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- 15302 discussions
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6d22f16a2ed75a03684e34b06e5393790dda9fdd
https://github.com/galaxyproject/galaxy/commit/6d22f16a2ed75a03684e34b06e53…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Add missing comma to workflow form code
Commit: 64f4d2192745f823f0c9d2021c6b543f14fa66cc
https://github.com/galaxyproject/galaxy/commit/64f4d2192745f823f0c9d2021c6b…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Merge pull request #2674 from guerler/fix_punctation
Add missing comma to workflow form code
Compare: https://github.com/galaxyproject/galaxy/compare/e625eed9c575...64f4d2192745
1
0
[galaxyproject/galaxy] 2ecc26: remove unused config; clarify sample; provide defa...
by GitHub 27 Jul '16
by GitHub 27 Jul '16
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2ecc26d83a517ac7e7452a50d84e9b96e1a9e8af
https://github.com/galaxyproject/galaxy/commit/2ecc26d83a517ac7e7452a50d84e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/config.py
M templates/base/base_panels.mako
Log Message:
-----------
remove unused config; clarify sample; provide default for inactive message
Commit: c223ebff6dff348acfe70d329657fc71fef605d1
https://github.com/galaxyproject/galaxy/commit/c223ebff6dff348acfe70d329657…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
explicitly disable activation for TS
because inherited user controller wants the property
Commit: e625eed9c57502996b3f5caa83060bdf001bcada
https://github.com/galaxyproject/galaxy/commit/e625eed9c57502996b3f5caa8306…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/config.py
M templates/base/base_panels.mako
Log Message:
-----------
Merge pull request #2158 from martenson/improve-activation
activation config touch
Compare: https://github.com/galaxyproject/galaxy/compare/3440334694cf...e625eed9c575
1
0
[galaxyproject/galaxy] 04b7d1: Add hg38 to main for ucsc_build_sites.txt.sample
by GitHub 27 Jul '16
by GitHub 27 Jul '16
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 04b7d11f053e66b14232440e6ff534a62ff26666
https://github.com/galaxyproject/galaxy/commit/04b7d11f053e66b14232440e6ff5…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
Log Message:
-----------
Add hg38 to main for ucsc_build_sites.txt.sample
Commit: 3440334694cfac5967009a45d945b97a06648f9e
https://github.com/galaxyproject/galaxy/commit/3440334694cfac5967009a45d945…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
Log Message:
-----------
Merge pull request #2670 from blankenberg/ucsc-hg38-display
Add hg38 to main for ucsc_build_sites.txt.sample
Compare: https://github.com/galaxyproject/galaxy/compare/59af87700ddc...3440334694cf
1
0
[galaxyproject/galaxy] a9809c: Use default job history on build_for_rerun unless ...
by GitHub 27 Jul '16
by GitHub 27 Jul '16
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a9809ca6925a450115a99e6dafb6f415c95357ad
https://github.com/galaxyproject/galaxy/commit/a9809ca6925a450115a99e6dafb6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Use default job history on build_for_rerun unless specified otherwise
Commit: 59af87700ddca4a6162d2ed55b148196867a9231
https://github.com/galaxyproject/galaxy/commit/59af87700ddca4a6162d2ed55b14…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #2668 from guerler/default_job_history
Use default job history on build_for_rerun if current history is unavailable
Compare: https://github.com/galaxyproject/galaxy/compare/d9e52c671f80...59af87700ddc
1
0
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a25278db670891de06c5159182b0838d47900050
https://github.com/galaxyproject/galaxy/commit/a25278db670891de06c5159182b0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form.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-view.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Change default refresh mode for form views
Commit: d9e52c671f803fd6b320fd2f1cf49d2c00570aa5
https://github.com/galaxyproject/galaxy/commit/d9e52c671f803fd6b320fd2f1cf4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form.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-view.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #2667 from guerler/add_form_refresh
Change default refresh mode for form views
Compare: https://github.com/galaxyproject/galaxy/compare/28e7f866cbab...d9e52c671f80
1
0
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3163dc77f504a1923046e184c3d86822e34f940a
https://github.com/galaxyproject/galaxy/commit/3163dc77f504a1923046e184c3d8…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2016-06-29 (Wed, 29 Jun 2016)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
add python-ldap module if used in auth-conf.xml
Commit: 8b9d77ee3b8832c767dd2a34f23eb8bcc60d6423
https://github.com/galaxyproject/galaxy/commit/8b9d77ee3b8832c767dd2a34f23e…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2016-06-29 (Wed, 29 Jun 2016)
Changed paths:
M lib/galaxy/dependencies/__init__.py
Log Message:
-----------
detect actviedirectory too
Commit: b08dfa2e72ec7d49a6b9e50241dba082825f8061
https://github.com/galaxyproject/galaxy/commit/b08dfa2e72ec7d49a6b9e50241db…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/graphviz/static/js/graphVis.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
A config/tool_destinations.yml.sample
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_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/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_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/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
A scripts/grt.py
A scripts/grt.yml.sample
M setup.cfg
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.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/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/style/blue/base.css
M templates/admin/impersonate.mako
M templates/ind_share_base.mako
M templates/user/change_password.mako
M templates/webapps/galaxy/history/grid.mako
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
A test/functional/tools/identifier_collection.xml
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/datatypes/test_data.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.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_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_toolbox.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into ldap
Commit: 28e7f866cbab76e93f63179d4a7e6c2fd962b5b1
https://github.com/galaxyproject/galaxy/commit/28e7f866cbab76e93f63179d4a7e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
Merge pull request #2576 from abretaud/ldap
Add python-ldap module to conditional requirements
Compare: https://github.com/galaxyproject/galaxy/compare/b74fd63feff0...28e7f866cbab
1
0
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b79474083b08860923f7f28fc1e7442b53f925db
https://github.com/galaxyproject/galaxy/commit/b79474083b08860923f7f28fc1e7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M config/tool_shed.ini.sample
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/util/shed_util_common.py
M static/maps/layout/page.js.map
M static/maps/mvc/citation/citation-model.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-library-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
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-library-view.js
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/workflow/run.mako
M test/tool_shed/base/twilltestcase.py
A test/tool_shed/functional/test_0310_hg_api_features.py
R test/tool_shed/functional/test_0310_hg_push_from_api.py
Log Message:
-----------
Merge pull request #2206 from dannon/master
Sanity check of master update.
Commit: e77d3f009a8e2fb51e97f41b4c47e397c90cbcea
https://github.com/galaxyproject/galaxy/commit/e77d3f009a8e2fb51e97f41b4c47…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-03 (Tue, 03 May 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/workflow/run.py
M templates/webapps/galaxy/library/common/browse_library.mako
M templates/webapps/galaxy/library/common/ldda_info.mako
M test/tool_shed/base/twilltestcase.py
Log Message:
-----------
Merge branch 'release_16.01'
Commit: e08dae34628d31f6685f9f7e031e2085c024f63b
https://github.com/galaxyproject/galaxy/commit/e08dae34628d31f6685f9f7e031e…
Author: balto <balto_59(a)hotmail.fr>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
A lib/galaxy/webapps/reports/controllers/history.py
A templates/webapps/reports/history_and_dataset_per_user.mako
A templates/webapps/reports/history_and_dataset_type.mako
M templates/webapps/reports/index.mako
Log Message:
-----------
Creation of the history category that contains two pages: history and dataset per type/user.
Commit: cd2b61a3a1426cdd62f9af3fe506affa3c097688
https://github.com/galaxyproject/galaxy/commit/cd2b61a3a1426cdd62f9af3fe506…
Author: balto <balto_59(a)hotmail.fr>
Date: 2016-05-09 (Mon, 09 May 2016)
Changed paths:
A lib/galaxy/webapps/reports/controllers/tools.py
Log Message:
-----------
Creation of the tools controller and each methods for each template.
Commit: e4d8c7d88556a201a91ac21b67d08feecd57f819
https://github.com/galaxyproject/galaxy/commit/e4d8c7d88556a201a91ac21b67d0…
Author: balto <balto_59(a)hotmail.fr>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M templates/webapps/reports/index.mako
A templates/webapps/reports/tool_error_messages.mako
A templates/webapps/reports/tool_execution_time.mako
A templates/webapps/reports/tool_execution_time_peer_month.mako
A templates/webapps/reports/tools_and_job_state.mako
A templates/webapps/reports/tools_and_job_state_peer_month.mako
Log Message:
-----------
Implementation of tools-related pages.
Commit: fdd778f244b6f647aa8c56e133c3226bbed8ed72
https://github.com/galaxyproject/galaxy/commit/fdd778f244b6f647aa8c56e133c3…
Author: balto <balto_59(a)hotmail.fr>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/users.py
A templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/index.mako
Log Message:
-----------
Implementation of a new page listing histories per users.
Commit: 71fc940c8f048d3c3b4e929320bd895c2361e342
https://github.com/galaxyproject/galaxy/commit/71fc940c8f048d3c3b4e929320bd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/history.py
Log Message:
-----------
Gets reports/controllers/history.py up to passing style.
Commit: a66800465614042b75c0f30217b0c1d9075aaed1
https://github.com/galaxyproject/galaxy/commit/a66800465614042b75c0f30217b0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-10 (Tue, 10 May 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/history.py
Log Message:
-----------
Slight bit of extra import cleanup in reports/controllers/history
Commit: 5c47820e01576854a111b54f220993415258ffc8
https://github.com/galaxyproject/galaxy/commit/5c47820e01576854a111b54f2209…
Author: BalthazarPavot <balthazar.pavot(a)hotmail.fr>
Date: 2016-07-07 (Thu, 07 Jul 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/history.py
Log Message:
-----------
Merge pull request #1 from dannon/dev_reports
This brings the history file up to style guidelines and will fix the build.
Commit: 3107cfed9d502ea9baf0cab14a19cbf3c8bdec61
https://github.com/galaxyproject/galaxy/commit/3107cfed9d502ea9baf0cab14a19…
Author: BalthazarPavot <balthazar.pavot(a)hotmail.fr>
Date: 2016-07-07 (Thu, 07 Jul 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/tools.py
Log Message:
-----------
Update tools.py
Commit: 12c65d4a6365e34660c78dab7bb43b2cf292eb61
https://github.com/galaxyproject/galaxy/commit/12c65d4a6365e34660c78dab7bb4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/tools.py
Log Message:
-----------
fix import of and_ operator
Commit: 28a990470738ac821a6a2851306dac9723767c12
https://github.com/galaxyproject/galaxy/commit/28a990470738ac821a6a2851306d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M templates/webapps/reports/history_and_dataset_per_user.mako
M templates/webapps/reports/history_and_dataset_type.mako
M templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/index.mako
M templates/webapps/reports/tool_execution_time.mako
R templates/webapps/reports/tool_execution_time_peer_month.mako
A templates/webapps/reports/tool_execution_time_per_month.mako
M templates/webapps/reports/tools_and_job_state.mako
R templates/webapps/reports/tools_and_job_state_peer_month.mako
A templates/webapps/reports/tools_and_job_state_per_month.mako
Log Message:
-----------
fix menu items to actually display new templates
reword certain texts
reorder imports and fix style
remove unnecessary imports
Commit: 295f3f93e1db89b13040b42c8945cd5491ccda02
https://github.com/galaxyproject/galaxy/commit/295f3f93e1db89b13040b42c8945…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M templates/webapps/reports/history_and_dataset_per_user.mako
M templates/webapps/reports/history_and_dataset_type.mako
M templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/tool_execution_time.mako
M templates/webapps/reports/tool_execution_time_per_month.mako
M templates/webapps/reports/tools_and_job_state.mako
M templates/webapps/reports/tools_and_job_state_per_month.mako
Log Message:
-----------
change css classes and html markup for new report pages
Commit: 8483f2ce8bffbdee0ee9ffd65b7212ed8c54e8a4
https://github.com/galaxyproject/galaxy/commit/8483f2ce8bffbdee0ee9ffd65b72…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/webapps/reports/controllers/tools.py
Log Message:
-----------
Fix E731
Commit: b74fd63feff0c2c324009b9a48757ff146d69cdc
https://github.com/galaxyproject/galaxy/commit/b74fd63feff0c2c324009b9a4875…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
A lib/galaxy/webapps/reports/controllers/history.py
A lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
A templates/webapps/reports/history_and_dataset_per_user.mako
A templates/webapps/reports/history_and_dataset_type.mako
A templates/webapps/reports/history_per_user.mako
M templates/webapps/reports/index.mako
A templates/webapps/reports/tool_error_messages.mako
A templates/webapps/reports/tool_execution_time.mako
A templates/webapps/reports/tool_execution_time_per_month.mako
A templates/webapps/reports/tools_and_job_state.mako
A templates/webapps/reports/tools_and_job_state_per_month.mako
Log Message:
-----------
Merge pull request #2664 from dannon/dev_reports
Reports: new pages and improvements
Compare: https://github.com/galaxyproject/galaxy/compare/fa4085be548a...b74fd63feff0
1
0
[galaxyproject/galaxy] 1cdc53: Reduce server sided refresh requests to changes in...
by GitHub 27 Jul '16
by GitHub 27 Jul '16
27 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1cdc532ff1817f59b5693cb9ef6e787be5374e9d
https://github.com/galaxyproject/galaxy/commit/1cdc532ff1817f59b5693cb9ef6e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-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/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Reduce server sided refresh requests to changes in data associated input fields
Commit: fa4085be548a6b893745f467deb71cd0ec0dfcec
https://github.com/galaxyproject/galaxy/commit/fa4085be548a6b893745f467deb7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-27 (Wed, 27 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M lib/galaxy/tools/parameters/basic.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-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/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Merge pull request #2652 from guerler/reduce_refreshs
Reduce server sided refresh requests to changes in data associated input fields
Compare: https://github.com/galaxyproject/galaxy/compare/8b597ed01a6f...fa4085be548a
1
0
26 Jul '16
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9
https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Generate metadata in separate conda environment
Galaxy supports generating metadata in a separate command (enable
beta_tool_command_isolation). This command has its own dependency resolution,
that may interfere with thedependency resolution of the actual tool, if the
same environment is being used. With this PR we create a new environment when
resolving metadata dependencies with conda, that will be active only for
metadata generation.
Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde
https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Fix whitespace and comma use
Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb
https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e61224…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore.
Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64
https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/__init__.py
M test/base/driver_util.py
Log Message:
-----------
Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it)
Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76
https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/web/framework/helpers/__init__.py
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #2662 from jmchilton/backport_2253
[16.04] Backport #2253 as requested by Eagle Eyes
Compare: https://github.com/galaxyproject/galaxy/compare/1de7beca98d0...8f978b8957f0
1
0
[galaxyproject/galaxy] c07bbe: Add import order linting using tox and flake8-impo...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c07bbe010ee350d6bb63006ff8829a16d0d9d4a9
https://github.com/galaxyproject/galaxy/commit/c07bbe010ee350d6bb63006ff882…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .travis.yml
M setup.cfg
M tox.ini
Log Message:
-----------
Add import order linting using tox and flake8-import-order.
Adds two tasks:
- Add a task that just lints everything the way Galaxy's default linting is (py27-lint-imports) and don't enforce it passes on Travis.
- Add a task that just lints a subset we expect to past, hopefully we can grow this subset over time.
Once the inverse of the subset we are testing is just the blacklist, we can eliminate bothtasks and just wrap this into Galaxy's default linting.
These tasks require an older flake8 until https://github.com/PyCQA/flake8-import-order/issues/79#issuecomment-2350522… is part of a released version of flake8.
Commit: 8b597ed01a6fd4335b78ba66875a40f430423c34
https://github.com/galaxyproject/galaxy/commit/8b597ed01a6fd4335b78ba66875a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .travis.yml
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #2661 from jmchilton/lint_imports
Add import order linting using tox and flake8-import-order.
Compare: https://github.com/galaxyproject/galaxy/compare/71151c6b2dd3...8b597ed01a6f
1
0
[galaxyproject/galaxy] 26b141: made changes to tool-form-base.js, this should all...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 26b141c83f906dbc7d11c14da968f323eaa632e8
https://github.com/galaxyproject/galaxy/commit/26b141c83f906dbc7d11c14da968…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.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/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
made changes to tool-form-base.js, this should allow the tool-form to listen to history. Thanks @guerler for walking me through backbone
Commit: c172641c9deda5d9c193e212a2d74d150eb64f79
https://github.com/galaxyproject/galaxy/commit/c172641c9deda5d9c193e212a2d7…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
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:
-----------
added refresh in _buildform as per @guerler 's suggestion
Commit: fd34553cb142e9ccff6b7b295247dd09801d3fb0
https://github.com/galaxyproject/galaxy/commit/fd34553cb142e9ccff6b7b295247…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
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:
-----------
removing options.needs_update as it is not used anymore, per @guerlers suggestion
Commit: 6414478ad1ab669c8725d0fb784e1b438ddb40dd
https://github.com/galaxyproject/galaxy/commit/6414478ad1ab669c8725d0fb784e…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
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:
-----------
added self.deferred() in refresh
Commit: a6e288fe301c00e88893e0ffe3cbe9f9572aba5e
https://github.com/galaxyproject/galaxy/commit/a6e288fe301c00e88893e0ffe3cb…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
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.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
changes'
Commit: 71151c6b2dd3038ac04a77bbb8543e77875b9cc1
https://github.com/galaxyproject/galaxy/commit/71151c6b2dd3038ac04a77bbb854…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.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/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #2476 from nturaga/tool_form_listen_history
Allow tool form to listen to history
Compare: https://github.com/galaxyproject/galaxy/compare/3d0f5577b105...71151c6b2dd3
1
0
[galaxyproject/galaxy] 7a8d86: Ensure Galaxy's python binary is used for metadata...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7a8d86aa9bd2b8adfbe8e6826e506dfedf997e22
https://github.com/galaxyproject/galaxy/commit/7a8d86aa9bd2b8adfbe8e6826e50…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Ensure Galaxy's python binary is used for metadata generation.
Commit: 3d0f5577b10507cd774f3e4f92f6c8364a8a4407
https://github.com/galaxyproject/galaxy/commit/3d0f5577b10507cd774f3e4f92f6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Merge pull request #2660 from jmchilton/ensure_galaxy_python_for_metadata
Ensure Galaxy's python binary is used for metadata generation.
Compare: https://github.com/galaxyproject/galaxy/compare/9607e528be01...3d0f5577b105
1
0
[galaxyproject/galaxy] 93ba35: Import pyparsing in testing so twill's older versi...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 93ba35fdd16a96b46ccac6884b7efcb4a5d3e8a3
https://github.com/galaxyproject/galaxy/commit/93ba35fdd16a96b46ccac6884b7e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M test/base/twilltestcase.py
Log Message:
-----------
Import pyparsing in testing so twill's older version doesn't get loaded.
There are unintended consequences if not, such as svgwrite not loading properly.
Commit: 9607e528be01234b1107db29e0a910043d12507e
https://github.com/galaxyproject/galaxy/commit/9607e528be01234b1107db29e0a9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M test/base/twilltestcase.py
Log Message:
-----------
Merge pull request #2656 from jmchilton/pyparsing_testing
Import pyparsing in testing so twill's older version doesn't get loaded.
Compare: https://github.com/galaxyproject/galaxy/compare/134f98854931...9607e528be01
1
0
[galaxyproject/galaxy] 8559dc: Ignore .tox directory. Used to be ignored by defa...
by GitHub 25 Jul '16
by GitHub 25 Jul '16
25 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8559dc00b606551de5947d6bc5d74bb9feb9f184
https://github.com/galaxyproject/galaxy/commit/8559dc00b606551de5947d6bc5d7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore.
Commit: 10745f252f6e0cf59a47f097620d5d05034b1c1a
https://github.com/galaxyproject/galaxy/commit/10745f252f6e0cf59a47f097620d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/__init__.py
M test/base/driver_util.py
Log Message:
-----------
Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it)
Commit: cf800dce03949e928333a13b675fba76e612226f
https://github.com/galaxyproject/galaxy/commit/cf800dce03949e928333a13b675f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Add eggs to blacklist as well, to ignore it in local testing for folks with it still around. (nsoranzo's suggestion)
Commit: 9f2237905b81205d0d6fec918fc15ddbea1e34ce
https://github.com/galaxyproject/galaxy/commit/9f2237905b81205d0d6fec918fc1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M test/base/driver_util.py
Log Message:
-----------
Remove two #noqas and specify __all__ for those modules. Specify many more #noqas to skip the precise relevant exception.
Commit: 0deae302852102c66e6386e16607c1db99cdeb07
https://github.com/galaxyproject/galaxy/commit/0deae302852102c66e6386e16607…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/forms.py
Log Message:
-----------
Remove two unused imports in forms controller.
Commit: 134f988549314a4a384144c2eedc3d8b4ff7e2f3
https://github.com/galaxyproject/galaxy/commit/134f988549314a4a384144c2eedc…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/galaxy/model/mapping.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #2650 from dannon/flake8_update_tox_default
Ignore .tox directory. Used to be ignored by default w/ flake8 appar…
Compare: https://github.com/galaxyproject/galaxy/compare/1e291e1ecdd1...134f98854931
1
0
25 Jul '16
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 796678f38f5545c1efc9eb1b2ba1ffa8d1244019
https://github.com/galaxyproject/usegalaxy-playbook/commit/796678f38f5545c1…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M common_roles
M production/galaxy_version.yml
Log Message:
-----------
update Main, update submodule
1
0
25 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0dd206d8f6851eeeb4fa513c42f053f801c6b757
https://github.com/galaxyproject/galaxy/commit/0dd206d8f6851eeeb4fa513c42f0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-buttons.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
M static/scripts/mvc/ui/ui-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Add optional progress bar to default buttons
Commit: d5a16deb00dc68176c04c8ed1ab1005e346f057c
https://github.com/galaxyproject/galaxy/commit/d5a16deb00dc68176c04c8ed1ab1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Increase bar size, modify wait label
Commit: bc6358ea35e6904cd7a9264fcb32ab5f8e0aa5d3
https://github.com/galaxyproject/galaxy/commit/bc6358ea35e6904cd7a9264fcb32…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M static/style/blue/base.css
Log Message:
-----------
Repack styles
Commit: 7ef6a99959511d600e64c01453b68fc4677323d7
https://github.com/galaxyproject/galaxy/commit/7ef6a99959511d600e64c01453b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
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/mvc/tool/tool-form-composite.js
Log Message:
-----------
Disable button before validation
Commit: ceaa5991e08e3e2b0a036f4b59d148b5608ec1ad
https://github.com/galaxyproject/galaxy/commit/ceaa5991e08e3e2b0a036f4b59d1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M config/datatypes_conf.xml.sample
A display_applications/ucsc/trackhub.xml
A lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/tools/execute.py
M lib/galaxy/workflow/extract.py
Log Message:
-----------
Merge branch 'dev' into progress_button
Commit: be7210e03bc6867baba513d3fb879e00bce169b4
https://github.com/galaxyproject/galaxy/commit/be7210e03bc6867baba513d3fb87…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/style/blue/base.css
Log Message:
-----------
Place steps into scrollable div, restyle step forms
Fix
Commit: 5120637b00c8c3ecef5e2caf95b7be32c4bac86d
https://github.com/galaxyproject/galaxy/commit/5120637b00c8c3ecef5e2caf95b7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
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/ui.less
M static/maps/mvc/tool/tool-form-base.js.map
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-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/style/blue/base.css
Log Message:
-----------
Remove operations from workflow step modules to simplify view
Commit: d0e222f529755e060edd3837d4fc57754c6b0447
https://github.com/galaxyproject/galaxy/commit/d0e222f529755e060edd3837d4fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M static/maps/mvc/form/form-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-view.js
Log Message:
-----------
Generalize input element highlighting
Commit: 95949c66bc658afc285dae854efd2fa8c8ede6e0
https://github.com/galaxyproject/galaxy/commit/95949c66bc658afc285dae854efd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M .gitignore
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/style/less/base.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/config.py
R lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.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/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/style/base.css
M static/style/blue/base.css
A templates/user/communication_settings.mako
M templates/user/index.mako
Log Message:
-----------
Merge branch 'dev' into progress_button
Commit: 8cf69f382a4e81bd0c1e2eced57fdf67acc29a69
https://github.com/galaxyproject/galaxy/commit/8cf69f382a4e81bd0c1e2eced57f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-24 (Sun, 24 Jul 2016)
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/mvc/tool/tool-form-composite.js
Log Message:
-----------
Remove unused history div, use reduce to calculate available screen space
Commit: 1e291e1ecdd17344aad4baed295f00bc827e36f7
https://github.com/galaxyproject/galaxy/commit/1e291e1ecdd17344aad4baed295f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.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/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/form/form-view.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/ui/ui-buttons.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/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #2647 from guerler/progress_button
Enhance workflow run button to indicate workflow loading progress, keep header fixed
Compare: https://github.com/galaxyproject/galaxy/compare/1b1e2876f562...1e291e1ecdd1
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 36938e8bcb5bba81dbac8df2a0314a96a881d50a
https://github.com/galaxyproject/galaxy/commit/36938e8bcb5bba81dbac8df2a031…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Reorder base templates meta tags
Move title below recommended first three meta tags:
https://github.com/joshbuchea/HEAD#recommended-minimum
Commit: 1b1e2876f562c39227a2834d1c8d47d4f2a064e3
https://github.com/galaxyproject/galaxy/commit/1b1e2876f562c39227a2834d1c8d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Merge pull request #2651 from carlfeberhard/templates.meta-reorder
Reorder base templates meta tags
Compare: https://github.com/galaxyproject/galaxy/compare/5e4986875d8c...1b1e2876f562
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ef58e62e6deeeecd37587c737b3113ede606f3c1
https://github.com/galaxyproject/galaxy/commit/ef58e62e6deeeecd37587c737b31…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M .gitignore
Log Message:
-----------
excluded IntelliJ IDEA files
Commit: f1a3086b87536a78c757b25d5dab51a82ee8259b
https://github.com/galaxyproject/galaxy/commit/f1a3086b87536a78c757b25d5dab…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M .ci/flake8_wrapper.sh
M .ci/py3_sources.txt
M .gitignore
M CONTRIBUTORS.md
M Makefile
M README.rst
R buildbot_setup.sh
M client/README.md
M client/bower.json
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
R client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-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/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
R client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
A client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/static/views/group.js
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
R config/plugins/visualizations/graphview/static/graphview.js
R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
R config/plugins/visualizations/graphview/templates/graphview.mako
M config/reports.ini.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.ini.sample
M contrib/galaxy.debian-init
A contrib/galaxy_supervisor.conf
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
A display_applications/biom/biom_simple.xml
M doc/source/lib/modules.rst
R doc/source/lib/pulsar.client.rst
R doc/source/lib/pulsar.client.staging.rst
R doc/source/lib/pulsar.client.transport.rst
R doc/source/lib/pulsar.rst
M doc/source/releases/16.01.rst
A doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
A doc/source/releases/16.07_announce.rst
M doc/source/releases/index.rst
R install_and_test_tool_shed_repositories.sh
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
A lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/5e5z.pdb
A lib/galaxy/datatypes/test/drugbank_drugs.cml
A lib/galaxy/datatypes/test/drugbank_drugs.inchi
A lib/galaxy/datatypes/test/drugbank_drugs.mol2
A lib/galaxy/datatypes/test/drugbank_drugs.sdf
A lib/galaxy/datatypes/test/drugbank_drugs.smi
A lib/galaxy/datatypes/test/issue1818.tabular
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
A lib/galaxy/datatypes/test/q.fps
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
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/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/util.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
A lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/__init__.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/linters/command.py
A lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
R lib/galaxy/tools/linters/top_level.py
M lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
R lib/galaxy/util/backports/importlib/__init__.py
R lib/galaxy/util/dictobj.py
M lib/galaxy/util/directory_hash.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.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_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.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/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.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/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
R lib/pulsar/__init__.py
R lib/pulsar/client/__init__.py
R lib/pulsar/client/action_mapper.py
R lib/pulsar/client/amqp_exchange.py
R lib/pulsar/client/amqp_exchange_factory.py
R lib/pulsar/client/client.py
R lib/pulsar/client/config_util.py
R lib/pulsar/client/decorators.py
R lib/pulsar/client/destination.py
R lib/pulsar/client/interface.py
R lib/pulsar/client/job_directory.py
R lib/pulsar/client/manager.py
R lib/pulsar/client/object_client.py
R lib/pulsar/client/path_mapper.py
R lib/pulsar/client/setup_handler.py
R lib/pulsar/client/staging/__init__.py
R lib/pulsar/client/staging/down.py
R lib/pulsar/client/staging/up.py
R lib/pulsar/client/transport/__init__.py
R lib/pulsar/client/transport/curl.py
R lib/pulsar/client/transport/poster.py
R lib/pulsar/client/transport/requests.py
R lib/pulsar/client/transport/ssh.py
R lib/pulsar/client/transport/standard.py
R lib/pulsar/client/util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.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/migrate/common.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.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/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.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
R lib/tool_shed/scripts/api/add_repository_registry_entry.py
R lib/tool_shed/scripts/api/common.py
R lib/tool_shed/scripts/api/create_categories.py
R lib/tool_shed/scripts/api/create_users.py
R lib/tool_shed/scripts/api/export.py
R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
R lib/tool_shed/scripts/api/import_capsule.py
R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/data_manager_example_execute.py
A scripts/api/filter_failed_datasets_from_collection.py
M scripts/api/search.py
M scripts/api/upload_to_history.py
M scripts/bootstrap_history.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/extract_dataset_part.py
M scripts/functional_tests.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/runtime_stats.py
M scripts/summarize_timings.py
A scripts/tool_shed/api/add_repository_registry_entry.py
A scripts/tool_shed/api/common.py
A scripts/tool_shed/api/create_categories.py
A scripts/tool_shed/api/create_users.py
A scripts/tool_shed/api/export.py
A scripts/tool_shed/api/get_filtered_repository_revisions.py
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M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
A test/unit/shed_unit/__init__.py
A test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_td_common_util.py
A test/unit/shed_unit/test_tool_panel_manager.py
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M test/unit/tools/test_select_parameters.py
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M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
A tool-data/biom_simple_display.loc.sample
M tools/data_source/biomart.xml
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.xml
M tools/filters/axt_to_fasta.xml
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav.xml
M tools/filters/bed2gff.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff2bed.xml
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M tools/filters/gtf2bedgraph.xml
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M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
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M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_thread_for_species.py
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M tools/maf/maf_to_fasta_multiple_sets.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/grouping.xml
M tools/stats/gsummary.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Commit: d2c53ee724041ed6947b6db35665fd9ebb624ca8
https://github.com/galaxyproject/galaxy/commit/d2c53ee724041ed6947b6db35665…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
add config objects for the communication server
Commit: 20f25f0e35a8ca8b979aa971626925e413e39130
https://github.com/galaxyproject/galaxy/commit/20f25f0e35a8ca8b979aa9716269…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M lib/galaxy/managers/configuration.py
Log Message:
-----------
add communication host/port to the URL
Commit: f8a20cb85fa072bc2539a59c1869599be0137bfd
https://github.com/galaxyproject/galaxy/commit/f8a20cb85fa072bc2539a59c1869…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
A scripts/communication_server.py
Log Message:
-----------
add rt-communication server based on flask
Commit: e9642720b81b8ef9aed083b49fb2bc191333b376
https://github.com/galaxyproject/galaxy/commit/e9642720b81b8ef9aed083b49fb2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
Log Message:
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updating files for real time communication-server and client
Commit: 19d333d427695e11080eee705dc7ad75af5f2cda
https://github.com/galaxyproject/galaxy/commit/19d333d427695e11080eee705dc7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/maps/layout/page.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:
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updated files for real time communication feature addition
Commit: f4273ce56e23be9088b181cf02539be334310cb2
https://github.com/galaxyproject/galaxy/commit/f4273ce56e23be9088b181cf0253…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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updated the chat server client template
Commit: e90de49f584e45cf897fd63cf153dfe1bd251e43
https://github.com/galaxyproject/galaxy/commit/e90de49f584e45cf897fd63cf153…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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Change you to Me, some style fixes,
Commit: fff6c5e519875588abebd1a649e9097c38df28d6
https://github.com/galaxyproject/galaxy/commit/fff6c5e519875588abebd1a649e9…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated chat server for few features
Commit: 053e5173cc9c179e3ad3b55177fd4f91c58839dc
https://github.com/galaxyproject/galaxy/commit/053e5173cc9c179e3ad3b55177fd…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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updating the chat client template
Commit: 574136ce3fc518cfafe7c9e984c35b1cb3036fcd
https://github.com/galaxyproject/galaxy/commit/574136ce3fc518cfafe7c9e984c3…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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style changes
Commit: b7cb80343607d9af997cb539e2c3fe0239ca2ac3
https://github.com/galaxyproject/galaxy/commit/b7cb80343607d9af997cb539e2c3…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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added show full chat history feature
Commit: a539846c043d79a605eaa847e00557d2662758d1
https://github.com/galaxyproject/galaxy/commit/a539846c043d79a605eaa847e005…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Log Message:
-----------
added show full chat history feature
Commit: 687f26edf706358ef06a84c6f4ae171575d00a69
https://github.com/galaxyproject/galaxy/commit/687f26edf706358ef06a84c6f4ae…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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updated full chat history feature and added sent date time
Commit: 69d422ca034841b3fef6ede498f3df82f8ccc40b
https://github.com/galaxyproject/galaxy/commit/69d422ca034841b3fef6ede498f3…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated chat template code
Commit: 233c752a0b27cbd98aee99b0cb422f6c119f5e4a
https://github.com/galaxyproject/galaxy/commit/233c752a0b27cbd98aee99b0cb42…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
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style changes
Commit: f2ccbc6f6c73786839acb6792c86043337e36ba3
https://github.com/galaxyproject/galaxy/commit/f2ccbc6f6c73786839acb6792c86…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
Log Message:
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style changes and only show the icon if the user has activated the communication app inside of user-preferences
Commit: 67bb0874c522db4c7980032bf15eac2924277a11
https://github.com/galaxyproject/galaxy/commit/67bb0874c522db4c7980032bf15e…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
add new config parameter to indicate if the communication application is active
Commit: e572be746fc4f93dd3326a41fdd508eaaebe4867
https://github.com/galaxyproject/galaxy/commit/e572be746fc4f93dd3326a41fdd5…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Convert "1" also to True inside of string_as_bool()
Commit: cb6f739712d47699ca1196e89d1fea830aeb1868
https://github.com/galaxyproject/galaxy/commit/cb6f739712d47699ca1196e89d1f…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M lib/galaxy/managers/users.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
add user.preferences to be serialised and available in the client
Commit: 1ba0ef705a4d3f3b7538e68a50b9a66d004273cd
https://github.com/galaxyproject/galaxy/commit/1ba0ef705a4d3f3b7538e68a50b9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
remove debug statements
Commit: e6843de2dfc10fae7d47671d9e3cc7d43ebcbbfd
https://github.com/galaxyproject/galaxy/commit/e6843de2dfc10fae7d47671d9e3c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M templates/user/index.mako
Log Message:
-----------
add new change_communication action to the user controller, to offer communication related options to the user preference panel
Commit: c91c4f4089ec2ffc0195bfcb280fbcf5ea6f755a
https://github.com/galaxyproject/galaxy/commit/c91c4f4089ec2ffc0195bfcb280f…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
A templates/user/communication_settings.mako
Log Message:
-----------
add communication setting to the user preference panel
Commit: b07cfa887d2e751fe35296d8a39749ac73c2deb2
https://github.com/galaxyproject/galaxy/commit/b07cfa887d2e751fe35296d8a397…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
Log Message:
-----------
make client updates
Commit: 1dac71a42ded24fd18db005de003f2fd69a3f551
https://github.com/galaxyproject/galaxy/commit/1dac71a42ded24fd18db005de003…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Merge branch 'rt_comm' of https://github.com/bgruening/galaxy into rt_comm
Commit: 48466e1a84dd5f11e6b4ac03ce657cddf9a49253
https://github.com/galaxyproject/galaxy/commit/48466e1a84dd5f11e6b4ac03ce65…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
adjusted previous changes with new ones for the communication server
Commit: 7ea4051820acf61a176f3a5294957d64f5e2577c
https://github.com/galaxyproject/galaxy/commit/7ea4051820acf61a176f3a529495…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
a lot of cleanups
Commit: 267e1fa3813003f9a18b338a892ce99dddd35a18
https://github.com/galaxyproject/galaxy/commit/267e1fa3813003f9a18b338a892c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
A static/style/base.css
Log Message:
-----------
create symlink
Commit: eb58c101d935fd54e4922f7e5d2e18cc79c61c91
https://github.com/galaxyproject/galaxy/commit/eb58c101d935fd54e4922f7e5d2e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M scripts/communication_server.py
A scripts/socket.js
Log Message:
-----------
adding socket.js and updating chat server
Commit: 230aa1c106da8f21037f24fa16a5700d54ac9615
https://github.com/galaxyproject/galaxy/commit/230aa1c106da8f21037f24fa16a5…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
R scripts/socket.js
Log Message:
-----------
remove socket.js file
Commit: ee647dbe80d57aa6f596833fdcf2b0ab93b2cf9b
https://github.com/galaxyproject/galaxy/commit/ee647dbe80d57aa6f596833fdcf2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
revert to fetching resources from the URLs and adjusted the size of chat window
Commit: 7abca061f5dca22b9d6ee9a63f29071f9c5b4c82
https://github.com/galaxyproject/galaxy/commit/7abca061f5dca22b9d6ee9a63f29…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
removed disconnet icon and moved the functionality to online status icon
Commit: 915a882ff492bccbb233d18730c060bccafdd122
https://github.com/galaxyproject/galaxy/commit/915a882ff492bccbb233d18730c0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
css changes
Commit: 0ef409dc1274af7b1530c3823c1c6a9ca4db21d0
https://github.com/galaxyproject/galaxy/commit/0ef409dc1274af7b1530c3823c1c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-30 (Mon, 30 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
adding close button and updating chat ui
Commit: 4491e6bb4765895a979eaaaf22330f5744f7190a
https://github.com/galaxyproject/galaxy/commit/4491e6bb4765895a979eaaaf2233…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated server to clean up
Commit: 499f76e1d93bf77aaade47f50c7c1906b8ba31ba
https://github.com/galaxyproject/galaxy/commit/499f76e1d93bf77aaade47f50c7c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
removed a couple of fontawesome icons
Commit: 2831ac80f74486d4126b8694e00939af1d69d095
https://github.com/galaxyproject/galaxy/commit/2831ac80f74486d4126b8694e009…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
adding feature of chat rooms tabs and notification color
Commit: 656b2c5c6857c32c43c9e3a0ec60224cc4166ca0
https://github.com/galaxyproject/galaxy/commit/656b2c5c6857c32c43c9e3a0ec60…
Author: Remi Marenco <remi.marenco(a)gmail.com>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
A scripts/communication/template/communication.html
M scripts/communication_server.py
Log Message:
-----------
Move the html template into a dedicated folder + Add info about button online/offline
Commit: 5b196571425babf004871390e99ed073b775974f
https://github.com/galaxyproject/galaxy/commit/5b196571425babf004871390e99e…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
A scripts/communication/template/communication.html
M scripts/communication_server.py
Log Message:
-----------
Merge pull request #11 from remimarenco/rt_comm
Add info for connection status + extract HTML into a template folder
Commit: 009cbe4cb4c1c79822ef061c7ed52f07d83ae4bb
https://github.com/galaxyproject/galaxy/commit/009cbe4cb4c1c79822ef061c7ed5…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication/template/communication.html
Log Message:
-----------
added horizontal scroll in case of multiple tabs/rooms
Commit: 7a93c845d6ae4a5a5ce81b484724c7766a31abd4
https://github.com/galaxyproject/galaxy/commit/7a93c845d6ae4a5a5ce81b484724…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Talk to Galaxy to parse cookies
Commit: 03b5622ab5bc3991d13020ff6c8acd533dbe3d05
https://github.com/galaxyproject/galaxy/commit/03b5622ab5bc3991d13020ff6c8a…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Debug mode + flask-login
Commit: ca14290dc95fea6d5b0617659a062f38f92578be
https://github.com/galaxyproject/galaxy/commit/ca14290dc95fea6d5b0617659a06…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Serve separate files using approved serve method
Commit: e08a7cd39a59e191b430dae01e816ab21c8dd11f
https://github.com/galaxyproject/galaxy/commit/e08a7cd39a59e191b430dae01e81…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
A scripts/communication/template/communication.css
M scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M scripts/communication_server.py
Log Message:
-----------
Separate out into three files for legibility
Commit: 346f4e21b039050544fbfbafcc841ebcd9997e17
https://github.com/galaxyproject/galaxy/commit/346f4e21b039050544fbfbafcc84…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Tiny reorg, prettier printing
Commit: c4d11500aca3353bb0c6cdddd92bb0de1712f3b8
https://github.com/galaxyproject/galaxy/commit/c4d11500aca3353bb0c6cdddd92b…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
Refactor to not use client provided usernames
Commit: 67d614e26cf0e8bf138ed9e5172a75dbe9e54aeb
https://github.com/galaxyproject/galaxy/commit/67d614e26cf0e8bf138ed9e5172a…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Do not trust clients. Also switch to logging from printing
Commit: 8576b634d5f812bd0119f82dcf1cb16e377df68b
https://github.com/galaxyproject/galaxy/commit/8576b634d5f812bd0119f82dcf1c…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
prod ready! (ish)
Commit: d5797fc706c42dc8135cb18d5d7457988a4bbf93
https://github.com/galaxyproject/galaxy/commit/d5797fc706c42dc8135cb18d5d74…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Whitespace + fix iframe URL
Commit: 640c5b4c7b6eefdb95382e535283609a86a7b452
https://github.com/galaxyproject/galaxy/commit/640c5b4c7b6eefdb95382e535283…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
A scripts/communication/template/communication.css
M scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M scripts/communication_server.py
Log Message:
-----------
Merge pull request #12 from erasche/rt-comm-2
Some small updates for security
Commit: 983328f817ff9da469df1000adc92367b455b015
https://github.com/galaxyproject/galaxy/commit/983328f817ff9da469df1000adc9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
change handling of id_secret slightly
Commit: 0bff02f95ddd19d5cd22ca9a70ca316913fd0f3d
https://github.com/galaxyproject/galaxy/commit/0bff02f95ddd19d5cd22ca9a70ca…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
A scripts/communication/communication_server.py
R scripts/communication_server.py
Log Message:
-----------
move everything under scripts/communication
Commit: a4970e71cf04acf336c4463c0103a7aa0f8de777
https://github.com/galaxyproject/galaxy/commit/a4970e71cf04acf336c4463c0103…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
adjust path to galaxy-lib
Commit: c79dadd931cdb989197ac78096b98c4163725568
https://github.com/galaxyproject/galaxy/commit/c79dadd931cdb989197ac78096b9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
client updates
Commit: 4d186982ce9fb907d9d25006dc7646e14e589d32
https://github.com/galaxyproject/galaxy/commit/4d186982ce9fb907d9d25006dc76…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
fix a few bugs, we should now be back to buisness
Commit: 3dbd6d8074c44d7cfb333c8b5a49de40e683af9a
https://github.com/galaxyproject/galaxy/commit/3dbd6d8074c44d7cfb333c8b5a49…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
Log Message:
-----------
fix error if no user is logged in
Commit: 5a3580c752c45e5a7d68fd742a0b6336a09169ea
https://github.com/galaxyproject/galaxy/commit/5a3580c752c45e5a7d68fd742a0b…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
client updates
Commit: 6bc64e74263097a969b5d097c9334b41b7b59425
https://github.com/galaxyproject/galaxy/commit/6bc64e74263097a969b5d097c933…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
enhance documentation
Commit: 74e3e05034e146bfa3b13c177557e78097265bb7
https://github.com/galaxyproject/galaxy/commit/74e3e05034e146bfa3b13c177557…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-09 (Thu, 09 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
fix js bug
Commit: 043b129c91b3b2b679d4bb4e31db4970c26219e8
https://github.com/galaxyproject/galaxy/commit/043b129c91b3b2b679d4bb4e31db…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-09 (Thu, 09 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
Merge branch 'rt_comm' of https://github.com/bgruening/galaxy into rt_comm
Commit: 0cd28c72515804f859cb9054a13a157fc8ebf2e6
https://github.com/galaxyproject/galaxy/commit/0cd28c72515804f859cb9054a13a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Added global chat rooms
Commit: 581108a442ec762dc9d87111f9425c01accc67c5
https://github.com/galaxyproject/galaxy/commit/581108a442ec762dc9d87111f942…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
backend work for persistent chat rooms
Commit: f75189aaaadf697d5759023cdc72fefa8f1d17c8
https://github.com/galaxyproject/galaxy/commit/f75189aaaadf697d5759023cdc72…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
style cleanups
Commit: e0c4e1cef04cde226bc140a62beb47670a25b85d
https://github.com/galaxyproject/galaxy/commit/e0c4e1cef04cde226bc140a62beb…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/managers/configuration.py
Log Message:
-----------
access the list of persistent chat rooms via Galaxy.config object
Commit: 80ee76cb39c06f8a922e3fbcf9930711c3eeb6ce
https://github.com/galaxyproject/galaxy/commit/80ee76cb39c06f8a922e3fbcf993…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Adding persistent rooms from config
Commit: 074fefeda2b10accec700e250e516aa8bd9e6a0b
https://github.com/galaxyproject/galaxy/commit/074fefeda2b10accec700e250e51…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Adding features-space enabled chat room names, ctrl+l for chat log deletion, removing delete icon, smooth transition on window load and code cleanup
Commit: f034f1778b7482e182f8a03d6c53774361875b56
https://github.com/galaxyproject/galaxy/commit/f034f1778b7482e182f8a03d6c53…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
Log Message:
-----------
make the communication window more packed
Commit: 111a1c62223d4d252f91f5bed5f009bf3c58bd2e
https://github.com/galaxyproject/galaxy/commit/111a1c62223d4d252f91f5bed5f0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Fixing the issue with persistent room names with spaces, adding fancy scroll bar, buttons instead of links for persistent rooms and UI changes for message area
Commit: 5ed647e34f69fb3ab05982a135fa2be7f65310f5
https://github.com/galaxyproject/galaxy/commit/5ed647e34f69fb3ab05982a135fa…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
release preparation
Commit: f27e80e46dd1a1af7991fe1fc62a428dbbe49715
https://github.com/galaxyproject/galaxy/commit/f27e80e46dd1a1af7991fe1fc62a…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
fix documenation
Commit: 52e1918e9e2807f30c0c5a64d9493d5a766f6312
https://github.com/galaxyproject/galaxy/commit/52e1918e9e2807f30c0c5a64d949…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
add
Commit: b18decddda86ddc0fa7a813c1bad64722123da83
https://github.com/galaxyproject/galaxy/commit/b18decddda86ddc0fa7a813c1bad…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
client updates
Commit: b8a92a3f80661f2b729160163343034216616e53
https://github.com/galaxyproject/galaxy/commit/b8a92a3f80661f2b729160163343…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
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Fixing issue with no persistent rooms
Commit: ab43e094c2c7f5d3c5ba6d2e82af3f7c5fd52970
https://github.com/galaxyproject/galaxy/commit/ab43e094c2c7f5d3c5ba6d2e82af…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Allow changing settings under remote_user
Commit: 83e61f1ca4c16b5383b7ae0dba36c1b0aab2dce8
https://github.com/galaxyproject/galaxy/commit/83e61f1ca4c16b5383b7ae0dba36…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
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Support gravatar and rework template
Commit: 0d9865b5c56c1d6e7d0f15c8e566e1b30fffd2f3
https://github.com/galaxyproject/galaxy/commit/0d9865b5c56c1d6e7d0f15c8e566…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M scripts/communication/communication_server.py
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
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Merge pull request #14 from erasche/rt_comm-gravatar
Gravatar suppot
Commit: 4a304b63b12073dc2c82e811fa9acde04337170b
https://github.com/galaxyproject/galaxy/commit/4a304b63b12073dc2c82e811fa9a…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
fix pep8
Commit: b690abb46a03c1d622e8395ae6d4752952354861
https://github.com/galaxyproject/galaxy/commit/b690abb46a03c1d622e8395ae6d4…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
make chat view a little bit more compact and fix bug in displaying "me" messages
Commit: c017b516663a312a866fd3000547982838a67b8a
https://github.com/galaxyproject/galaxy/commit/c017b516663a312a866fd3000547…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
Log Message:
-----------
Fixed UI issues and log deletion functionality in main tab
Commit: e477d728d407cde21449549c5e464da8b54044f0
https://github.com/galaxyproject/galaxy/commit/e477d728d407cde21449549c5e46…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
do not show gravatar for server messages
Commit: 10c2764f097beb1b5c2b221377424002c698d7ca
https://github.com/galaxyproject/galaxy/commit/10c2764f097beb1b5c2b22137742…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
add the identicon to gravatar
Commit: feb00567e4f08970be67f75ccee8df7940b9067a
https://github.com/galaxyproject/galaxy/commit/feb00567e4f08970be67f75ccee8…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
Log Message:
-----------
Adjusted the vertical position of gravatar icons
Commit: 008220d88d4d2699f901b9e2e656afd7510473c0
https://github.com/galaxyproject/galaxy/commit/008220d88d4d2699f901b9e2e656…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
Adjusted the vertical position of gravatar icons
Commit: 464e9a42615bed11197a43fbd082f0c31076ca71
https://github.com/galaxyproject/galaxy/commit/464e9a42615bed11197a43fbd082…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Fixed issue with Firefox auto scrolling
Commit: 1f1c35f70873b87e0923fc04b1c11d546e100a04
https://github.com/galaxyproject/galaxy/commit/1f1c35f70873b87e0923fc04b1c1…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M .gitignore
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/style/base.css
A templates/user/communication_settings.mako
M templates/user/index.mako
Log Message:
-----------
merge
Commit: 474a8889e346b21f24d557880929b9c0eb989a8a
https://github.com/galaxyproject/galaxy/commit/474a8889e346b21f24d557880929…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
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
Log Message:
-----------
update client
Commit: b81034554377d3e0a3f971eae579c42a032c0685
https://github.com/galaxyproject/galaxy/commit/b81034554377d3e0a3f971eae579…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
fix pep8 warning
Commit: 93c33b4188548ff4575befcbb5b7787585085364
https://github.com/galaxyproject/galaxy/commit/93c33b4188548ff4575befcbb5b7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/style/less/base.less
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
M static/style/blue/base.css
Log Message:
-----------
A bit of clean of menu.js for the chat tab
Commit: 66c3e418a6d55fbee8211a95fb0913e7e0418b17
https://github.com/galaxyproject/galaxy/commit/66c3e418a6d55fbee8211a95fb09…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
A client/galaxy/scripts/layout/generic-nav-view.js
Log Message:
-----------
Adding generic nav view
Commit: ff23df05216750b5df4c7f2050fe30f009d24832
https://github.com/galaxyproject/galaxy/commit/ff23df05216750b5df4c7f2050fe…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
M static/maps/layout/menu.js.map
Log Message:
-----------
adding static menu map file
Commit: 28744e1235a0decc26f2fb5545f4946e6cece25a
https://github.com/galaxyproject/galaxy/commit/28744e1235a0decc26f2fb5545f4…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
M .gitignore
Log Message:
-----------
ignore IDEA files
Commit: 0d915ce131e1928fe1feab82633ef6bf90ebce0f
https://github.com/galaxyproject/galaxy/commit/0d915ce131e1928fe1feab82633e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/style/less/base.less
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding maximize/minimize feature to the communication channel
Commit: 5b0641fe4a5dc681b75a357f04578f7b53ccb733
https://github.com/galaxyproject/galaxy/commit/5b0641fe4a5dc681b75a357f0457…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/graphviz/static/js/graphVis.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/tool_data_table_conf.xml.sample
A config/tool_destinations.yml.sample
A display_applications/igv/bigwig.xml
A display_applications/ucsc/trackhub.xml
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_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/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_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/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M run_tests.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
A scripts/grt.py
A scripts/grt.yml.sample
M scripts/set_dataset_sizes.py
M setup.cfg
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.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/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/admin/impersonate.mako
M templates/ind_share_base.mako
M templates/user/change_password.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/history/grid.mako
M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
A test/functional/tools/identifier_collection.xml
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/datatypes/test_data.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.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_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_toolbox.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Commit: 6b8b0cde5b6a2725177e409ebc84ba1591f5bd40
https://github.com/galaxyproject/galaxy/commit/6b8b0cde5b6a2725177e409ebc84…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/graphviz/static/js/graphVis.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/tool_data_table_conf.xml.sample
A config/tool_destinations.yml.sample
A display_applications/igv/bigwig.xml
A display_applications/ucsc/trackhub.xml
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_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/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_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/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M run_tests.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
A scripts/grt.py
A scripts/grt.yml.sample
M scripts/set_dataset_sizes.py
M setup.cfg
A static/maps/layout/generic-nav-view.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.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
A static/scripts/layout/generic-nav-view.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/admin/impersonate.mako
M templates/ind_share_base.mako
M templates/user/change_password.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/history/grid.mako
M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
A test/functional/tools/identifier_collection.xml
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/datatypes/test_data.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.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_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_toolbox.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
make client
Commit: b0566ad9ce8daf42a10bd013f7bd5d9efdfc4fa4
https://github.com/galaxyproject/galaxy/commit/b0566ad9ce8daf42a10bd013f7bd…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M .gitignore
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/style/less/base.less
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.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/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/style/base.css
M static/style/blue/base.css
A templates/user/communication_settings.mako
M templates/user/index.mako
Log Message:
-----------
Merge pull request #2515 from bgruening/realtime_communication
Add a simple Galaxy Communication Server for realtime communication between Galaxy users.
Compare: https://github.com/galaxyproject/galaxy/compare/47522208c6d7...b0566ad9ce8d
1
0
23 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c27d3f296d1d653b96eb2191d203e9a2daa272a6
https://github.com/galaxyproject/galaxy/commit/c27d3f296d1d653b96eb2191d203…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Allow uploading strict BED datatypes.
Commit: 47522208c6d7a109d12c8d4dda153fd6bbaf0c1b
https://github.com/galaxyproject/galaxy/commit/47522208c6d7a109d12c8d4dda15…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #2648 from blankenberg/bedstrict-up
Allow uploading strict BED datatypes.
Compare: https://github.com/galaxyproject/galaxy/compare/4da167be7b48...47522208c6d7
1
0
[galaxyproject/galaxy] 897f2f: Merge hubAssembly.py in tracks.py , fix Python3 co...
by GitHub 22 Jul '16
by GitHub 22 Jul '16
22 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 897f2fe9331e8232a616a6329e0ea23f3237e44e
https://github.com/galaxyproject/galaxy/commit/897f2fe9331e8232a616a6329e0e…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
R lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Merge hubAssembly.py in tracks.py , fix Python3 compatibility
Fix unaddressed comments from #2348.
Commit: 4da167be7b480c9a0a2050d0bf2b18c9808e548b
https://github.com/galaxyproject/galaxy/commit/4da167be7b480c9a0a2050d0bf2b…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
R lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Merge pull request #2646 from nsoranzo/fixes_for_2348
Merge hubAssembly.py in tracks.py , fix Python3 compatibility
Compare: https://github.com/galaxyproject/galaxy/compare/7763aaa39b88...4da167be7b48
1
0
[galaxyproject/galaxy] 193c27: Move execute button and new history form to top of...
by GitHub 22 Jul '16
by GitHub 22 Jul '16
22 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 193c27e3dbc21ca539d9634b29618f86ab1c84b6
https://github.com/galaxyproject/galaxy/commit/193c27e3dbc21ca539d9634b2961…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-buttons.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
M static/scripts/mvc/ui/ui-buttons.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Move execute button and new history form to top of workflow execution form
Commit: 7b49080dc1ea410842ffb16825f86c69a95e0989
https://github.com/galaxyproject/galaxy/commit/7b49080dc1ea410842ffb16825f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.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-buttons.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Adjust/fix button link variation, add test cases
Commit: 842a98106257e21e9609370af7a55e31fdc99a6a
https://github.com/galaxyproject/galaxy/commit/842a98106257e21e9609370af7a5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.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-buttons.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Adjust check state button and add test cases
Commit: 80d20900efb6c319a6373bd6adb63ba547cafd16
https://github.com/galaxyproject/galaxy/commit/80d20900efb6c319a6373bd6adb6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-buttons.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-buttons.js
M static/style/blue/base.css
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Adjust icon button, add test cases
Commit: 9e82e59baff3ae23fe356aa6ad145324dcd30bf9
https://github.com/galaxyproject/galaxy/commit/9e82e59baff3ae23fe356aa6ad14…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-buttons.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-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Adjust menu button
Commit: 361f89e8717738809fe2eecc08954809f271a049
https://github.com/galaxyproject/galaxy/commit/361f89e8717738809fe2eecc0895…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.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-buttons.js
Log Message:
-----------
Remove unused download attribute from button menu options
Fix spacing
Commit: 4781aafb472e7299e5a2204661584c4aeb52b98d
https://github.com/galaxyproject/galaxy/commit/4781aafb472e7299e5a220466158…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-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/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
Log Message:
-----------
Adjust upload button, unify model and option attributes
Commit: 31a8dbf670bed9666d5c4afeaf7c4fb2c55d70ce
https://github.com/galaxyproject/galaxy/commit/31a8dbf670bed9666d5c4afeaf7c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-buttons.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-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Fix margin handling
Commit: 072b28b091c66316d7eedb3482800f1aa2bc77e4
https://github.com/galaxyproject/galaxy/commit/072b28b091c66316d7eedb348280…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
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/mvc/tool/tool-form-composite.js
Log Message:
-----------
Fix workflow wait label for workflow submission
Commit: 01d14a0435d52666df69b21844e60a24b83fa25f
https://github.com/galaxyproject/galaxy/commit/01d14a0435d52666df69b21844e6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Reduce distance between icon and title
Commit: 35ef492e21b6e6a70fe52b4d089f67c137909925
https://github.com/galaxyproject/galaxy/commit/35ef492e21b6e6a70fe52b4d089f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/job_conf.xml.sample_advanced
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
A config/tool_destinations.yml.sample
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/web/framework/base.py
A scripts/grt.py
A scripts/grt.yml.sample
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.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-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/style/blue/base.css
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.py
M test/unit/tools/test_conda_resolution.py
Log Message:
-----------
Merge branch 'dev' into move_workflow_run
Commit: 45038d1399bf9e619ee815dad587f8ec3b3c4815
https://github.com/galaxyproject/galaxy/commit/45038d1399bf9e619ee815dad587…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M config/tool_data_table_conf.xml.sample
M lib/galaxy/tools/wrappers.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/render.py
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.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-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge branch 'dev' into move_workflow_run
Commit: 881af45dfedc8415f0a444e958be4c1c1eeeeb68
https://github.com/galaxyproject/galaxy/commit/881af45dfedc8415f0a444e958be…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M test/qunit/tests/upload_dialog_tests.js
Log Message:
-----------
Fix upload dialog test cases
Commit: 7763aaa39b882e6fd9076055266b271abbf69829
https://github.com/galaxyproject/galaxy/commit/7763aaa39b882e6fd9076055266b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-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/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/style/blue/base.css
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
Log Message:
-----------
Merge pull request #2643 from guerler/move_workflow_run
Move workflow run and history options to top, add loading indicator
Compare: https://github.com/galaxyproject/galaxy/compare/40fde4ecf6e4...7763aaa39b88
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0a9d038a5d75560bc27e1f20d833e435b2f90e6e
https://github.com/galaxyproject/galaxy/commit/0a9d038a5d75560bc27e1f20d833…
Author: remiarenco <remimarenco(a)gmail.com>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M config/datatypes_conf.xml.sample
A display_applications/ucsc/huba.xml
A lib/galaxy/datatypes/hubAssembly.py
Log Message:
-----------
Add the composite datatype
Commit: 4002e4ed1dbf6bbdad89e2e2420295e37c6789f0
https://github.com/galaxyproject/galaxy/commit/4002e4ed1dbf6bbdad89e2e24202…
Author: remiarenco <remimarenco(a)gmail.com>
Date: 2016-05-11 (Wed, 11 May 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/hubAssembly.py
Log Message:
-----------
Pass pylint and better xml formatting
Commit: e0ffb2d8d021248019c3a9a9d9e18ca0cdd9cf26
https://github.com/galaxyproject/galaxy/commit/e0ffb2d8d021248019c3a9a9d9e1…
Author: remiarenco <remimarenco(a)gmail.com>
Date: 2016-05-13 (Fri, 13 May 2016)
Changed paths:
M config/datatypes_conf.xml.sample
R display_applications/ucsc/huba.xml
A display_applications/ucsc/trackhub.xml
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Following advices: renamed the extension to 'trackhub', renamed the huba.xml to trackhub.xml, changed iteritems to items, removed hubAssembly.py to port it into tracks.py
Commit: 873a5d9f725cf574550b88805c543ebb33ee3ffc
https://github.com/galaxyproject/galaxy/commit/873a5d9f725cf574550b88805c54…
Author: remiarenco <remimarenco(a)gmail.com>
Date: 2016-05-14 (Sat, 14 May 2016)
Changed paths:
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Fix the uppercase in the extension (did not seem to affect the loading of the datatype/its use in Galaxy
Commit: 1f6d3bc47069b054c86687bf00a8cad2afdd43bd
https://github.com/galaxyproject/galaxy/commit/1f6d3bc47069b054c86687bf00a8…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-05-17 (Tue, 17 May 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Update datatypes_conf.xml.sample
Typo in the extension
Commit: 7cf435438817672854d524f8359c92675c36b046
https://github.com/galaxyproject/galaxy/commit/7cf435438817672854d524f8359c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-18 (Wed, 18 May 2016)
Changed paths:
M lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Remove blank lines in file.
Commit: 50fa525a440b0d3dc76a97053c58fead86b4bc2f
https://github.com/galaxyproject/galaxy/commit/50fa525a440b0d3dc76a97053c58…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-05-18 (Wed, 18 May 2016)
Changed paths:
M lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Merge pull request #1 from dannon/huba_datatype
Remove blank lines in file.
Commit: e66cf8358940e9bf298de4e3416b952d44987c65
https://github.com/galaxyproject/galaxy/commit/e66cf8358940e9bf298de4e3416b…
Author: remimarenco <remi.marenco(a)gmail.com>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Remove the support of Galaxy version <= 16.01
Commit: 611ade3552d2cfe665156a64214e7a1e58d14683
https://github.com/galaxyproject/galaxy/commit/611ade3552d2cfe665156a64214e…
Author: remimarenco <remi.marenco(a)gmail.com>
Date: 2016-06-03 (Fri, 03 Jun 2016)
Changed paths:
M display_applications/ucsc/trackhub.xml
Log Message:
-----------
Remove the strip_https attribute because we don't need it anymore
Commit: 40fde4ecf6e4e8b2951c6fd2738205450144a07b
https://github.com/galaxyproject/galaxy/commit/40fde4ecf6e4e8b2951c6fd27382…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M config/datatypes_conf.xml.sample
A display_applications/ucsc/trackhub.xml
A lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
Log Message:
-----------
Merge pull request #2348 from remimarenco/huba_datatype
Add the trackhub composite datatype
Compare: https://github.com/galaxyproject/galaxy/compare/1839e8144231...40fde4ecf6e4
1
0
[galaxyproject/galaxy] 43523d: Fix flushing so mapped output collections created ...
by GitHub 22 Jul '16
by GitHub 22 Jul '16
22 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 43523dac98c6a7dda819caa7835349c11adf0a6c
https://github.com/galaxyproject/galaxy/commit/43523dac98c6a7dda819caa78353…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-18 (Mon, 18 Jul 2016)
Changed paths:
M lib/galaxy/tools/execute.py
Log Message:
-----------
Fix flushing so mapped output collections created uniformly.
Commit: 9ede8e556be1f6038361b579c1457068e50e951a
https://github.com/galaxyproject/galaxy/commit/9ede8e556be1f6038361b579c145…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-18 (Mon, 18 Jul 2016)
Changed paths:
M lib/galaxy/workflow/extract.py
Log Message:
-----------
Fix duplicated entries when using collections in history extract.
This would "sometimes" correctly pick the first job to represent a collection creation step but in many cases not. Explicitly grab the "first".
Commit: 1839e8144231abfcdd9a158ce221badcfd2c1d66
https://github.com/galaxyproject/galaxy/commit/1839e8144231abfcdd9a158ce221…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M lib/galaxy/tools/execute.py
M lib/galaxy/workflow/extract.py
Log Message:
-----------
Merge pull request #2625 from jmchilton/history_extract_fixes_2
Fixes for workflow extraction of mapping collection jobs.
Compare: https://github.com/galaxyproject/galaxy/compare/a8c1dfc16163...1839e8144231
1
0
[galaxyproject/galaxy] f947fb: Remove dependency of select2 to regular select fie...
by GitHub 22 Jul '16
by GitHub 22 Jul '16
22 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f947fb604e28992b445d82d60df063e53553622e
https://github.com/galaxyproject/galaxy/commit/f947fb604e28992b445d82d60df0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-12 (Tue, 12 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.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-select-default.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Remove dependency of select2 to regular select fields
Commit: 67c3ec899d510c2956a876236e9a4e8d67f2c0dc
https://github.com/galaxyproject/galaxy/commit/67c3ec899d510c2956a876236e9a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-12 (Tue, 12 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.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-select-default.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Reinsert classic multiple select field box
Commit: 4fac8884b6e3ac85b91e078a8dab3f4750cd5505
https://github.com/galaxyproject/galaxy/commit/4fac8884b6e3ac85b91e078a8dab…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-12 (Tue, 12 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/mvc/ui/ui-select-default.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Preserve selection order, allow empty string as valid selection
Commit: b4ee77d28279f3fdfc5e81ea34bf822477c30522
https://github.com/galaxyproject/galaxy/commit/b4ee77d28279f3fdfc5e81ea34bf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-12 (Tue, 12 Jul 2016)
Changed paths:
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Adjust content selector tests
Commit: a030aaf6ee31bcea782940a819611e6ac8a96c23
https://github.com/galaxyproject/galaxy/commit/a030aaf6ee31bcea782940a81961…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-12 (Tue, 12 Jul 2016)
Changed paths:
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:
-----------
Repack scripts
Commit: 8ae831aa9e669265c1b67dd3b630241d303cfc3b
https://github.com/galaxyproject/galaxy/commit/8ae831aa9e669265c1b67dd3b630…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-13 (Wed, 13 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Add query feature to select2 options list
Commit: 8e933f6e92e1276da7617b2a22ec69cb5164c549
https://github.com/galaxyproject/galaxy/commit/8e933f6e92e1276da7617b2a22ec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-13 (Wed, 13 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.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-select-default.js
Log Message:
-----------
Add select2 pagination
Commit: 4a289ce4a083163e4027d61ff312b502f587fd31
https://github.com/galaxyproject/galaxy/commit/4a289ce4a083163e4027d61ff312…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-13 (Wed, 13 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/ui/ui-select-content.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-select-content.js
Log Message:
-----------
Add pagination criteria to content selector
Commit: cc81cdb9465c742b4f089b31081a5e9eb8c64ad6
https://github.com/galaxyproject/galaxy/commit/cc81cdb9465c742b4f089b31081a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-13 (Wed, 13 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.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-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Hide select all button optionally
Commit: f239a0a927c0635f6ade3a39d7a42650dd2d890e
https://github.com/galaxyproject/galaxy/commit/f239a0a927c0635f6ade3a39d7a4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.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-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
Log Message:
-----------
Add search word filtering
Commit: 0372bdb4add3f44eef28febabf5658f7e2bbebd7
https://github.com/galaxyproject/galaxy/commit/0372bdb4add3f44eef28febabf56…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-default.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-select-default.js
Log Message:
-----------
Optimize logic for first value and button all selection
Commit: 576e09fe63baaa1c5f7f90967d32f0b957d474e3
https://github.com/galaxyproject/galaxy/commit/576e09fe63baaa1c5f7f90967d32…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.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-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge branch 'select_performance' into dev
Commit: a8c1dfc16163ab1fd6ef1096ce4cd9a636fdab36
https://github.com/galaxyproject/galaxy/commit/a8c1dfc16163ab1fd6ef1096ce4c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M static/maps/mvc/ui/ui-select-default.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-select-default.js
Log Message:
-----------
Rebuild client, borked merge of #2615.
Compare: https://github.com/galaxyproject/galaxy/compare/09278b2afbda...a8c1dfc16163
1
0
22 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 92948b5b0fc062ce904c5987c1d48d3831730a9a
https://github.com/galaxyproject/galaxy/commit/92948b5b0fc062ce904c5987c1d4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-18 (Mon, 18 Jul 2016)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Overload select wrapper`s concat function
Commit: e4a35f943b42401c92646d8f6b7b1c1fd515a9c1
https://github.com/galaxyproject/galaxy/commit/e4a35f943b42401c92646d8f6b7b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-19 (Tue, 19 Jul 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/render.py
Log Message:
-----------
Paste handles encoding automatically when thrown unicode, but uwsgi does
not. This was resulting in unencoded (unicode) workflow drawings (svg)
not appearing at all when the gen_image was invoked. Also took the
opportunity to add a correct header for a standalone svg document.
Commit: 68a64182c14af9f4cc10915c466177292d24ebfc
https://github.com/galaxyproject/galaxy/commit/68a64182c14af9f4cc10915c4661…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/render.py
Log Message:
-----------
Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix
[16.04] Workflow SVG generation fix
Commit: 1de7beca98d0bc8b11b9dca46a4984ac1cee9428
https://github.com/galaxyproject/galaxy/commit/1de7beca98d0bc8b11b9dca46a49…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-21 (Thu, 21 Jul 2016)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Merge pull request #2623 from guerler/fix_select_value_concat
[16.04] Overload select wrapper`s concat function
Commit: 09278b2afbdacbf871df6e8560ba8739206b9dda
https://github.com/galaxyproject/galaxy/commit/09278b2afbdacbf871df6e8560ba…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M lib/galaxy/tools/wrappers.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/render.py
Log Message:
-----------
Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/0808015c9a42...09278b2afbda
1
0