galaxy-commits November 2016

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[galaxyproject/galaxy] c5a519: Change wording to be more clear about how workflow...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5a51967173b7e5b0ecf6bbb1340db9ff54a3aed https://github.com/galaxyproject/galaxy/commit/c5a51967173b7e5b0ecf6bbb1340… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Change wording to be more clear about how workflow output cleanup works. Also adjust styling so that the rows in the workflow editor box are less smashed together. Commit: 277d3c3e58d28904752674c9210f02b88e481eb7 https://github.com/galaxyproject/galaxy/commit/277d3c3e58d28904752674c9210f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Slight wording tweak. Commit: 8966b741317431275100c24ab3cc69a221de646c https://github.com/galaxyproject/galaxy/commit/8966b741317431275100c24ab3cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Swap to section row selector Commit: 5028e2a25107e8f4cd2f136ab275853b5e31bb7f https://github.com/galaxyproject/galaxy/commit/5028e2a25107e8f4cd2f136ab275… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M 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tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into workflow_intermediates_ux Commit: e5b69a711d14fa8e8876041f92160db19da3e9bf https://github.com/galaxyproject/galaxy/commit/e5b69a711d14fa8e8876041f9216… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #2966 from dannon/workflow_intermediates_ux Change wording to be more clear about how workflow output cleanup wor… Compare: https://github.com/galaxyproject/galaxy/compare/ac5b7efc5f88...e5b69a711d14

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[galaxyproject/galaxy] fb69af: Update ToolPanelElements instance locally
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb69afae28c434f35860ccaa4591e95fe3acfe91 https://github.com/galaxyproject/galaxy/commit/fb69afae28c434f35860ccaa4591… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update ToolPanelElements instance locally in addition to Galaxy's IPC call via send_control_task. Commit: ac5b7efc5f88da9b337a8d98f36dbdbfe29bb3f6 https://github.com/galaxyproject/galaxy/commit/ac5b7efc5f88da9b337a8d98f36d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3130 from mvdbeek/fix_invalid_section_key Update ToolPanelElements instance locally Compare: https://github.com/galaxyproject/galaxy/compare/2f08dd72c3e0...ac5b7efc5f88

1 0

[galaxyproject/galaxy] 45259b: Fix typo
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45259b7f168f6c1eb17f4f6aec738ad9f9231518 https://github.com/galaxyproject/galaxy/commit/45259b7f168f6c1eb17f4f6aec73… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Fix typo Commit: 2f08dd72c3e028855b37dc1d113636dda2db9eab https://github.com/galaxyproject/galaxy/commit/2f08dd72c3e028855b37dc1d1136… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3184 from afgane/dev Fix a typo in the intro tour Compare: https://github.com/galaxyproject/galaxy/compare/2f2d21aea25f...2f08dd72c3e0

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[galaxyproject/galaxy] dd5560: Fix import broken in b4c77b761799b3a8752a6fec50071...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd556090c158b5062f0b7f6e0775281fcaabcb7e https://github.com/galaxyproject/galaxy/commit/dd556090c158b5062f0b7f6e0775… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M test/manual/workflows_scaling.py Log Message: ----------- Fix import broken in b4c77b761799b3a8752a6fec500717b1a6f3818b Commit: a8746c4f52295e5133950c0bffc3a9f07a2818ec https://github.com/galaxyproject/galaxy/commit/a8746c4f52295e5133950c0bffc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.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_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.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/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Fix import order and Python3 compatibility for test/unit/ Commit: 2f2d21aea25f45508bccf046f179041f3599c3b0 https://github.com/galaxyproject/galaxy/commit/2f2d21aea25f45508bccf046f179… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M test/manual/workflows_scaling.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.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_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.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/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #3177 from nsoranzo/flake8-import-order Fix import order and Python3 compatibility for test/unit/ Compare: https://github.com/galaxyproject/galaxy/compare/a86a457230e8...2f2d21aea25f

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[galaxyproject/galaxy] 063bb6: add links to local tours to sample welcome
by GitHub 15 Nov '16

15 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 063bb61d07177f2736805521a888003d705e516e https://github.com/galaxyproject/galaxy/commit/063bb61d07177f2736805521a888… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- add links to local tours to sample welcome Commit: 2c756ff170da94b88829866f43082861a625b9fb https://github.com/galaxyproject/galaxy/commit/2c756ff170da94b88829866f4308… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- drop leading slash to work with proxy prefix, thanks @dannon Commit: a86a457230e87ab02de29bba13686ad0c1243a63 https://github.com/galaxyproject/galaxy/commit/a86a457230e87ab02de29bba1368… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #3176 from martenson/add-tours-to-welcome add links to local tours to sample welcome Compare: https://github.com/galaxyproject/galaxy/compare/594e44b4fbca...a86a457230e8

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[galaxyproject/usegalaxy-playbook] 3e87c1: Cert updates, Test updates, mutable config file up...
by GitHub 15 Nov '16

15 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3e87c1b24618bca4b1750dade5307009963164f4 https://github.com/galaxyproject/usegalaxy-playbook/commit/3e87c1b24618bca4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M common/secret_vars/ssl.yml M common_roles M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M files/ssl/athena.galaxyproject.org_cert.pem M files/ssl/radegast.galaxyproject.org_cert.pem M files/ssl/usegalaxy.org_cert.pem M files/ssl/wildcard_cert.pem M stage/galaxy_version.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Cert updates, Test updates, mutable config file updates.

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[galaxyproject/galaxy] 1d17a2: Fixes for pycodestyle 2.2.0
by GitHub 15 Nov '16

15 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d17a29c7947993ae7cca998eff25c1ff998ebdb https://github.com/galaxyproject/galaxy/commit/1d17a29c7947993ae7cca998eff2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/source_material/circle.py 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/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.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/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.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/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.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/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/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/util/workflow_util.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py 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/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.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/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api_asserts.py M test/base/driver_util.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Fixes for pycodestyle 2.2.0 Commit: 594e44b4fbca2a1d128f81c8a10d5a4e0c334b01 https://github.com/galaxyproject/galaxy/commit/594e44b4fbca2a1d128f81c8a10d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/source_material/circle.py 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/parse_builds.py M cron/parse_builds_3_sites.py M doc/parse_gx_xsd.py M doc/patch.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.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/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.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/display_applications/parameters.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.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/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/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/mimeparse.py M lib/tool_shed/util/workflow_util.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py 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/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.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/communication/communication_server.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api_asserts.py M test/base/driver_util.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #3170 from nsoranzo/dev Fixes for pycodestyle 2.2.0 Compare: https://github.com/galaxyproject/galaxy/compare/3f4033c05d1f...594e44b4fbca

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[galaxyproject/galaxy] afbea0: Present tool help from history entry. Issue 2100
by GitHub 15 Nov '16

15 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afbea0dbfda0ad231a101aa0d7c25ee3822d9f7e https://github.com/galaxyproject/galaxy/commit/afbea0dbfda0ad231a101aa0d7c2… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Present tool help from history entry. Issue 2100 Commit: 32d0db8bb3b3b64a96beb1f09908cb1e3c1e3c28 https://github.com/galaxyproject/galaxy/commit/32d0db8bb3b3b64a96beb1f09908… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Job ID comes from creating_job value in dataset metadata. Commit: 5a2d01b267398bb01620faeec0d665291ac953ad https://github.com/galaxyproject/galaxy/commit/5a2d01b267398bb01620faeec0d6… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Move help button to last position of left group, add 5px padding to help text. Commit: 3f4033c05d1f2f1437d42da21e5d26e8e3b46ced https://github.com/galaxyproject/galaxy/commit/3f4033c05d1f2f1437d42da21e5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-15 (Tue, 15 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge remote-tracking branch 'tmcgowan/issue_2100' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7e988bbe097f...3f4033c05d1f

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[galaxyproject/galaxy] 00b147: Bring in updates from galaxy-lib.
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 00b147a6649b8fd1112fa76c573fa78db8e58621 https://github.com/galaxyproject/galaxy/commit/00b147a6649b8fd1112fa76c573f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/rods.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Bring in updates from galaxy-lib. Commit: 7e988bbe097f4f4e3d1f7c5dc3d149ee0c201bd8 https://github.com/galaxyproject/galaxy/commit/7e988bbe097f4f4e3d1f7c5dc3d1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/rods.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3169 from jmchilton/galaxy-lib-update-3 Bring in updates from galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/66cc4c3bbe4a...7e988bbe097f

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[galaxyproject/usegalaxy-playbook] 8b9276: Updated slide rotation. Featuring PRABI this mont...
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8b9276ec927a630df3ec1b1e6d9f7c7d9ae21cd2 https://github.com/galaxyproject/usegalaxy-playbook/commit/8b9276ec927a630d… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: A files/galaxy/common/static/welcome_img/PRABIGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation. Featuring PRABI this month.

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