproject/galaxy/commit/e3a4bf5d9ed02fe22a6732637511…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
A client/galaxy/scripts/mvc/history/history-list.js
Log Message:
-----------
Add history list module
Commit: 84adc659bc67b6b65206ad7f9e9ee10916237f30
https://github.com/galaxyproject/galaxy/commit/84adc659bc67b6b65206ad7f9e9e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-list.js
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/history-list.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/grid/grid-view.js
M static/scripts/mvc/history/history-list.js
Log Message:
-----------
Augment grid view event handler to allow custom client side operations
Commit: d931df2ca9d107d07af1c97a3d5de326f8ef378b
https://github.com/galaxyproject/galaxy/commit/d931df2ca9d107d07af1c97a3d5d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/history-list.js
M static/maps/mvc/history/history-list.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-list.js
Log Message:
-----------
Reimplement copy operation
Commit: c3305581426fc2b344499079a5f94a65c9f5400a
https://github.com/galaxyproject/galaxy/commit/c3305581426fc2b344499079a5f9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.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/history/options-menu.js
Log Message:
-----------
Reroute link form history panel to saved grids
Commit: 72d038504128a5b8e7ce721375b254b18805c450
https://github.com/galaxyproject/galaxy/commit/72d038504128a5b8e7ce721375b2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-07 (Wed, 07 Jun 2017)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.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/history/options-menu.js
Log Message:
-----------
Fix target handling
Commit: b9461eba40fbc3e8d3129fff94b954f2618c5ddf
https://github.com/galaxyproject/galaxy/commit/b9461eba40fbc3e8d3129fff94b9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/mvc/page/page-list.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
A lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_search.py
M lib/galaxy/tools/deps/mulled/util.py
A lib/galaxy/tools/deps/singularity_util.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M static/maps/layout/menu.js.map
M static/maps/mvc/grid/grid-view.js.map
A static/maps/mvc/page/page-list.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/menu.js
M static/scripts/mvc/grid/grid-view.js
A static/scripts/mvc/page/page-list.js
M templates/sharing_base.mako
R templates/webapps/galaxy/dataset/grid.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
A test/functional/tools/mulled_example_multi_versionless.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'dev' into grid_histories
Commit: c2ebb5776bc26d62179fbc7ffe07bb7bec4288cf
https://github.com/galaxyproject/galaxy/commit/c2ebb5776bc26d62179fbc7ffe07…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-14 (Wed, 14 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use explicit routes
Commit: 434d944e5da46cf889b74a6759f3cce88c2f6aa4
https://github.com/galaxyproject/galaxy/commit/434d944e5da46cf889b74a6759f3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-06-14 (Wed, 14 Jun 2017)
Changed paths:
M .gitignore
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/onload.js
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
A config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/static/script.js
A config/plugins/webhooks/demo/tour_generator/static/styles.css
M cron/updateucsc.sh.sample
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.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/menu.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/webhooks.js
M static/scripts/onload.js
M templates/js-app.mako
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/functional/webhooks/trans_object/helper/__init__.py
Log Message:
-----------
Merge branch 'dev' into grid_histories
Commit: 6a0401e08ebce9797901812c57d7fca69a887c0b
https://github.com/galaxyproject/galaxy/commit/6a0401e08ebce9797901812c57d7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-06-20 (Tue, 20 Jun 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/options-menu.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/layout/menu.js.map
M static/maps/mvc/grid/grid-view.js.map
A static/maps/mvc/history/history-list.js.map
M static/maps/mvc/history/options-menu.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/grid/grid-view.js
A static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/options-menu.js
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
Log Message:
-----------
Merge pull request #4167 from guerler/grid_histories
Remove histories grid mako
Compare: https://github.com/galaxyproject/galaxy/compare/89851e4c7154...6a0401e08ebc
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 76c6b6f5bae1fbf7b2b564ecdb46a556590a6daa
https://github.com/galaxyproject/galaxy/commit/76c6b6f5bae1fbf7b2b564ecdb46…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Fix mulled Docker resolution.
I broke a bunch of Docker stuff when I abstracted it out for Singularity - things like ignoring namespaces because Singularity doesn't use that concept.
Also fetching mulled-v2 images from quay.io was broken - I didn't notice this because previously there were no published images mulit-container images.
Commit: ea1cf742f0f8e2f6277762c540e0173dbaf45964
https://github.com/galaxyproject/galaxy/commit/ea1cf742f0f8e2f6277762c540e0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
Log Message:
-----------
Bring in Singularity fixes from galaxy-lib.
xref https://github.com/galaxyproject/galaxy-lib/pull/67
Commit: 89851e4c7154b451c02f83e1561a65ded45ae502
https://github.com/galaxyproject/galaxy/commit/89851e4c7154b451c02f83e1561a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
Log Message:
-----------
Merge pull request #4207 from jmchilton/mulled_container_fixes
Various mulled container fixes.
Compare: https://github.com/galaxyproject/galaxy/compare/2a5dc90003c6...89851e4c7154