[galaxy-commits] [galaxyproject/galaxy] 633061: WIP: Stop using eggs, start using prebuilt wheels.

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 633061f3e0e95041383901378e33f8b41b83717e https://github.com/galaxyproject/galaxy/commit/633061f3e0e95041383901378e33f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/__init__.py M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py A lib/galaxy/wheels.py R lib/pkg_resources.py M run.sh R scripts/check_eggs.py M scripts/common_startup.sh R scripts/dist-scramble.py R scripts/fetch_eggs.py R scripts/make_egg_packager.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py R scripts/test_dist_egg.py Log Message: ----------- WIP: Stop using eggs, start using prebuilt wheels. Commit: a24134c447818fc8f55e0f7b7a0f33690155444b https://github.com/galaxyproject/galaxy/commit/a24134c447818fc8f55e0f7b7a0f3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install modified pip for fetching Linux wheels, fetch wheels from wheels.galaxyproject.org Commit: 0de745188e28b5b53097b7cb1d69454bf681f523 https://github.com/galaxyproject/galaxy/commit/0de745188e28b5b53097b7cb1d694... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: R dist-eggs.ini R eggs.ini Log Message: ----------- Remove (dist-)eggs.ini. Commit: 33095318f777bf55fcf01cff4fe9d00910ff2868 https://github.com/galaxyproject/galaxy/commit/33095318f777bf55fcf01cff4fe9d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/wheels.py Log Message: ----------- Fix problems in wheels.py found by flake8 Commit: 55019173466628c117a8a41eb068a605c1282f06 https://github.com/galaxyproject/galaxy/commit/55019173466628c117a8a41eb068a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install modified pip in develop/edit mode so it won't be reinstalled every time (courtesy @jxtx). Commit: e6446b05d35e7950675f4bcd95cf8c9e1c89ef1d https://github.com/galaxyproject/galaxy/commit/e6446b05d35e7950675f4bcd95cf8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M requirements.txt Log Message: ----------- Add nose to requirements.txt. Commit: 033b1e88da99b86ffbd33321374aa59d1d72484c https://github.com/galaxyproject/galaxy/commit/033b1e88da99b86ffbd33321374aa... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/lwr_client/config_util.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove all imports of `galaxy.eggs` and all calls to `{eggs,pkg_resources}.require`. Probably broke some stuff where we were trying to be smart about whether a particular egg was available, but Galaxy does at least start. Commit: 431ebf93bd75437fb5f5c41e40791c5c9e6e9aad https://github.com/galaxyproject/galaxy/commit/431ebf93bd75437fb5f5c41e40791... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M requirements.txt Log Message: ----------- Updating requirements.txt as I get wheels ready. TODO: automate OS X wheels. Commit: 90279909209983fc620e26c6d7fabb6031d57dfd https://github.com/galaxyproject/galaxy/commit/90279909209983fc620e26c6d7fab... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M requirements.txt Log Message: ----------- Pin requirements Commit: 40bde6e102ae7bd66973a9f81b79fa9a08836c55 https://github.com/galaxyproject/galaxy/commit/40bde6e102ae7bd66973a9f81b79f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/wheels.py M scripts/common_startup.sh Log Message: ----------- Install required dependencies from requirements.txt rather than convoluted galaxy.wheels method. Not sure why I was doing that. Hackathons are dangerous places. Commit: 97ad53f570800fc2518925555dc99f5a56356bdc https://github.com/galaxyproject/galaxy/commit/97ad53f570800fc2518925555dc99... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt A CODE_OF_CONDUCT.md M CONTRIBUTING.md M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/handlebars.runtime.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/history/copy-dialog.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-panel-edit.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.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/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A 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-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/reports_webapp/run_stats.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/utils/config.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/galaxy/style/less/trackster.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M cron/parse_builds_3_sites.py M doc/patch.py A doc/source/api/guidelines.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst M doc/source/conf.py A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/project/organization.rst A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/_header.rst M doc/source/releases/index.rst A doc/source/ts_api_doc.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py 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 M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/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/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.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/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/eggs/__init__.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/__init__.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.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/local.py M lib/galaxy/jobs/runners/lwr.py M lib/galaxy/jobs/runners/lwr_client/amqp_exchange.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/state_handler_factory.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/main.py M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.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/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/0018_ordered_tags_and_page_tags.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/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.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/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/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.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/0053_item_ratings.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/0058_history_import_export.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/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.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/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.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/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.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/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/bunch.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/debugging.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/expressions.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/inflection.py M lib/galaxy/util/log/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/lrucache.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/specs.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/template.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/cigar.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/params.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/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/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/error.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py A lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py A lib/galaxy/webapps/util.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py M lib/log_tempfile.py M lib/mimeparse.py M lib/psyco_full.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/galaxy_install/utility_containers/__init__.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grid_filter_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/scripts/api/add_repository_registry_entry.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/api/create_categories.py M lib/tool_shed/scripts/api/create_users.py M lib/tool_shed/scripts/api/export.py M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py M lib/tool_shed/scripts/api/import_capsule.py M lib/tool_shed/scripts/api/remove_repository_registry_entry.py M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M run_tests.sh M scripts/api/common.py A scripts/auth/pam_auth_helper.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/edam_mapping.py M scripts/egg_packager_template.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/get_platforms.py M scripts/helper.py M scripts/metagenomics/convert_title.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_table.py M scripts/migrate_tools/migrate_tools.py M scripts/nosetests.py M scripts/paster.py M scripts/runtime_stats.py M scripts/set_dataset_sizes.py M scripts/set_metadata.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/transfer.py M scripts/update_shed_config_path.py M setup.cfg R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/maps/galaxy-app-base.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.menu.js.map M static/maps/galaxy.panels.js.map M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/handlebars.runtime.js.map A static/maps/libs/jquery.sparklines.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/toastr.js.map M static/maps/libs/tracekit.js.map A static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.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-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/ui/ui-button-check.js.map R static/maps/mvc/ui/ui-button-menu.js.map A static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/reports_webapp/run_stats.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.menu.js M static/scripts/galaxy.panels.js M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/handlebars.runtime.js A static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/toastr.js M static/scripts/libs/tracekit.js A static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-view.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/ui/ui-button-check.js R static/scripts/mvc/ui/ui-button-menu.js A static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/reports_webapp/run_stats.js R static/scripts/templates/compile_templates.py M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js A static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/masthead.css A static/style/blue/reports.css M static/style/blue/sprite-fugue.png M static/style/blue/sprite-history-buttons.png M static/style/blue/sprite-history-states.png M static/style/blue/trackster.css R static/welcome.rst M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/base.mako M templates/display_base.mako A templates/page_base.mako M templates/search/index.mako M templates/show_params.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako R templates/webapps/galaxy/cloud/index.mako M templates/webapps/galaxy/galaxy.masthead.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/galaxy/root/index.mako R templates/webapps/galaxy/root/tool_menu.mako M templates/webapps/galaxy/tool_form.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako A templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako A test-data/3.bam M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/asserts/__init__.py M test/base/interactor.py M test/base/test_db_util.py A test/base/test_logging.py M test/base/tool_shed_util.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/casperjs_runner.py M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/casperjs/server_env.py M test/docker/README.md M test/docker/base/Dockerfile M test/functional/test_admin_features.py M test/functional/test_data_managers.py M test/functional/test_data_security.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml R test/functional/tools/compare_bam_as_sam.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/metadata_bam.xml A test/functional/tools/output_collection_filter.xml M test/functional/tools/output_format.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/qunit/README.txt M test/qunit/package.json A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/base.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_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox_filters.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample M tool_list.py M tools/data_source/data_source.py M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into smash_eggs Conflicts: eggs.ini lib/galaxy/__init__.py lib/galaxy/datatypes/binary.py lib/galaxy/datatypes/converters/bgzip.py lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py lib/galaxy/datatypes/converters/interval_to_coverage.py lib/galaxy/datatypes/converters/interval_to_fli.py lib/galaxy/datatypes/converters/interval_to_tabix_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.py lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py lib/galaxy/datatypes/coverage.py lib/galaxy/eggs/__init__.py lib/galaxy/eggs/dist.py lib/galaxy/eggs/scramble.py lib/galaxy/exceptions/__init__.py lib/galaxy/jobs/runners/pbs.py lib/galaxy/jobs/transfer_manager.py lib/galaxy/model/__init__.py lib/galaxy/model/migrate/check.py lib/galaxy/model/orm/__init__.py lib/galaxy/model/tool_shed_install/migrate/check.py lib/galaxy/web/framework/__init__.py lib/galaxy/web/framework/helpers/__init__.py lib/galaxy/web/framework/middleware/sentry.py lib/galaxy/web/framework/openid_manager.py lib/galaxy/web/framework/webapp.py lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py lib/galaxy/webapps/galaxy/controllers/dataset.py lib/galaxy/webapps/galaxy/controllers/library_common.py lib/galaxy/webapps/reports/controllers/workflows.py lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/search/repo_search.py lib/galaxy/webapps/tool_shed/search/tool_search.py lib/galaxy_ext/metadata/set_metadata.py lib/pulsar/client/config_util.py lib/tool_shed/galaxy_install/install_manager.py lib/tool_shed/galaxy_install/migrate/check.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/repository_types/repository_suite_definition.py lib/tool_shed/repository_types/tool_dependency_definition.py lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py lib/tool_shed/scripts/check_repositories_for_functional_tests.py lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py lib/tool_shed/util/basic_util.py lib/tool_shed/util/encoding_util.py lib/tool_shed/util/hg_util.py scripts/check_eggs.py scripts/dist-scramble.py scripts/fetch_eggs.py scripts/make_egg_packager.py scripts/scramble.py scripts/scramble/lib/scramble_lib.py scripts/scramble/scripts/DRMAA_python-macosx.py scripts/scramble/scripts/DRMAA_python-solaris.py scripts/scramble/scripts/DRMAA_python.py scripts/scramble/scripts/MySQL_python-solaris.py scripts/scramble/scripts/MySQL_python.py scripts/scramble/scripts/PyRods.py scripts/scramble/scripts/bx_python-solaris.py scripts/scramble/scripts/generic.py scripts/scramble/scripts/pbs_python.py scripts/scramble/scripts/psycopg2-linux.py scripts/scramble/scripts/psycopg2-macosx.py scripts/scramble/scripts/psycopg2-solaris.py scripts/scramble/scripts/psycopg2.py scripts/scramble/scripts/pysam-solaris.py scripts/scramble/scripts/pysqlite.py scripts/test_dist_egg.py Commit: 975fddeb4092097c5f6eb02f36cac65dcddf0d6a https://github.com/galaxyproject/galaxy/commit/975fddeb4092097c5f6eb02f36cac... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/wheels.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py Log Message: ----------- Fix linting errors Commit: 0469ed29e064a4aed213dcc0230e8a06e711fc24 https://github.com/galaxyproject/galaxy/commit/0469ed29e064a4aed213dcc0230e8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M scripts/api/common.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py M scripts/functional_tests.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/summarize_timings.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py Log Message: ----------- Remove egg cruft from scripts/ Commit: b727174326292fcc713adc79471065d483ce42a8 https://github.com/galaxyproject/galaxy/commit/b727174326292fcc713adc7947106... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M tox.ini Log Message: ----------- tox: Install nose and NoseHTML for unit tests. Commit: 93410ecf2538e32bdac7bed45367dbd6c993fb04 https://github.com/galaxyproject/galaxy/commit/93410ecf2538e32bdac7bed45367d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M scripts/nosetests.py M scripts/summarize_timings.py Log Message: ----------- Fix additional lint errors created by modifying stuff in scripts/ Commit: 165d6bdc9ded10c751e4eecbcca4390d231875ee https://github.com/galaxyproject/galaxy/commit/165d6bdc9ded10c751e4eecbcca43... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py Log Message: ----------- Fix ctabix import errors (would these converters ever have worked?) Commit: 222bb4294a3dd9c9c58ae9f0785a10eb361c1e77 https://github.com/galaxyproject/galaxy/commit/222bb4294a3dd9c9c58ae9f0785a1... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/objectstore/rods.py Log Message: ----------- Conditional import for irods Commit: bf50d44ee50f5ace7d34db3e69c39779283167c7 https://github.com/galaxyproject/galaxy/commit/bf50d44ee50f5ace7d34db3e69c39... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/wheels.py Log Message: ----------- Conditional imports for optional dependencies. Commit: f33476462722ec17947522d0a88661c88b688438 https://github.com/galaxyproject/galaxy/commit/f33476462722ec17947522d0a8866... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Egg cleaning in test/ Commit: a44b2c2170c9c326a2d5e1fec35beb44fd9834df https://github.com/galaxyproject/galaxy/commit/a44b2c2170c9c326a2d5e1fec35be... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/requirements.txt R lib/galaxy/wheels.py M requirements.txt M run.sh M scripts/common_startup.sh Log Message: ----------- Rename galaxy.wheels to the more generalized galaxy.dependencies (since technically we don't care whether they are wheels), handle optional deps more correctly. Add error handling to common_startup.sh. Commit: c0cb01c2f65ccf94e96120b080eb7b5aa06bf31b https://github.com/galaxyproject/galaxy/commit/c0cb01c2f65ccf94e96120b080eb7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt Log Message: ----------- Fixes for job_conf.xml conditional dependencies Commit: e6337269b6fcd2b6c9d76045ff068a22d1dc39f8 https://github.com/galaxyproject/galaxy/commit/e6337269b6fcd2b6c9d76045ff068... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/users.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/template.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Remove pkg_resources.requires from lib/ Commit: 7c9c0cecdc3c31b9e86356470611ad1c7c0e87f4 https://github.com/galaxyproject/galaxy/commit/7c9c0cecdc3c31b9e86356470611a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing WebError requirement Commit: 95b102371b5a2cdf617f988ab0d9e3bebcd03ebe https://github.com/galaxyproject/galaxy/commit/95b102371b5a2cdf617f988ab0d9e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add Pygments as a dependency of WebError and update SQLAlchemy version Commit: 02aed9c79e9f886990d2f5b747b35183f64a2cf7 https://github.com/galaxyproject/galaxy/commit/02aed9c79e9f886990d2f5b747b35... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Update Mercurial to 3.5 Commit: 2955ac414ac572a0c7a32c8b7ae61e0707d90524 https://github.com/galaxyproject/galaxy/commit/2955ac414ac572a0c7a32c8b7ae61... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt Log Message: ----------- pysqlite is not a dependency (we expect Python's sqlite module to exist) Commit: 665c4c299d93b8a028b92ec34988371ac8171617 https://github.com/galaxyproject/galaxy/commit/665c4c299d93b8a028b92ec349883... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Handle the case where there are no conditional (heh) requirements Commit: 94a6f4c1704e30b839ba0de8abedff04155db5d2 https://github.com/galaxyproject/galaxy/commit/94a6f4c1704e30b839ba0de8abedf... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- psycopg2 is not a hard requirement Commit: 4a4bfb55ec6a721f4b915ea1a7023d0ff945557d https://github.com/galaxyproject/galaxy/commit/4a4bfb55ec6a721f4b915ea1a7023... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Slurm runner is a subclass of DRMAA so its use should trigger the conditional dependency code for the drmaa wheel. Commit: 5994311d8274d8b946f51d28efcca17d31a05bbc https://github.com/galaxyproject/galaxy/commit/5994311d8274d8b946f51d28efcca... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Pass Galaxy's virtualenv to jobs (local and remote) if a venv is not set. Can be overridden with <env file="/path/to/activate"/> on the destination. Commit: 7df95d15ab67dd5e1f22107a200913d1b874749e https://github.com/galaxyproject/galaxy/commit/7df95d15ab67dd5e1f22107a20091... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix flake8 error Commit: 6449db2a4ccc78e35193d7c14d315b4686f12532 https://github.com/galaxyproject/galaxy/commit/6449db2a4ccc78e35193d7c14d315... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M test/unit/jobs/test_runner_local.py Log Message: ----------- Fix broken unit test caused by addition of the job wrapper's galaxy_virtual_env attribute Commit: 744835bbfe8bb07041600326af2f2f5d203365f5 https://github.com/galaxyproject/galaxy/commit/744835bbfe8bb07041600326af2f2... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M run_tests.sh M scripts/common_startup.sh M tox.ini Log Message: ----------- Allow the use of common_startup.sh's --skip-eggs from run_tests.sh, and have tox pass this flag (so that dependencies are installed in the tox envs) Commit: 433b79de2b001369a62d4da3b8cc46f75dac86bb https://github.com/galaxyproject/galaxy/commit/433b79de2b001369a62d4da3b8cc4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.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/hda-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-panel-edit-current.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-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/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.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-select-default.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/grunt-tasks/scripts.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg A doc/source/admin/interactive_environments_success.png M doc/source/dev/faq.rst M doc/source/index.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.gg M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.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/local.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py A lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/pulsar/client/amqp_exchange.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py R run_functional_tests.sh M run_tests.sh M scripts/common_startup.sh M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.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-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/history-panel-edit-current.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/upload-row.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.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-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-panel-edit-current.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/upload-row.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M templates/base/base_panels.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/root/index.mako A templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako R templates/webapps/galaxy/tool_form.mako A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py M test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/docker/base/Dockerfile M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/multi_data_param.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/tool_shed/functional/test_1140_tool_help_images.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_execution.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml R tools/data_source/echo.py R tools/data_source/echo.xml R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: d92787557a56fbf542a488c795a33f43b54b325f https://github.com/galaxyproject/galaxy/commit/d92787557a56fbf542a488c795a33... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Move vvers and vurl vars to a more relevant scope. Commit: 735e1c1bb0ea6ee857d04cd1f137c696303af5b0 https://github.com/galaxyproject/galaxy/commit/735e1c1bb0ea6ee857d04cd1f137c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/pulsar/client/config_util.py Log Message: ----------- Fix a bad merge in pulsar client lib caught (as always) by @nsoranzo Commit: 22297e3b839f1985b70944088eeb02c1bf9f26e0 https://github.com/galaxyproject/galaxy/commit/22297e3b839f1985b70944088eeb0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/pulsar/client/config_util.py Log Message: ----------- Missed the rest of the bad merge in the previous commit Commit: b6fde86369bcd715c976e6d8bd3002ffa25a2136 https://github.com/galaxyproject/galaxy/commit/b6fde86369bcd715c976e6d8bd300... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/util/plugin_config.py Log Message: ----------- More graceful handling of failure to import yaml (a la Pulsar) Commit: f22ab8a60b06512596d68080b1bae4011110f4f1 https://github.com/galaxyproject/galaxy/commit/f22ab8a60b06512596d68080b1bae... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Conditional boto import in s3_multipart_upload.py Commit: 367ceae2560efac06e85018f9822207011240bd6 https://github.com/galaxyproject/galaxy/commit/367ceae2560efac06e85018f98222... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M create_db.sh M manage_db.sh M manage_tools.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M set_metadata.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Dockerized tests need to create and activate .venv if it does not exist. Do this by calling common_startup.sh prior to manage_db.sh in run_test_wrapper.sh. Will require a rebuild of the testing-base image. Also, have scripts in Galaxy root activate .venv if it exists. Commit: f7d0d76c509a8d468f29cb07a4fbd98ad1640d8f https://github.com/galaxyproject/galaxy/commit/f7d0d76c509a8d468f29cb07a4fbd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add boto as an explicit requirement (as a dependency of bioblend) Commit: c893afda008f4c47550f9bc94feb1a1256c470e7 https://github.com/galaxyproject/galaxy/commit/c893afda008f4c47550f9bc94feb1... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/version.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.py M test/docker/base/run_test_wrapper.sh M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'dev' into smash_eggs Commit: 26f78a5870a551630a5f4b91533b07b64bd3cb10 https://github.com/galaxyproject/galaxy/commit/26f78a5870a551630a5f4b91533b0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Bump docker test image to 15.10.1 Commit: 6aea26caf307d9931c9f8349c324ed1a90c1a5d7 https://github.com/galaxyproject/galaxy/commit/6aea26caf307d9931c9f8349c324e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add requests as a dependency of bioblend Commit: 6e00db2d35be741247fbd43d154f107585bb81c3 https://github.com/galaxyproject/galaxy/commit/6e00db2d35be741247fbd43d154f1... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Make galaxy.dependencies env-config-var-aware. Commit: 50bfed49f55a7d9c39308f46648616906ce20eb4 https://github.com/galaxyproject/galaxy/commit/50bfed49f55a7d9c39308f4664861... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Rename conditional_requirements.txt ('_' -> '-'), add dev-requirements.txt, fix a flake8 violation that doesn't violate PEP-8. =P Commit: 4a05d5ea12142046eac2d4593030f4d4dcd3c4b1 https://github.com/galaxyproject/galaxy/commit/4a05d5ea12142046eac2d4593030f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/style/less/base.less M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/library_upload_dir.py M scripts/functional_tests.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M static/style/blue/base.css M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: 2b48f5676527a83b76cb4205950670cf16c4b2cb https://github.com/galaxyproject/galaxy/commit/2b48f5676527a83b76cb420595067... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Add lxml as a dev requirement for twill Commit: 5098b7cb27f2c64603c57ee9991bd9516e0d25bb https://github.com/galaxyproject/galaxy/commit/5098b7cb27f2c64603c57ee9991bd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Downgrade twill to 0.9.1 so we don't have to install lxml, which won't compile because libxml-dev isn't installed in the testing image, so we'd have to rebuild it yet again... Commit: af89922aee11a8dffbdeabbc36cf1003828f3a73 https://github.com/galaxyproject/galaxy/commit/af89922aee11a8dffbdeabbc36cf1... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Update the BAM datatype for pysam API changes. index_file also no longer exists (the index must be filename + b".bai" or filename[:-4] + b".bai") =/. Removing it here is okay since the impact is that we can't fetch() random regions or use .pileup(), neither of which are done here. But it might be a problem for galaxy.visualization.data_providers.genome. Commit: 048f0be1bebb233edfb47a3625e8e0a9f751a696 https://github.com/galaxyproject/galaxy/commit/048f0be1bebb233edfb47a3625e8e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Talked to Dan, who corrected me on a few things. Also, forgot that the whole reason we use a modified pysam is for the index_filename param... Commit: 7e372d3cd0e18e3a533d2b36fadc5ab9c755d2ca https://github.com/galaxyproject/galaxy/commit/7e372d3cd0e18e3a533d2b36fadc5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Updates to vis data providers for pysam API changes Commit: 0cbaf3b8c57138d694f8e1e06e353d97b211215f https://github.com/galaxyproject/galaxy/commit/0cbaf3b8c57138d694f8e1e06e353... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use proper PEP-440 local version identifiers for modified dependencies. Commit: 4a5f5f44dc09be5194c9ee4ebc6b0b6a4a057480 https://github.com/galaxyproject/galaxy/commit/4a5f5f44dc09be5194c9ee4ebc6b0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install our modified pip as a wheel from wheels.galaxyproject.org rather than an editable directly from github. Also, use `set -e` in scripts/common_startup.sh to fail if anything fails, rather than chaining a bunch of things with `&&` but not properly handling failure cases. Commit: 737596413f88174edc24345282aee9a1c1b53cac https://github.com/galaxyproject/galaxy/commit/737596413f88174edc24345282aee... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M run.sh Log Message: ----------- Pass relevant args from run.sh to common_startup.sh. Commit: 88683c3c40821581d80b3e984da486032c746c06 https://github.com/galaxyproject/galaxy/commit/88683c3c40821581d80b3e984da48... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is provided. Commit: e423ab6246088fec6a41c31fb67bc34c0ff40a89 https://github.com/galaxyproject/galaxy/commit/e423ab6246088fec6a41c31fb67bc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M create_db.sh R dist-eggs.ini R eggs.ini M lib/galaxy/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/util/gff_util.py A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/template.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py R lib/pkg_resources.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M manage_db.sh M manage_tools.sh M requirements.txt M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py R scripts/check_eggs.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py R scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py R scripts/fetch_eggs.py M scripts/functional_tests.py R scripts/make_egg_packager.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py M scripts/summarize_timings.py R scripts/test_dist_egg.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M set_metadata.sh M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Merge pull request #428 from natefoo/smash_eggs Replace eggs with wheels Compare: https://github.com/galaxyproject/galaxy/compare/112c0390d586...e423ab624608