- galaxy-commits - lists.galaxyproject.org

[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 16 Nov '16

16 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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[galaxyproject/galaxy] 6c4d43: Add note about building docs to Makefile.
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c4d430d75781dac112f0c7b56fe61208d081f1c https://github.com/galaxyproject/galaxy/commit/6c4d430d75781dac112f0c7b56fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M Makefile Log Message: ----------- Add note about building docs to Makefile. Commit: 66cc4c3bbe4a90cd68d935574691c31b8053804e https://github.com/galaxyproject/galaxy/commit/66cc4c3bbe4a90cd68d935574691… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #3167 from jmchilton/doc_note Add note about building docs to Makefile. Compare: https://github.com/galaxyproject/galaxy/compare/ca4e8914ecdd...66cc4c3bbe4a

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[galaxyproject/galaxy] 20f98d: Finish job for Torque SSH runner
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20f98df554f502bddff1f22879bf867f97ab7288 https://github.com/galaxyproject/galaxy/commit/20f98df554f502bddff1f22879bf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Finish job for Torque SSH runner Commit: 61d25720661cb120afc7b44c57f41a1b245e21e4 https://github.com/galaxyproject/galaxy/commit/61d25720661cb120afc7b44c57f4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- More explcit logging of CLI runner state change (thx @nsoranzo) Commit: a3ac57dbc532320c98e0b4a72772663293ab3b06 https://github.com/galaxyproject/galaxy/commit/a3ac57dbc532320c98e0b4a72772… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove verbose_install_check option This option was introduced with #2554 and #2538, in reponse to a false positive conda install. This would have been caught by simply checking the exit code, which we are doing by default now. The additional verification is too strigent and not in line with the conda resolver. Activating this option will report perfectly well installed conda environments as having failed and will cause them to be uninstalled. Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs Commit: b748ad1565a1e5064f6e08640c19b09a41b4b2bc https://github.com/galaxyproject/galaxy/commit/b748ad1565a1e5064f6e08640c19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #3157 from galaxyproject/gie-doc-fix [16.07] Fix typo in GIE nginx proxy docs Commit: ae3bdf31dc815dfce305316fe67776bc6802ec1a https://github.com/galaxyproject/galaxy/commit/ae3bdf31dc815dfce305316fe677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07 [16.07] Remove verbose_install_check option Commit: 727270261750fc71979e7ba9fec96b10091ff104 https://github.com/galaxyproject/galaxy/commit/727270261750fc71979e7ba9fec9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #3085 from mvdbeek/fix_torque_ssh [16.07] Finish job for Torque SSH/CLI runner Commit: ca4e8914ecddbba007c1f65ff17f51e719c0c149 https://github.com/galaxyproject/galaxy/commit/ca4e8914ecddbba007c1f65ff17f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M lib/galaxy/jobs/runners/cli.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/conda_util.py Compare: https://github.com/galaxyproject/galaxy/compare/bfabe00ea8f0...ca4e8914ecdd

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[galaxyproject/galaxy] 20f98d: Finish job for Torque SSH runner
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 20f98df554f502bddff1f22879bf867f97ab7288 https://github.com/galaxyproject/galaxy/commit/20f98df554f502bddff1f22879bf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Finish job for Torque SSH runner Commit: 61d25720661cb120afc7b44c57f41a1b245e21e4 https://github.com/galaxyproject/galaxy/commit/61d25720661cb120afc7b44c57f4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- More explcit logging of CLI runner state change (thx @nsoranzo) Commit: 727270261750fc71979e7ba9fec96b10091ff104 https://github.com/galaxyproject/galaxy/commit/727270261750fc71979e7ba9fec9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #3085 from mvdbeek/fix_torque_ssh [16.07] Finish job for Torque SSH/CLI runner Compare: https://github.com/galaxyproject/galaxy/compare/ae3bdf31dc81...727270261750

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[galaxyproject/galaxy] a3ac57: Remove verbose_install_check option
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: a3ac57dbc532320c98e0b4a72772663293ab3b06 https://github.com/galaxyproject/galaxy/commit/a3ac57dbc532320c98e0b4a72772… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove verbose_install_check option This option was introduced with #2554 and #2538, in reponse to a false positive conda install. This would have been caught by simply checking the exit code, which we are doing by default now. The additional verification is too strigent and not in line with the conda resolver. Activating this option will report perfectly well installed conda environments as having failed and will cause them to be uninstalled. Commit: ae3bdf31dc815dfce305316fe67776bc6802ec1a https://github.com/galaxyproject/galaxy/commit/ae3bdf31dc815dfce305316fe677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07 [16.07] Remove verbose_install_check option Compare: https://github.com/galaxyproject/galaxy/compare/b748ad1565a1...ae3bdf31dc81

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[galaxyproject/galaxy] 510506: Rework dependency shell command handling
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51050653b44c24328d9225b69d9b1b6971b0354c https://github.com/galaxyproject/galaxy/commit/51050653b44c24328d9225b69d9b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Rework dependency shell command handling The approach is to always log a warning with stdout and stderr when the exit code is not 0. With this change, one can expect logs like the follwing: ``` galaxy.tools.deps.conda_util DEBUG 2016-11-05 15:14:17,373 Executing command: /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie(a)0.12.7 bowtie=0.12.7 127.0.0.1 - - [05/nov./2016:15:14:19 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" 127.0.0.1 - - [05/nov./2016:15:14:22 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" galaxy.tools.deps.conda_util WARNING 2016-11-05 15:14:24,029 Failed to execute command-line /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie(a)0.12.7 bowtie=0.12.7, stderr was: -------->>begin stderr<<-------- PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels: - bowtie 0.12.7* You can search for packages on anaconda.org with anaconda search -t conda bowtie You may need to install the anaconda-client command line client with conda install anaconda-client -------->>end stderr<<-------- -------->>begin stdout<<-------- Fetching package metadata ............... Solving package specifications: . -------->>end stdout<<-------- galaxy.tools.deps.resolvers.conda DEBUG 2016-11-05 15:14:24,030 Removing failed conda install of bowtie, version '0.12.7' ``` This should be helpful for the more obscure errors that can occur with conda. Commit: bfabe00ea8f07782f0af307b124da8090f2906f2 https://github.com/galaxyproject/galaxy/commit/bfabe00ea8f07782f0af307b124d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3129 from mvdbeek/conda_error_reporting Pass dependency shell command errors to log Compare: https://github.com/galaxyproject/galaxy/compare/7955077e635f...bfabe00ea8f0

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[galaxyproject/galaxy] d3f751: Remove unnecessary set_output_history parameter
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3f7510b2db932228c76402062bad9095549f5f0 https://github.com/galaxyproject/galaxy/commit/d3f7510b2db932228c76402062ba… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Remove unnecessary set_output_history parameter Also fix import order and Python3 compatibility. Commit: 7955077e635f09b4a0c3fda621406686affe0c0f https://github.com/galaxyproject/galaxy/commit/7955077e635f09b4a0c3fda62140… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #3155 from nsoranzo/remove_set_output_history Remove unnecessary set_output_history parameter Compare: https://github.com/galaxyproject/galaxy/compare/46bd40bdc4c0...7955077e635f

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[galaxyproject/galaxy] 133fd3: Quote all paths in converter tools
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 133fd3adfc76216d8808ed7200e7278bdaf87488 https://github.com/galaxyproject/galaxy/commit/133fd3adfc76216d8808ed7200e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Quote all paths in converter tools Commit: 89e6f77feb4404ecb9e0ba025b5d2168e627ed71 https://github.com/galaxyproject/galaxy/commit/89e6f77feb4404ecb9e0ba025b5d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Don't quote Commit: 46bd40bdc4c0dbad20084937e1e3ac606def9a3a https://github.com/galaxyproject/galaxy/commit/46bd40bdc4c0dbad20084937e1e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Merge pull request #3165 from mvdbeek/quote_data_converters Quote all paths in converter tool xml Compare: https://github.com/galaxyproject/galaxy/compare/3ec7be27952b...46bd40bdc4c0

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[galaxyproject/galaxy]
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/gie-doc-fix Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 019f55: Copy hid attribute to converted datasets for hdas ...
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 019f554e4e8425635c4ba36d7d2500d3a3a7502c https://github.com/galaxyproject/galaxy/commit/019f554e4e8425635c4ba36d7d25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Copy hid attribute to converted datasets for hdas only Commit: 3ec7be27952b57cf7e0ad87fdf067cacc5e66856 https://github.com/galaxyproject/galaxy/commit/3ec7be27952b57cf7e0ad87fdf06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #3149 from guerler/fix_hid Explicitly specify attributes which should be copied to converted datasets Compare: https://github.com/galaxyproject/galaxy/compare/2d8cf6b3376b...3ec7be27952b

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[galaxyproject/galaxy] d144f1: Fix typo in GIE nginx proxy docs
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs Commit: b748ad1565a1e5064f6e08640c19b09a41b4b2bc https://github.com/galaxyproject/galaxy/commit/b748ad1565a1e5064f6e08640c19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #3157 from galaxyproject/gie-doc-fix [16.07] Fix typo in GIE nginx proxy docs Compare: https://github.com/galaxyproject/galaxy/compare/53a66c9d4678...b748ad1565a1

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[galaxyproject/galaxy] d144f1: Fix typo in GIE nginx proxy docs
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/gie-doc-fix Home: https://github.com/galaxyproject/galaxy Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs

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[galaxyproject/galaxy] 9c37c6: Fixes for flake8-import-order 0.11
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c37c6df896312de5d07f93d2c6e1bdcaeff3e53 https://github.com/galaxyproject/galaxy/commit/9c37c6df896312de5d07f93d2c6e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Fixes for flake8-import-order 0.11 Also fix Python3 compatibility. Commit: 2d8cf6b3376b41a6dd9a9ff3f4a82aaae1baa209 https://github.com/galaxyproject/galaxy/commit/2d8cf6b3376b41a6dd9a9ff3f4a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/tool_shed/tools/tool_validator.py M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Merge pull request #3154 from nsoranzo/fixes_for_new_flake8_import_order Fixes for flake8-import-order 0.11 Compare: https://github.com/galaxyproject/galaxy/compare/4b2e875802dc...2d8cf6b3376b

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[galaxyproject/usegalaxy-playbook] 6731a5: Updated dynamic rules
by GitHub 10 Nov '16

10 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6731a5819bfbca076126e12cb48ccd5282333dd0 https://github.com/galaxyproject/usegalaxy-playbook/commit/6731a5819bfbca07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: A files/galaxy/common/dynamic_rules/bridges_select.py M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Updated dynamic rules

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[galaxyproject/usegalaxy-playbook] c544f1: Upding slide rotation. Swapping events.
by GitHub 10 Nov '16

10 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c544f1a17001df1d42fe03983129867a10491159 https://github.com/galaxyproject/usegalaxy-playbook/commit/c544f1a17001df1d… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: A files/galaxy/common/static/welcome_img/EDGW2017.jpg A files/galaxy/common/static/welcome_img/GAMe2017TalkAbstracts.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Upding slide rotation. Swapping events.

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[galaxyproject/galaxy] d3a5c4: Catch and display exceptions triggered by tool fil...
by GitHub 09 Nov '16

09 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3a5c4c7205b269830547fcb647528e3e2a9663f https://github.com/galaxyproject/galaxy/commit/d3a5c4c7205b269830547fcb6475… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Catch and display exceptions triggered by tool filter functions Commit: 300c9616306f69579b1d492aa78a17985e21f738 https://github.com/galaxyproject/galaxy/commit/300c9616306f69579b1d492aa78a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Use as instead of comma Commit: 1c740833e0c1884d43a42dc4417eb3f02adfafab https://github.com/galaxyproject/galaxy/commit/1c740833e0c1884d43a42dc4417e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix import order Commit: 7456b1f9218dabd6eab0d2fa6c3acc285c6c20c3 https://github.com/galaxyproject/galaxy/commit/7456b1f9218dabd6eab0d2fa6c3a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove unnecessary slashes Commit: 4d623a4d5a391a6aed2faf4b45f03c87b8f11a90 https://github.com/galaxyproject/galaxy/commit/4d623a4d5a391a6aed2faf4b45f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Ensure that label key exists before attempting removal Commit: 4b2e875802dcdc0015fb1c05d669e31eb60f01ab https://github.com/galaxyproject/galaxy/commit/4b2e875802dcdc0015fb1c05d669… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3123 from guerler/fix_tool_filters Display an error message when toolbox filters fails Compare: https://github.com/galaxyproject/galaxy/compare/93a09d2eb033...4b2e875802dc

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[galaxyproject/galaxy] 7f630e: Fix flake8 linting broken in 7bee2651aa8f08ea0495d...
by GitHub 09 Nov '16

09 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f630ea2ddb279ce963070d87573bac4c66d5027 https://github.com/galaxyproject/galaxy/commit/7f630ea2ddb279ce963070d87573… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/reports/config.py Log Message: ----------- Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 Also fix import order and Python3 compatibility. Commit: 93a09d2eb033d8bc8b98a7ca94e80bbb1a80fe60 https://github.com/galaxyproject/galaxy/commit/93a09d2eb033d8bc8b98a7ca94e8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/reports/config.py Log Message: ----------- Merge pull request #3141 from nsoranzo/followup_on_3139 Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9 Compare: https://github.com/galaxyproject/galaxy/compare/00edc474274a...93a09d2eb033

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[galaxyproject/galaxy] 1e142d: User activation emails are sent without a From: ad...
by GitHub 08 Nov '16

08 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e142dd33d505436e081306bc08f044bb7b5886a https://github.com/galaxyproject/galaxy/commit/1e142dd33d505436e081306bc08f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- User activation emails are sent without a From: address if email_from is unset. Fix this by using `galaxy-no-reply@host` as with other emails we send. Commit: 00edc474274a671c1ba4d7e2a64335e0abb614c5 https://github.com/galaxyproject/galaxy/commit/00edc474274a671c1ba4d7e2a643… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3140 from natefoo/activation-from Ensure a From: address is set for user activation emails Compare: https://github.com/galaxyproject/galaxy/compare/3d69a2d1a5f7...00edc474274a

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