- 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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