- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c3ef54: Eliminate LWR from Galaxy.
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3ef5467c71e69aa4570613e27bb8bd46d7de4f4 https://github.com/galaxyproject/galaxy/commit/c3ef5467c71e69aa4570613e27bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Eliminate LWR from Galaxy. Commit: 903823f2986fad624770166a7d31f7936ce1a9f1 https://github.com/galaxyproject/galaxy/commit/903823f2986fad624770166a7d31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #857 from jmchilton/lwr_remove Eliminate LWR from Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/920f7950fdb1...903823f2986f

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[galaxyproject/galaxy] 31c89e: UI, Collections: allow expansion to fetch details ...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31c89ea29c2c504878f336d90dfcf320b873b2ee https://github.com/galaxyproject/galaxy/commit/31c89ea29c2c504878f336d90dfc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- UI, Collections: allow expansion to fetch details for DatasetDCEs (assuming they're HDAs); move rerunnable and creating_job fetch to HDAs Commit: 69cd5a98dcda30771ce78118ebd3a934dfb09c65 https://github.com/galaxyproject/galaxy/commit/69cd5a98dcda30771ce78118ebd3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- Merge pull request #854 from carlfeberhard/release_15.10 [15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… Compare: https://github.com/galaxyproject/galaxy/compare/cc23adb0a962...69cd5a98dcda

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[galaxyproject/galaxy] fd1fd5: flake8 lib/galaxy/model/migrate/versions/ .
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd1fd5e73c1828f79526ac712e3a4d9d5e9afa1c https://github.com/galaxyproject/galaxy/commit/fd1fd5e73c1828f79526ac712e3a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.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/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/0104_update_genome_downloader_job_parameters.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/0115_longer_user_password_field.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/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 Log Message: ----------- flake8 lib/galaxy/model/migrate/versions/ . Fix 1429 linting errors. Commit: 920f7950fdb10a4df4a237406c680f65e721942b https://github.com/galaxyproject/galaxy/commit/920f7950fdb10a4df4a237406c68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.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/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/0104_update_genome_downloader_job_parameters.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/0115_longer_user_password_field.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/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 Log Message: ----------- Merge pull request #832 from nsoranzo/flake8_fixes Flake8 lib/galaxy/model/migrate/versions/ . Compare: https://github.com/galaxyproject/galaxy/compare/c8533f6e3a86...920f7950fdb1

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[galaxyproject/galaxy] 6d3c8a: Do not split parameter of type "text" during funct...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d3c8a8b08367a6063c06b75778b006df596d4e8 https://github.com/galaxyproject/galaxy/commit/6d3c8a8b08367a6063c06b75778b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-04 (Sun, 04 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Do not split parameter of type "text" during functional tests. Commit: 35dcbc5afb697a663866033372aaefed6912aaa6 https://github.com/galaxyproject/galaxy/commit/35dcbc5afb697a663866033372aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Unindent value.type check Commit: c8533f6e3a8602531c438b379c559a8bd9102e25 https://github.com/galaxyproject/galaxy/commit/c8533f6e3a8602531c438b379c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Merge pull request #837 from mvdbeek/No_split_text_functional_tests Do not split parameter of type text during functional tests. Compare: https://github.com/galaxyproject/galaxy/compare/fd3cadc371d7...c8533f6e3a86

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[galaxyproject/galaxy] d4fba9: graph visualization added
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d4fba962310ea8357516526a941df05572fa2a9e https://github.com/galaxyproject/galaxy/commit/d4fba962310ea8357516526a941d… Author: Eteri <eteri(a)eteri-HP-ENVY-Sleekbook-4-PC.(none)> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- graph visualization added Commit: fd3cadc371d738ae9dfad68988f08c2508790bfd https://github.com/galaxyproject/galaxy/commit/fd3cadc371d738ae9dfad68988f0… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Merge pull request #378 from eteriSokhoyan/dev graph visualization added Compare: https://github.com/galaxyproject/galaxy/compare/cc23adb0a962...fd3cadc371d7

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[galaxyproject/galaxy]
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] ea2828: Add new run_tests.sh command to mount the external...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea28282b59e286570d6a4fb2c93259f99db0d1df https://github.com/galaxyproject/galaxy/commit/ea28282b59e286570d6a4fb2c932… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Add new run_tests.sh command to mount the external tmp directory. This is an attempt to potentially end these "Text file busy" problems on test: https://jenkins.galaxyproject.org/job/docker-api/170/testReport/junit/api.t…. Commit: cc23adb0a962f1c9780b838604718319a0a71888 https://github.com/galaxyproject/galaxy/commit/cc23adb0a962f1c9780b83860471… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #843 from jmchilton/text_file_busy_2 Allow reuse of parent /tmp directory in dockerized testing. Compare: https://github.com/galaxyproject/galaxy/compare/b5b36c0ab184...cc23adb0a962

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[galaxyproject/galaxy] 47113b: Merge branch 'dev' of github.com:galaxyproject/gal...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47113bedcabe3c82ad99ea1ef16307f8c3c5512f https://github.com/galaxyproject/galaxy/commit/47113bedcabe3c82ad99ea1ef163… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M .ci/flake8_blacklist.txt 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-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.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/0021_change_repository_type_value.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/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/pulsar/client/amqp_exchange.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tools/tools-form.js M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 5f4502b6500ca0aae57d6d76da12804d5d2fb9d1 https://github.com/galaxyproject/galaxy/commit/5f4502b6500ca0aae57d6d76da12… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin images for next release of Galaxy Commit: e9a3ec95b9485ea3b5b15bce4f8a96751f225b53 https://github.com/galaxyproject/galaxy/commit/e9a3ec95b9485ea3b5b15bce4f8a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Update faq.rst Commit: b5b36c0ab184d38b611fe0b293424bedd687cb28 https://github.com/galaxyproject/galaxy/commit/b5b36c0ab184d38b611fe0b29342… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #849 from erasche/gie-pinning-15.10 GIE pinning 15.10 Compare: https://github.com/galaxyproject/galaxy/compare/092fc17ec008...b5b36c0ab184

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[galaxyproject/galaxy] 1aebbc: Remove likely broken UCSC proxy and associated too...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aebbc3f68ad5a82834edb82ef52e3840fec697b https://github.com/galaxyproject/galaxy/commit/1aebbc3f68ad5a82834edb82ef52… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml R tools/data_source/ucsc_testproxy.xml Log Message: ----------- Remove likely broken UCSC proxy and associated tools. Unused for many, many years and likely no longer works. Commit: a6f9e62c1a4048d3f7669d5783a836d38d6f8f96 https://github.com/galaxyproject/galaxy/commit/a6f9e62c1a4048d3f7669d5783a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Add citations to ucsc browser tools. Commit: 092fc17ec008f092f016014f30317bdf68b9c567 https://github.com/galaxyproject/galaxy/commit/092fc17ec008f092f016014f3031… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml Log Message: ----------- Merge pull request #846 from jmchilton/ucsc_cleanup UCSC Tool Cleanup Compare: https://github.com/galaxyproject/galaxy/compare/f90c49e2705e...092fc17ec008

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[galaxyproject/galaxy] 591519: Add citations to a few more tools.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 591519009b0ead989ddf5a87fee9d5c69216b97c https://github.com/galaxyproject/galaxy/commit/591519009b0ead989ddf5a87fee9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Add citations to a few more tools. Commit: 88239abf5c2473af841eea139edc0164b3a4856c https://github.com/galaxyproject/galaxy/commit/88239abf5c2473af841eea139edc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml Log Message: ----------- Add more distribution tool citations. xref #361. Commit: f90c49e2705ed66bfa668de96568ea53126edc94 https://github.com/galaxyproject/galaxy/commit/f90c49e2705ed66bfa668de96568… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Merge pull request #847 from jmchilton/citations_5 Add more distribution tool citations. Compare: https://github.com/galaxyproject/galaxy/compare/3201005739ab...f90c49e2705e

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