Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: dc9c2e4b7569726263fac8ab06cefb889c2b8af5
https://github.com/galaxyproject/galaxy/commit/dc9c2e4b7569726263fac8ab06ce…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE.
Commit: 7bcbf140936bfc9d25b8e6bed8a0bc14270b0cf2
https://github.com/galaxyproject/galaxy/commit/7bcbf140936bfc9d25b8e6bed8a0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M static/maps/mvc/grid/grid-view.js.map
M static/scripts/mvc/grid/grid-view.js
Log Message:
-----------
Merge pull request #978 from dannon/graft_to_stable
[15.10] Fix grid bulk operations
Compare: https://github.com/galaxyproject/galaxy/compare/dab1ce3f03c2...7bcbf140936b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 291f4d77d62be708bd9ead6bfc546722eb2a66cf
https://github.com/galaxyproject/galaxy/commit/291f4d77d62be708bd9ead6bfc54…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-10-20 (Tue, 20 Oct 2015)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M lib/galaxy/managers/configuration.py
M static/maps/galaxy.library.js.map
M static/scripts/galaxy.library.js
Log Message:
-----------
add google analytics tracking to newlibs, propagate ga_code to JS config
Commit: f0fbd25526032ce35c824c8e2af7f72794327707
https://github.com/galaxyproject/galaxy/commit/f0fbd25526032ce35c824c8e2af7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M CONTRIBUTING.md
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/libs/jquery/jquery.dynatree.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/style/less/library.less
M client/galaxy/style/less/list-item.less
M create_db.sh
R dist-eggs.ini
M doc/source/index.rst
A doc/source/project/issues.rst
R eggs.ini
M lib/galaxy/__init__.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/util/gff_util.py
A lib/galaxy/dependencies/__init__.py
A lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/dependencies/dev-requirements.txt
A lib/galaxy/dependencies/requirements.txt
M lib/galaxy/eggs/__init__.py
R lib/galaxy/eggs/dist.py
R lib/galaxy/eggs/scramble.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.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 lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/orm/__init__.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/template.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/__init__.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/util.py
M lib/galaxy/workflow/render.py
M lib/galaxy_ext/metadata/set_metadata.py
R lib/pkg_resources.py
M lib/pulsar/client/config_util.py
M lib/pulsar/client/transport/poster.py
M lib/pulsar/client/transport/requests.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M manage_db.sh
M manage_tools.sh
M requirements.txt
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/common.py
A scripts/binary_compatibility.py
R scripts/check_eggs.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/common_startup.sh
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
R scripts/dist-scramble.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
R scripts/egg_packager_template.py
R scripts/fetch_eggs.py
M scripts/functional_tests.py
R scripts/make_egg_packager.py
M scripts/manage_db.py
M scripts/manage_tools.py
M scripts/nosetests.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
R scripts/scramble.py
R scripts/scramble/lib/scramble_lib.py
R scripts/scramble/patches/Cheetah/SetupConfig.py
R scripts/scramble/patches/MySQL_python/site.cfg
R scripts/scramble/patches/PasteScript/setup.py
R scripts/scramble/patches/python_daemon/setup.py
R scripts/scramble/scripts/DRMAA_python-macosx.py
R scripts/scramble/scripts/DRMAA_python-solaris.py
R scripts/scramble/scripts/DRMAA_python.py
R scripts/scramble/scripts/MySQL_python-solaris.py
R scripts/scramble/scripts/MySQL_python.py
R scripts/scramble/scripts/PyRods.py
R scripts/scramble/scripts/bx_python-solaris.py
R scripts/scramble/scripts/generic.py
R scripts/scramble/scripts/pbs_python.py
R scripts/scramble/scripts/psycopg2-linux.py
R scripts/scramble/scripts/psycopg2-macosx.py
R scripts/scramble/scripts/psycopg2-solaris.py
R scripts/scramble/scripts/psycopg2.py
R scripts/scramble/scripts/pysam-solaris.py
R scripts/scramble/scripts/pysqlite.py
M scripts/summarize_timings.py
R scripts/test_dist_egg.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tools/maf/check_loc_file.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M set_metadata.sh
M static/maps/libs/jquery/jquery.dynatree.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/history-panel.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/libs/jquery/jquery.dynatree.js
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/reports_webapp/run_stats.js
M static/style/blue/base.css
R static/style/blue/dynatree_skin/cbChecked.gif
R static/style/blue/dynatree_skin/cbChecked_hover.gif
R static/style/blue/dynatree_skin/cbIntermediate.gif
R static/style/blue/dynatree_skin/cbIntermediate_hover.gif
R static/style/blue/dynatree_skin/cbUnchecked.gif
R static/style/blue/dynatree_skin/cbUnchecked_hover.gif
R static/style/blue/dynatree_skin/customDoc1.gif
R static/style/blue/dynatree_skin/customFolder1.gif
A static/style/blue/dynatree_skin/icons-rtl.gif
A static/style/blue/dynatree_skin/icons.gif
A static/style/blue/dynatree_skin/loading.gif
R static/style/blue/dynatree_skin/ltD_ne.gif
R static/style/blue/dynatree_skin/ltD_nes.gif
R static/style/blue/dynatree_skin/ltDoc.gif
R static/style/blue/dynatree_skin/ltError.gif
R static/style/blue/dynatree_skin/ltFld.gif
R static/style/blue/dynatree_skin/ltFld_o.gif
R static/style/blue/dynatree_skin/ltL_.gif
R static/style/blue/dynatree_skin/ltL_ne.gif
R static/style/blue/dynatree_skin/ltL_nes.gif
R static/style/blue/dynatree_skin/ltL_ns.gif
R static/style/blue/dynatree_skin/ltM_ne.gif
R static/style/blue/dynatree_skin/ltM_nes.gif
R static/style/blue/dynatree_skin/ltP_ne.gif
R static/style/blue/dynatree_skin/ltP_nes.gif
R static/style/blue/dynatree_skin/ltWait.gif
R static/style/blue/dynatree_skin/rbChecked.gif
R static/style/blue/dynatree_skin/rbChecked_hover.gif
R static/style/blue/dynatree_skin/rbIntermediate.gif
R static/style/blue/dynatree_skin/rbIntermediate_hover.gif
R static/style/blue/dynatree_skin/rbUnchecked.gif
R static/style/blue/dynatree_skin/rbUnchecked_hover.gif
M static/style/blue/dynatree_skin/ui.dynatree.css
A static/style/blue/dynatree_skin/vline-rtl.gif
A static/style/blue/dynatree_skin/vline.gif
M static/style/blue/library.css
M templates/admin/requests/select_datasets_to_transfer.mako
M templates/admin/tool_shed_repository/common.mako
M templates/base/base_panels.mako
M templates/webapps/galaxy/root/index.mako
M templates/webapps/tool_shed/repository/common.mako
M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/test_db_util.py
M test/base/twilltestcase.py
M test/casperjs/anon-history-tests.js
M test/casperjs/api-hda-tests.js
M test/casperjs/api-history-tests.js
M test/casperjs/hda-state-tests.js
M test/casperjs/history-panel-tests.js
M test/casperjs/modules/historypanel.js
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/functional/test_metadata_editing.py
M test/functional/tools/simple_constructs.yml
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/manual/workflows_scaling.py
M test/tool_shed/base/test_db_util.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional_tests.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_execution.py
M test/unit/workflows/test_modules.py
M tools/filters/cutWrapper.xml
M tools/genomespace/genomespace_importer.xml
M tox.ini
Log Message:
-----------
Merge branch 'dev' into track-newlibs
Conflicts:
static/maps/galaxy.library.js.map
static/scripts/galaxy.library.js
Commit: a71f504b1e9e1b10a188804bc2c359218d815483
https://github.com/galaxyproject/galaxy/commit/a71f504b1e9e1b10a188804bc2c3…
Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M lib/galaxy/managers/configuration.py
M static/maps/galaxy.library.js.map
M static/scripts/galaxy.library.js
Log Message:
-----------
Merge pull request #959 from martenson/track-newlibs
add google analytics tracking to newlibs, propagate ga_code to JS config
Compare: https://github.com/galaxyproject/galaxy/compare/e31ec7b0c8bc...a71f504b1e9e
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: ee079f369c5e05952b006b73512bc431837ce58d
https://github.com/galaxyproject/usegalaxy-playbook/commit/ee079f369c5e0595…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M roles/galaxyprojectdotorg.galaxy/README.md
M roles/galaxyprojectdotorg.galaxy/defaults/main.yml
M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info
M roles/galaxyprojectdotorg.galaxy/meta/main.yml
M roles/galaxyprojectdotorg.galaxy/tasks/clone.yml
A roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml
M roles/galaxyprojectdotorg.galaxy/tasks/main.yml
Log Message:
-----------
Update galaxyprojectdotorg.galaxy to 0.6
Branch: refs/heads/master
Home: https://github.com/galaxyproject/ansible-galaxy
Commit: c2c4afeb19d608ed381554ea943d2566ca14cd18
https://github.com/galaxyproject/ansible-galaxy/commit/c2c4afeb19d608ed3815…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M tasks/dependencies.yml
Log Message:
-----------
Ensure $VIRTUAL_ENV is always set when running pip (it is not activated,
but reading binary-compatibility.cfg depends on it).
Add a task for running Galaxy's binary_compatibility.py script so that
CentOS can install RHEL wheels.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f3bfa2f56bb71f737ff8faa622271102652c7592
https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
remove the autorefresh on Reports app
because of how long each page takes on Main the request for a subpage
would timeout because new autorefresh request would be automatically
issued
Commit: ee327702d75415261085796af1e5c1ff5b1308ee
https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix workflow extraction from history
Fix history extraction by returning value dictionary
Remove previous fix
Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207
https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Undo commit, wrong branch
Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453
https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix workflow extraction from history
Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7
https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Merge pull request #967 from martenson/remove-reports-autorefresh
[15.10] remove the autorefresh on Reports app homepage
Commit: 3fe148dd1981b516452df9ace6db75e95879df03
https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #970 from guerler/fix_history_extract_001
[15.10] Fix workflow extraction from history
Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be
https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec…
Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
Log Message:
-----------
Fix for missing included files on history export and import.
Notes:
If a history was exported previously, galaxy would just serve the cached version.
In that case, it is better to make some changes to the history for example, by re-running
the last job and then exporting it.
Export of histories that haven't been exported previously should work without problems.
(cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960)
Commit: dfb59002ba78373dac32d8aebefd7b2de324260b
https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd…
Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Use object store for imported history datasets and included files
(cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7)
Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d
https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
Log Message:
-----------
Merge pull request #973 from natefoo/composite-history-import-export
[15.10] Fix for missing included files on history export and import
Commit: 6d7be0a2186882c6090584a1cd58c59c18a0a519
https://github.com/galaxyproject/galaxy/commit/6d7be0a2186882c6090584a1cd58…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M lib/galaxy/tools/__init__.py
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Merge branch 'release_15.10' of https://github.com/galaxyproject/galaxy into dev
Compare: https://github.com/galaxyproject/galaxy/compare/5f3fbdefbeb5...6d7be0a21868
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: f3bfa2f56bb71f737ff8faa622271102652c7592
https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
remove the autorefresh on Reports app
because of how long each page takes on Main the request for a subpage
would timeout because new autorefresh request would be automatically
issued
Commit: ee327702d75415261085796af1e5c1ff5b1308ee
https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix workflow extraction from history
Fix history extraction by returning value dictionary
Remove previous fix
Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207
https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Undo commit, wrong branch
Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453
https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix workflow extraction from history
Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7
https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
Log Message:
-----------
Merge pull request #967 from martenson/remove-reports-autorefresh
[15.10] remove the autorefresh on Reports app homepage
Commit: 3fe148dd1981b516452df9ace6db75e95879df03
https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #970 from guerler/fix_history_extract_001
[15.10] Fix workflow extraction from history
Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be
https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec…
Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
Log Message:
-----------
Fix for missing included files on history export and import.
Notes:
If a history was exported previously, galaxy would just serve the cached version.
In that case, it is better to make some changes to the history for example, by re-running
the last job and then exporting it.
Export of histories that haven't been exported previously should work without problems.
(cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960)
Commit: dfb59002ba78373dac32d8aebefd7b2de324260b
https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd…
Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Use object store for imported history datasets and included files
(cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7)
Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d
https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
Log Message:
-----------
Merge pull request #973 from natefoo/composite-history-import-export
[15.10] Fix for missing included files on history export and import
Compare: https://github.com/galaxyproject/galaxy/compare/ab7ec7b3abbb...dab1ce3f03c2