Branch: refs/heads/dev
Home:
https://github.com/galaxyproject/galaxy
Commit: ef58e62e6deeeecd37587c737b3113ede606f3c1
https://github.com/galaxyproject/galaxy/commit/ef58e62e6deeeecd37587c737b...
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/f1a3086b87536a78c757b25d5d...
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
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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
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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
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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
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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
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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
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M lib/galaxy/webapps/galaxy/api/library_contents.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
M test/unit/test_lazy_process.py
M test/unit/test_objectstore.py
R test/unit/tool_shed_unit_tests/__init__.py
R test/unit/tool_shed_unit_tests/test_fabric_util.py
R test/unit/tool_shed_unit_tests/test_td_common_util.py
R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_select_parameters.py
M test/unit/unittest_utils/galaxy_mock.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 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
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf2bedgraph.xml
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
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
M tools/maf/maf_to_fasta_concat.py
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/d2c53ee724041ed6947b6db356...
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/20f25f0e35a8ca8b979aa97162...
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/f8a20cb85fa072bc2539a59c18...
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/e9642720b81b8ef9aed083b49f...
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:
-----------
updating files for real time communication-server and client
Commit: 19d333d427695e11080eee705dc7ad75af5f2cda
https://github.com/galaxyproject/galaxy/commit/19d333d427695e11080eee705d...
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:
-----------
updated files for real time communication feature addition
Commit: f4273ce56e23be9088b181cf02539be334310cb2
https://github.com/galaxyproject/galaxy/commit/f4273ce56e23be9088b181cf02...
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated the chat server client template
Commit: e90de49f584e45cf897fd63cf153dfe1bd251e43
https://github.com/galaxyproject/galaxy/commit/e90de49f584e45cf897fd63cf1...
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:
-----------
Change you to Me, some style fixes,
Commit: fff6c5e519875588abebd1a649e9097c38df28d6
https://github.com/galaxyproject/galaxy/commit/fff6c5e519875588abebd1a649...
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/053e5173cc9c179e3ad3b55177...
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updating the chat client template
Commit: 574136ce3fc518cfafe7c9e984c35b1cb3036fcd
https://github.com/galaxyproject/galaxy/commit/574136ce3fc518cfafe7c9e984...
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:
-----------
style changes
Commit: b7cb80343607d9af997cb539e2c3fe0239ca2ac3
https://github.com/galaxyproject/galaxy/commit/b7cb80343607d9af997cb539e2...
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
added show full chat history feature
Commit: a539846c043d79a605eaa847e00557d2662758d1
https://github.com/galaxyproject/galaxy/commit/a539846c043d79a605eaa847e0...
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/687f26edf706358ef06a84c6f4...
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 full chat history feature and added sent date time
Commit: 69d422ca034841b3fef6ede498f3df82f8ccc40b
https://github.com/galaxyproject/galaxy/commit/69d422ca034841b3fef6ede498...
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/233c752a0b27cbd98aee99b0cb...
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:
-----------
style changes
Commit: f2ccbc6f6c73786839acb6792c86043337e36ba3
https://github.com/galaxyproject/galaxy/commit/f2ccbc6f6c73786839acb6792c...
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:
-----------
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/67bb0874c522db4c7980032bf1...
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/e572be746fc4f93dd3326a41fd...
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/cb6f739712d47699ca1196e89d...
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/1ba0ef705a4d3f3b7538e68a50...
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/e6843de2dfc10fae7d47671d9e...
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/c91c4f4089ec2ffc0195bfcb28...
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/b07cfa887d2e751fe35296d8a3...
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/1dac71a42ded24fd18db005de0...
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/48466e1a84dd5f11e6b4ac03ce...
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/7ea4051820acf61a176f3a5294...
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/267e1fa3813003f9a18b338a89...
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/eb58c101d935fd54e4922f7e5d...
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/230aa1c106da8f21037f24fa16...
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/ee647dbe80d57aa6f596833fdc...
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/7abca061f5dca22b9d6ee9a63f...
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/915a882ff492bccbb233d18730...
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/0ef409dc1274af7b1530c3823c...
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/4491e6bb4765895a979eaaaf22...
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/499f76e1d93bf77aaade47f50c...
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/2831ac80f74486d4126b8694e0...
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/656b2c5c6857c32c43c9e3a0ec...
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/5b196571425babf004871390e9...
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/009cbe4cb4c1c79822ef061c7e...
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/7a93c845d6ae4a5a5ce81b4847...
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/03b5622ab5bc3991d13020ff6c...
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/ca14290dc95fea6d5b0617659a...
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/e08a7cd39a59e191b430dae01e...
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/346f4e21b039050544fbfbafcc...
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/c4d11500aca3353bb0c6cdddd9...
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/67d614e26cf0e8bf138ed9e517...
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/8576b634d5f812bd0119f82dcf...
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/d5797fc706c42dc8135cb18d5d...
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/640c5b4c7b6eefdb95382e5352...
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/983328f817ff9da469df1000ad...
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/0bff02f95ddd19d5cd22ca9a70...
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/a4970e71cf04acf336c4463c01...
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/c79dadd931cdb989197ac78096...
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/4d186982ce9fb907d9d25006dc...
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/3dbd6d8074c44d7cfb333c8b5a...
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/5a3580c752c45e5a7d68fd742a...
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/6bc64e74263097a969b5d097c9...
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/74e3e05034e146bfa3b13c1775...
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/043b129c91b3b2b679d4bb4e31...
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/0cd28c72515804f859cb9054a1...
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/581108a442ec762dc9d87111f9...
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/f75189aaaadf697d5759023cdc...
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/e0c4e1cef04cde226bc140a62b...
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/80ee76cb39c06f8a922e3fbcf9...
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/074fefeda2b10accec700e250e...
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/f034f1778b7482e182f8a03d6c...
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/111a1c62223d4d252f91f5bed5...
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/5ed647e34f69fb3ab05982a135...
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/f27e80e46dd1a1af7991fe1fc6...
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/52e1918e9e2807f30c0c5a64d9...
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/b18decddda86ddc0fa7a813c1b...
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/b8a92a3f80661f2b7291601633...
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:
-----------
Fixing issue with no persistent rooms
Commit: ab43e094c2c7f5d3c5ba6d2e82af3f7c5fd52970
https://github.com/galaxyproject/galaxy/commit/ab43e094c2c7f5d3c5ba6d2e82...
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/83e61f1ca4c16b5383b7ae0dba...
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:
-----------
Support gravatar and rework template
Commit: 0d9865b5c56c1d6e7d0f15c8e566e1b30fffd2f3
https://github.com/galaxyproject/galaxy/commit/0d9865b5c56c1d6e7d0f15c8e5...
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:
-----------
Merge pull request #14 from erasche/rt_comm-gravatar
Gravatar suppot
Commit: 4a304b63b12073dc2c82e811fa9acde04337170b
https://github.com/galaxyproject/galaxy/commit/4a304b63b12073dc2c82e811fa...
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/b690abb46a03c1d622e8395ae6...
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/c017b516663a312a866fd30005...
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/e477d728d407cde21449549c5e...
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/10c2764f097beb1b5c2b221377...
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/feb00567e4f08970be67f75cce...
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/008220d88d4d2699f901b9e2e6...
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/464e9a42615bed11197a43fbd0...
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/1f1c35f70873b87e0923fc04b1...
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/474a8889e346b21f24d5578809...
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/b81034554377d3e0a3f971eae5...
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/93c33b4188548ff4575befcbb5...
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/66c3e418a6d55fbee8211a95fb...
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/ff23df05216750b5df4c7f2050...
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/28744e1235a0decc26f2fb5545...
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/0d915ce131e1928fe1feab8263...
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/5b0641fe4a5dc681b75a357f04...
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
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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/6b8b0cde5b6a2725177e409ebc...
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/b0566ad9ce8daf42a10bd013f7...
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