October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d90ba8: Add a --dev-wheels arg to common_startup.sh (calle...
by GitHub 26 Oct '15

26 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d90ba82e92e65a6f5779e149663b45d18e3aecdf https://github.com/galaxyproject/galaxy/commit/d90ba82e92e65a6f5779e149663b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Add a --dev-wheels arg to common_startup.sh (called by run_tests.sh by default) that will install things in dev-requirements.txt. Commit: 5f3fbdefbeb5aa0d1eac0cd4c8ffa1ac45eec2e7 https://github.com/galaxyproject/galaxy/commit/5f3fbdefbeb5aa0d1eac0cd4c8ff… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #988 from natefoo/smash_eggs Add a --dev-wheels arg to common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/ef08ef4eadd6...5f3fbdefbeb5

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[galaxyproject/galaxy] 797579: Do not attempt to read the `load` attribute of job...
by GitHub 26 Oct '15

26 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7975798afb7975d13578ea791b3e7824641c9973 https://github.com/galaxyproject/galaxy/commit/7975798afb7975d13578ea791b3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Do not attempt to read the `load` attribute of job runner plugins that do not have a `load` attribute. `load` is an optional attrib on the <plugin> tag in job_conf.xml, used by the dynamic runner (which is always/automatically loaded) to pass plugin params. Galaxy servers using a `load`-less plugin will fail to start if using run.sh without this fix. Commit: ef08ef4eadd6f0202b317c76e5766a2feb97f921 https://github.com/galaxyproject/galaxy/commit/ef08ef4eadd6f0202b317c76e576… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Merge pull request #986 from natefoo/smash_eggs Do not attempt to read the `load` attribute of job runner plugins that do not have a `load` attribute. Compare: https://github.com/galaxyproject/galaxy/compare/e423ab624608...ef08ef4eadd6

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[galaxyproject/ansible-galaxy] 6dbcb9: Support installation of dependency via wheels.
by GitHub 26 Oct '15

26 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 6dbcb90fc1bb37a85337e5ff2d30a7b17e718b22 https://github.com/galaxyproject/ansible-galaxy/commit/6dbcb90fc1bb37a85337… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M README.md M defaults/main.yml A tasks/dependencies.yml R tasks/eggs.yml M tasks/main.yml Log Message: ----------- Support installation of dependency via wheels.

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[galaxyproject/usegalaxy-playbook] e869d2: edit Test secret vars
by GitHub 23 Oct '15

23 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e869d268c93f0f314564e5530530bd86a8a8e37f https://github.com/galaxyproject/usegalaxy-playbook/commit/e869d268c93f0f31… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-23 (Fri, 23 Oct 2015) Changed paths: M stage/secret_vars/galaxyservers.yml Log Message: ----------- edit Test secret vars

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[galaxyproject/galaxy] 633061: WIP: Stop using eggs, start using prebuilt wheels.
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 633061f3e0e95041383901378e33f8b41b83717e https://github.com/galaxyproject/galaxy/commit/633061f3e0e95041383901378e33… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/__init__.py M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py A lib/galaxy/wheels.py R lib/pkg_resources.py M run.sh R scripts/check_eggs.py M scripts/common_startup.sh R scripts/dist-scramble.py R scripts/fetch_eggs.py R scripts/make_egg_packager.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py R scripts/test_dist_egg.py Log Message: ----------- WIP: Stop using eggs, start using prebuilt wheels. Commit: a24134c447818fc8f55e0f7b7a0f33690155444b https://github.com/galaxyproject/galaxy/commit/a24134c447818fc8f55e0f7b7a0f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install modified pip for fetching Linux wheels, fetch wheels from wheels.galaxyproject.org Commit: 0de745188e28b5b53097b7cb1d69454bf681f523 https://github.com/galaxyproject/galaxy/commit/0de745188e28b5b53097b7cb1d69… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: R dist-eggs.ini R eggs.ini Log Message: ----------- Remove (dist-)eggs.ini. Commit: 33095318f777bf55fcf01cff4fe9d00910ff2868 https://github.com/galaxyproject/galaxy/commit/33095318f777bf55fcf01cff4fe9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/wheels.py Log Message: ----------- Fix problems in wheels.py found by flake8 Commit: 55019173466628c117a8a41eb068a605c1282f06 https://github.com/galaxyproject/galaxy/commit/55019173466628c117a8a41eb068… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install modified pip in develop/edit mode so it won't be reinstalled every time (courtesy @jxtx). Commit: e6446b05d35e7950675f4bcd95cf8c9e1c89ef1d https://github.com/galaxyproject/galaxy/commit/e6446b05d35e7950675f4bcd95cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M requirements.txt Log Message: ----------- Add nose to requirements.txt. Commit: 033b1e88da99b86ffbd33321374aa59d1d72484c https://github.com/galaxyproject/galaxy/commit/033b1e88da99b86ffbd33321374a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/lwr_client/config_util.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove all imports of `galaxy.eggs` and all calls to `{eggs,pkg_resources}.require`. Probably broke some stuff where we were trying to be smart about whether a particular egg was available, but Galaxy does at least start. Commit: 431ebf93bd75437fb5f5c41e40791c5c9e6e9aad https://github.com/galaxyproject/galaxy/commit/431ebf93bd75437fb5f5c41e4079… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M requirements.txt Log Message: ----------- Updating requirements.txt as I get wheels ready. TODO: automate OS X wheels. Commit: 90279909209983fc620e26c6d7fabb6031d57dfd https://github.com/galaxyproject/galaxy/commit/90279909209983fc620e26c6d7fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M requirements.txt Log Message: ----------- Pin requirements Commit: 40bde6e102ae7bd66973a9f81b79fa9a08836c55 https://github.com/galaxyproject/galaxy/commit/40bde6e102ae7bd66973a9f81b79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/wheels.py M scripts/common_startup.sh Log Message: ----------- Install required dependencies from requirements.txt rather than convoluted galaxy.wheels method. Not sure why I was doing that. Hackathons are dangerous places. Commit: 97ad53f570800fc2518925555dc99f5a56356bdc https://github.com/galaxyproject/galaxy/commit/97ad53f570800fc2518925555dc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt A CODE_OF_CONDUCT.md M CONTRIBUTING.md M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/handlebars.runtime.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/reports_webapp/run_stats.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/utils/config.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/galaxy/style/less/trackster.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M cron/parse_builds_3_sites.py M doc/patch.py A doc/source/api/guidelines.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst M doc/source/conf.py A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/project/organization.rst A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/_header.rst M doc/source/releases/index.rst A doc/source/ts_api_doc.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M 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test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample M tool_list.py M tools/data_source/data_source.py M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into smash_eggs Conflicts: eggs.ini lib/galaxy/__init__.py lib/galaxy/datatypes/binary.py lib/galaxy/datatypes/converters/bgzip.py lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py lib/galaxy/datatypes/converters/interval_to_coverage.py lib/galaxy/datatypes/converters/interval_to_fli.py lib/galaxy/datatypes/converters/interval_to_tabix_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.py lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py lib/galaxy/datatypes/coverage.py lib/galaxy/eggs/__init__.py lib/galaxy/eggs/dist.py lib/galaxy/eggs/scramble.py lib/galaxy/exceptions/__init__.py lib/galaxy/jobs/runners/pbs.py lib/galaxy/jobs/transfer_manager.py lib/galaxy/model/__init__.py lib/galaxy/model/migrate/check.py lib/galaxy/model/orm/__init__.py lib/galaxy/model/tool_shed_install/migrate/check.py lib/galaxy/web/framework/__init__.py lib/galaxy/web/framework/helpers/__init__.py lib/galaxy/web/framework/middleware/sentry.py lib/galaxy/web/framework/openid_manager.py lib/galaxy/web/framework/webapp.py lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py lib/galaxy/webapps/galaxy/controllers/dataset.py lib/galaxy/webapps/galaxy/controllers/library_common.py lib/galaxy/webapps/reports/controllers/workflows.py lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/search/repo_search.py lib/galaxy/webapps/tool_shed/search/tool_search.py lib/galaxy_ext/metadata/set_metadata.py lib/pulsar/client/config_util.py lib/tool_shed/galaxy_install/install_manager.py lib/tool_shed/galaxy_install/migrate/check.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/repository_types/repository_suite_definition.py lib/tool_shed/repository_types/tool_dependency_definition.py lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py lib/tool_shed/scripts/check_repositories_for_functional_tests.py lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py lib/tool_shed/util/basic_util.py lib/tool_shed/util/encoding_util.py lib/tool_shed/util/hg_util.py scripts/check_eggs.py scripts/dist-scramble.py scripts/fetch_eggs.py scripts/make_egg_packager.py scripts/scramble.py scripts/scramble/lib/scramble_lib.py scripts/scramble/scripts/DRMAA_python-macosx.py scripts/scramble/scripts/DRMAA_python-solaris.py scripts/scramble/scripts/DRMAA_python.py scripts/scramble/scripts/MySQL_python-solaris.py scripts/scramble/scripts/MySQL_python.py scripts/scramble/scripts/PyRods.py scripts/scramble/scripts/bx_python-solaris.py scripts/scramble/scripts/generic.py scripts/scramble/scripts/pbs_python.py scripts/scramble/scripts/psycopg2-linux.py scripts/scramble/scripts/psycopg2-macosx.py scripts/scramble/scripts/psycopg2-solaris.py scripts/scramble/scripts/psycopg2.py scripts/scramble/scripts/pysam-solaris.py scripts/scramble/scripts/pysqlite.py scripts/test_dist_egg.py Commit: 975fddeb4092097c5f6eb02f36cac65dcddf0d6a https://github.com/galaxyproject/galaxy/commit/975fddeb4092097c5f6eb02f36ca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/wheels.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py Log Message: ----------- Fix linting errors Commit: 0469ed29e064a4aed213dcc0230e8a06e711fc24 https://github.com/galaxyproject/galaxy/commit/0469ed29e064a4aed213dcc0230e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M scripts/api/common.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py M scripts/functional_tests.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/summarize_timings.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py Log Message: ----------- Remove egg cruft from scripts/ Commit: b727174326292fcc713adc79471065d483ce42a8 https://github.com/galaxyproject/galaxy/commit/b727174326292fcc713adc794710… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M tox.ini Log Message: ----------- tox: Install nose and NoseHTML for unit tests. Commit: 93410ecf2538e32bdac7bed45367dbd6c993fb04 https://github.com/galaxyproject/galaxy/commit/93410ecf2538e32bdac7bed45367… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M scripts/nosetests.py M scripts/summarize_timings.py Log Message: ----------- Fix additional lint errors created by modifying stuff in scripts/ Commit: 165d6bdc9ded10c751e4eecbcca4390d231875ee https://github.com/galaxyproject/galaxy/commit/165d6bdc9ded10c751e4eecbcca4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py Log Message: ----------- Fix ctabix import errors (would these converters ever have worked?) Commit: 222bb4294a3dd9c9c58ae9f0785a10eb361c1e77 https://github.com/galaxyproject/galaxy/commit/222bb4294a3dd9c9c58ae9f0785a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/objectstore/rods.py Log Message: ----------- Conditional import for irods Commit: bf50d44ee50f5ace7d34db3e69c39779283167c7 https://github.com/galaxyproject/galaxy/commit/bf50d44ee50f5ace7d34db3e69c3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/wheels.py Log Message: ----------- Conditional imports for optional dependencies. Commit: f33476462722ec17947522d0a88661c88b688438 https://github.com/galaxyproject/galaxy/commit/f33476462722ec17947522d0a886… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Egg cleaning in test/ Commit: a44b2c2170c9c326a2d5e1fec35beb44fd9834df https://github.com/galaxyproject/galaxy/commit/a44b2c2170c9c326a2d5e1fec35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/requirements.txt R lib/galaxy/wheels.py M requirements.txt M run.sh M scripts/common_startup.sh Log Message: ----------- Rename galaxy.wheels to the more generalized galaxy.dependencies (since technically we don't care whether they are wheels), handle optional deps more correctly. Add error handling to common_startup.sh. Commit: c0cb01c2f65ccf94e96120b080eb7b5aa06bf31b https://github.com/galaxyproject/galaxy/commit/c0cb01c2f65ccf94e96120b080eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt Log Message: ----------- Fixes for job_conf.xml conditional dependencies Commit: e6337269b6fcd2b6c9d76045ff068a22d1dc39f8 https://github.com/galaxyproject/galaxy/commit/e6337269b6fcd2b6c9d76045ff06… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/users.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/template.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Remove pkg_resources.requires from lib/ Commit: 7c9c0cecdc3c31b9e86356470611ad1c7c0e87f4 https://github.com/galaxyproject/galaxy/commit/7c9c0cecdc3c31b9e86356470611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing WebError requirement Commit: 95b102371b5a2cdf617f988ab0d9e3bebcd03ebe https://github.com/galaxyproject/galaxy/commit/95b102371b5a2cdf617f988ab0d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add Pygments as a dependency of WebError and update SQLAlchemy version Commit: 02aed9c79e9f886990d2f5b747b35183f64a2cf7 https://github.com/galaxyproject/galaxy/commit/02aed9c79e9f886990d2f5b747b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Update Mercurial to 3.5 Commit: 2955ac414ac572a0c7a32c8b7ae61e0707d90524 https://github.com/galaxyproject/galaxy/commit/2955ac414ac572a0c7a32c8b7ae6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt Log Message: ----------- pysqlite is not a dependency (we expect Python's sqlite module to exist) Commit: 665c4c299d93b8a028b92ec34988371ac8171617 https://github.com/galaxyproject/galaxy/commit/665c4c299d93b8a028b92ec34988… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Handle the case where there are no conditional (heh) requirements Commit: 94a6f4c1704e30b839ba0de8abedff04155db5d2 https://github.com/galaxyproject/galaxy/commit/94a6f4c1704e30b839ba0de8abed… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- psycopg2 is not a hard requirement Commit: 4a4bfb55ec6a721f4b915ea1a7023d0ff945557d https://github.com/galaxyproject/galaxy/commit/4a4bfb55ec6a721f4b915ea1a702… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Slurm runner is a subclass of DRMAA so its use should trigger the conditional dependency code for the drmaa wheel. Commit: 5994311d8274d8b946f51d28efcca17d31a05bbc https://github.com/galaxyproject/galaxy/commit/5994311d8274d8b946f51d28efcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Pass Galaxy's virtualenv to jobs (local and remote) if a venv is not set. Can be overridden with <env file="/path/to/activate"/> on the destination. Commit: 7df95d15ab67dd5e1f22107a200913d1b874749e https://github.com/galaxyproject/galaxy/commit/7df95d15ab67dd5e1f22107a2009… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix flake8 error Commit: 6449db2a4ccc78e35193d7c14d315b4686f12532 https://github.com/galaxyproject/galaxy/commit/6449db2a4ccc78e35193d7c14d31… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M test/unit/jobs/test_runner_local.py Log Message: ----------- Fix broken unit test caused by addition of the job wrapper's galaxy_virtual_env attribute Commit: 744835bbfe8bb07041600326af2f2f5d203365f5 https://github.com/galaxyproject/galaxy/commit/744835bbfe8bb07041600326af2f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M run_tests.sh M scripts/common_startup.sh M tox.ini Log Message: ----------- Allow the use of common_startup.sh's 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templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako R templates/webapps/galaxy/tool_form.mako A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py M test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/docker/base/Dockerfile M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/multi_data_param.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/tool_shed/functional/test_1140_tool_help_images.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_execution.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml R tools/data_source/echo.py R tools/data_source/echo.xml R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: d92787557a56fbf542a488c795a33f43b54b325f https://github.com/galaxyproject/galaxy/commit/d92787557a56fbf542a488c795a3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Move vvers and vurl vars to a more relevant scope. Commit: 735e1c1bb0ea6ee857d04cd1f137c696303af5b0 https://github.com/galaxyproject/galaxy/commit/735e1c1bb0ea6ee857d04cd1f137… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/pulsar/client/config_util.py Log Message: ----------- Fix a bad merge in pulsar client lib caught (as always) by @nsoranzo Commit: 22297e3b839f1985b70944088eeb02c1bf9f26e0 https://github.com/galaxyproject/galaxy/commit/22297e3b839f1985b70944088eeb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/pulsar/client/config_util.py Log Message: ----------- Missed the rest of the bad merge in the previous commit Commit: b6fde86369bcd715c976e6d8bd3002ffa25a2136 https://github.com/galaxyproject/galaxy/commit/b6fde86369bcd715c976e6d8bd30… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/util/plugin_config.py Log Message: ----------- More graceful handling of failure to import yaml (a la Pulsar) Commit: f22ab8a60b06512596d68080b1bae4011110f4f1 https://github.com/galaxyproject/galaxy/commit/f22ab8a60b06512596d68080b1ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Conditional boto import in s3_multipart_upload.py Commit: 367ceae2560efac06e85018f9822207011240bd6 https://github.com/galaxyproject/galaxy/commit/367ceae2560efac06e85018f9822… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M create_db.sh M manage_db.sh M manage_tools.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M set_metadata.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Dockerized tests need to create and activate .venv if it does not exist. Do this by calling common_startup.sh prior to manage_db.sh in run_test_wrapper.sh. Will require a rebuild of the testing-base image. Also, have scripts in Galaxy root activate .venv if it exists. Commit: f7d0d76c509a8d468f29cb07a4fbd98ad1640d8f https://github.com/galaxyproject/galaxy/commit/f7d0d76c509a8d468f29cb07a4fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add boto as an explicit requirement (as a dependency of bioblend) Commit: c893afda008f4c47550f9bc94feb1a1256c470e7 https://github.com/galaxyproject/galaxy/commit/c893afda008f4c47550f9bc94feb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/version.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.py M test/docker/base/run_test_wrapper.sh M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'dev' into smash_eggs Commit: 26f78a5870a551630a5f4b91533b07b64bd3cb10 https://github.com/galaxyproject/galaxy/commit/26f78a5870a551630a5f4b91533b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Bump docker test image to 15.10.1 Commit: 6aea26caf307d9931c9f8349c324ed1a90c1a5d7 https://github.com/galaxyproject/galaxy/commit/6aea26caf307d9931c9f8349c324… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add requests as a dependency of bioblend Commit: 6e00db2d35be741247fbd43d154f107585bb81c3 https://github.com/galaxyproject/galaxy/commit/6e00db2d35be741247fbd43d154f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Make galaxy.dependencies env-config-var-aware. Commit: 50bfed49f55a7d9c39308f46648616906ce20eb4 https://github.com/galaxyproject/galaxy/commit/50bfed49f55a7d9c39308f466486… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Rename conditional_requirements.txt ('_' -> '-'), add dev-requirements.txt, fix a flake8 violation that doesn't violate PEP-8. =P Commit: 4a05d5ea12142046eac2d4593030f4d4dcd3c4b1 https://github.com/galaxyproject/galaxy/commit/4a05d5ea12142046eac2d4593030… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/style/less/base.less M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/library_upload_dir.py M scripts/functional_tests.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M static/style/blue/base.css M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: 2b48f5676527a83b76cb4205950670cf16c4b2cb https://github.com/galaxyproject/galaxy/commit/2b48f5676527a83b76cb42059506… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Add lxml as a dev requirement for twill Commit: 5098b7cb27f2c64603c57ee9991bd9516e0d25bb https://github.com/galaxyproject/galaxy/commit/5098b7cb27f2c64603c57ee9991b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Downgrade twill to 0.9.1 so we don't have to install lxml, which won't compile because libxml-dev isn't installed in the testing image, so we'd have to rebuild it yet again... Commit: af89922aee11a8dffbdeabbc36cf1003828f3a73 https://github.com/galaxyproject/galaxy/commit/af89922aee11a8dffbdeabbc36cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Update the BAM datatype for pysam API changes. index_file also no longer exists (the index must be filename + b".bai" or filename[:-4] + b".bai") =/. Removing it here is okay since the impact is that we can't fetch() random regions or use .pileup(), neither of which are done here. But it might be a problem for galaxy.visualization.data_providers.genome. Commit: 048f0be1bebb233edfb47a3625e8e0a9f751a696 https://github.com/galaxyproject/galaxy/commit/048f0be1bebb233edfb47a3625e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Talked to Dan, who corrected me on a few things. Also, forgot that the whole reason we use a modified pysam is for the index_filename param... Commit: 7e372d3cd0e18e3a533d2b36fadc5ab9c755d2ca https://github.com/galaxyproject/galaxy/commit/7e372d3cd0e18e3a533d2b36fadc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Updates to vis data providers for pysam API changes Commit: 0cbaf3b8c57138d694f8e1e06e353d97b211215f https://github.com/galaxyproject/galaxy/commit/0cbaf3b8c57138d694f8e1e06e35… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use proper PEP-440 local version identifiers for modified dependencies. Commit: 4a5f5f44dc09be5194c9ee4ebc6b0b6a4a057480 https://github.com/galaxyproject/galaxy/commit/4a5f5f44dc09be5194c9ee4ebc6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install our modified pip as a wheel from wheels.galaxyproject.org rather than an editable directly from github. Also, use `set -e` in scripts/common_startup.sh to fail if anything fails, rather than chaining a bunch of things with `&&` but not properly handling failure cases. Commit: 737596413f88174edc24345282aee9a1c1b53cac https://github.com/galaxyproject/galaxy/commit/737596413f88174edc24345282ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M run.sh Log Message: ----------- Pass relevant args from run.sh to common_startup.sh. Commit: 88683c3c40821581d80b3e984da486032c746c06 https://github.com/galaxyproject/galaxy/commit/88683c3c40821581d80b3e984da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is provided. Commit: e423ab6246088fec6a41c31fb67bc34c0ff40a89 https://github.com/galaxyproject/galaxy/commit/e423ab6246088fec6a41c31fb67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M create_db.sh R dist-eggs.ini R eggs.ini M lib/galaxy/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/util/gff_util.py A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/template.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py R lib/pkg_resources.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M manage_db.sh M manage_tools.sh M requirements.txt M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py R scripts/check_eggs.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py R scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py R scripts/fetch_eggs.py M scripts/functional_tests.py R scripts/make_egg_packager.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py M scripts/summarize_timings.py R scripts/test_dist_egg.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M set_metadata.sh M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Merge pull request #428 from natefoo/smash_eggs Replace eggs with wheels Compare: https://github.com/galaxyproject/galaxy/compare/112c0390d586...e423ab624608

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[galaxyproject/galaxy] c3db6a: Fix grid batch operations. This should correctly ...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3db6af560b86f1fcfccb52e4241f756d836cce1 https://github.com/galaxyproject/galaxy/commit/c3db6af560b86f1fcfccb52e4241… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. Commit: 6260bd1d0f370ed4fd3b7a00ba76b0efcd5e9221 https://github.com/galaxyproject/galaxy/commit/6260bd1d0f370ed4fd3b7a00ba76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Strip whitespace in grid-view.js Commit: 112c0390d586c5d53802e8e67e8b0a98093b364e https://github.com/galaxyproject/galaxy/commit/112c0390d586c5d53802e8e67e8b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #971 from dannon/grid_batch_fixes Grid batch operation fixes Compare: https://github.com/galaxyproject/galaxy/compare/eca98ec82815...112c0390d586

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[galaxyproject/usegalaxy-playbook] 828b68: update mutable confs for Test (installed new deept...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 828b682e63b56109ecaea0c42849ac09c6d278a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/828b682e63b56109… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: 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/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update mutable confs for Test (installed new deeptools)

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[galaxyproject/galaxy] bad9cc: Update dynatree to what will be the final release; ...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bad9cce30f3f4079a6ee11e4b6ca2dbd823702de https://github.com/galaxyproject/galaxy/commit/bad9cce30f3f4079a6ee11e4b6ca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M static/maps/libs/jquery/jquery.dynatree.js.map M static/scripts/libs/jquery/jquery.dynatree.js R static/style/blue/dynatree_skin/cbChecked.gif R static/style/blue/dynatree_skin/cbChecked_hover.gif R static/style/blue/dynatree_skin/cbIntermediate.gif R static/style/blue/dynatree_skin/cbIntermediate_hover.gif R static/style/blue/dynatree_skin/cbUnchecked.gif R static/style/blue/dynatree_skin/cbUnchecked_hover.gif R static/style/blue/dynatree_skin/customDoc1.gif R static/style/blue/dynatree_skin/customFolder1.gif A static/style/blue/dynatree_skin/icons-rtl.gif A static/style/blue/dynatree_skin/icons.gif A static/style/blue/dynatree_skin/loading.gif R static/style/blue/dynatree_skin/ltD_ne.gif R static/style/blue/dynatree_skin/ltD_nes.gif R static/style/blue/dynatree_skin/ltDoc.gif R static/style/blue/dynatree_skin/ltError.gif R static/style/blue/dynatree_skin/ltFld.gif R static/style/blue/dynatree_skin/ltFld_o.gif R static/style/blue/dynatree_skin/ltL_.gif R static/style/blue/dynatree_skin/ltL_ne.gif R static/style/blue/dynatree_skin/ltL_nes.gif R static/style/blue/dynatree_skin/ltL_ns.gif R static/style/blue/dynatree_skin/ltM_ne.gif R static/style/blue/dynatree_skin/ltM_nes.gif R static/style/blue/dynatree_skin/ltP_ne.gif R static/style/blue/dynatree_skin/ltP_nes.gif R static/style/blue/dynatree_skin/ltWait.gif R static/style/blue/dynatree_skin/rbChecked.gif R static/style/blue/dynatree_skin/rbChecked_hover.gif R static/style/blue/dynatree_skin/rbIntermediate.gif R static/style/blue/dynatree_skin/rbIntermediate_hover.gif R static/style/blue/dynatree_skin/rbUnchecked.gif R static/style/blue/dynatree_skin/rbUnchecked_hover.gif M static/style/blue/dynatree_skin/ui.dynatree.css A static/style/blue/dynatree_skin/vline-rtl.gif A static/style/blue/dynatree_skin/vline.gif Log Message: ----------- Update dynatree to what will be the final release; we probably want to just replace it at some point. Commit: 54ee8cfdc0a3560f5cbffacdd121272d730d35d7 https://github.com/galaxyproject/galaxy/commit/54ee8cfdc0a3560f5cbffacdd121… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Update old dynatree usage to 1.0 standards, clean up some of the extra-chatty debugging and an invalid ajaxComplete attachment that we don't need. Commit: eca98ec828158ef30af06aac8ecee91b204f2759 https://github.com/galaxyproject/galaxy/commit/eca98ec828158ef30af06aac8ece… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M static/maps/libs/jquery/jquery.dynatree.js.map M static/scripts/libs/jquery/jquery.dynatree.js R static/style/blue/dynatree_skin/cbChecked.gif R static/style/blue/dynatree_skin/cbChecked_hover.gif R static/style/blue/dynatree_skin/cbIntermediate.gif R static/style/blue/dynatree_skin/cbIntermediate_hover.gif R static/style/blue/dynatree_skin/cbUnchecked.gif R static/style/blue/dynatree_skin/cbUnchecked_hover.gif R static/style/blue/dynatree_skin/customDoc1.gif R static/style/blue/dynatree_skin/customFolder1.gif A static/style/blue/dynatree_skin/icons-rtl.gif A static/style/blue/dynatree_skin/icons.gif A static/style/blue/dynatree_skin/loading.gif R static/style/blue/dynatree_skin/ltD_ne.gif R static/style/blue/dynatree_skin/ltD_nes.gif R static/style/blue/dynatree_skin/ltDoc.gif R static/style/blue/dynatree_skin/ltError.gif R static/style/blue/dynatree_skin/ltFld.gif R static/style/blue/dynatree_skin/ltFld_o.gif R static/style/blue/dynatree_skin/ltL_.gif R static/style/blue/dynatree_skin/ltL_ne.gif R static/style/blue/dynatree_skin/ltL_nes.gif R static/style/blue/dynatree_skin/ltL_ns.gif R static/style/blue/dynatree_skin/ltM_ne.gif R static/style/blue/dynatree_skin/ltM_nes.gif R static/style/blue/dynatree_skin/ltP_ne.gif R static/style/blue/dynatree_skin/ltP_nes.gif R static/style/blue/dynatree_skin/ltWait.gif R static/style/blue/dynatree_skin/rbChecked.gif R static/style/blue/dynatree_skin/rbChecked_hover.gif R static/style/blue/dynatree_skin/rbIntermediate.gif R static/style/blue/dynatree_skin/rbIntermediate_hover.gif R static/style/blue/dynatree_skin/rbUnchecked.gif R static/style/blue/dynatree_skin/rbUnchecked_hover.gif M static/style/blue/dynatree_skin/ui.dynatree.css A static/style/blue/dynatree_skin/vline-rtl.gif A static/style/blue/dynatree_skin/vline.gif M templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #856 from dannon/dynatree_upgrade Dynatree upgrade Compare: https://github.com/galaxyproject/galaxy/compare/1c527d37849f...eca98ec82815

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[galaxyproject/galaxy] 951a4e: Initial outline of issue handling, project plannin...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 951a4e123ba70b024911fa4f001960954fd39e91 https://github.com/galaxyproject/galaxy/commit/951a4e123ba70b024911fa4f0019… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M CONTRIBUTING.md A project/CONTRIBUTING.md A project/ISSUES.md A project/ROADMAP.md Log Message: ----------- Initial outline of issue handling, project planning, and roadmap approach using GitHub. Commit: ecde79bbe9b96925dc03824c333cd2038e82bb5a https://github.com/galaxyproject/galaxy/commit/ecde79bbe9b96925dc03824c333c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M CONTRIBUTING.md R project/CONTRIBUTING.md Log Message: ----------- Move CONTRIBUTING.md back, changed my mind. Commit: 021e1006662d254785a5b3da6a36c4107b310926 https://github.com/galaxyproject/galaxy/commit/021e1006662d254785a5b3da6a36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Updates based on feedback, some tweaking of states to not have a duplicate 'triage' tag. Commit: 578263cc4a91fe1c971fdbe3d95d2d48a1bb9e4d https://github.com/galaxyproject/galaxy/commit/578263cc4a91fe1c971fdbe3d95d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Fix duplicate 'good enough' Commit: de4f4b2d15920c4cd65bc8a5cbe35d19490bd9e6 https://github.com/galaxyproject/galaxy/commit/de4f4b2d15920c4cd65bc8a5cbe3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Fix one more focus/area swap. Commit: a3eca0fd30e67c85b43b51403b131ab7a8f66308 https://github.com/galaxyproject/galaxy/commit/a3eca0fd30e67c85b43b51403b13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Add refactoring 'kind' Commit: 11b450e84c17ad8c45af533087a7f44671bdcd96 https://github.com/galaxyproject/galaxy/commit/11b450e84c17ad8c45af533087a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Remove status/new as it is redundant with triage. Commit: b7266846e99fc9c25e9de2b28b617e2b0a6ae564 https://github.com/galaxyproject/galaxy/commit/b7266846e99fc9c25e9de2b28b61… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Clean up some more language that was editorial in nature and, while useful for context, shouldn't be part of the final doc. Commit: b71de2503ab259c0ad8853c20a1741a9f9f1393d https://github.com/galaxyproject/galaxy/commit/b71de2503ab259c0ad8853c20a17… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Add section detailing the process for deferring issues. Commit: 30d7d2fec3bf5447accad86e0b5f2a18d91b5b8d https://github.com/galaxyproject/galaxy/commit/30d7d2fec3bf5447accad86e0b5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Move documentation from kind to area. Drop test as an area since it is a kind. Commit: efb0661c6d899624fc3090ef37c7a7a988dbb7cf https://github.com/galaxyproject/galaxy/commit/efb0661c6d899624fc3090ef37c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Add tests kind/tests label. Commit: c38da9de3c7d8fb7445128514d795c126cf1010a https://github.com/galaxyproject/galaxy/commit/c38da9de3c7d8fb7445128514d79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Standardize on lowercase'd tags Commit: 0fde68aa5e93e5116f6fa3a7fd9ce66e44f159d7 https://github.com/galaxyproject/galaxy/commit/0fde68aa5e93e5116f6fa3a7fd9c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- kind/tests -> kind/testing Commit: 86d0db5b147e98c3a29bd6c76bf98537b5508946 https://github.com/galaxyproject/galaxy/commit/86d0db5b147e98c3a29bd6c76bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M project/ISSUES.md R project/ROADMAP.md Log Message: ----------- Kill ROADMAP.md Commit: fe984c5c39bf1e94a8cd623b41e3a6eb4766c468 https://github.com/galaxyproject/galaxy/commit/fe984c5c39bf1e94a8cd623b41e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M project/ISSUES.md Log Message: ----------- Merge pull request #6 from jmchilton/doc_to_area Move documentation from kind to area. Commit: f7a97e35e55cf704da6d5c2a2ccca1428ac53522 https://github.com/galaxyproject/galaxy/commit/f7a97e35e55cf704da6d5c2a2ccc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A doc/source/project/ISSUES.md R project/ISSUES.md Log Message: ----------- Relocate issues.md to docs Commit: 05c5ecdd59c9e6c9f99b0eebd6085610b7902116 https://github.com/galaxyproject/galaxy/commit/05c5ecdd59c9e6c9f99b0eebd608… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: R doc/source/project/ISSUES.md A doc/source/project/issues.rst Log Message: ----------- Swap from markdown to rst, since it's in docs now. Gross. Commit: a4e69f44cd59a7028c47690413642d055143ae92 https://github.com/galaxyproject/galaxy/commit/a4e69f44cd59a7028c4769041364… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Add reference to organization document regarding 'procedures' tag. Commit: 614ec9de90651945480e50792368f217d6123e54 https://github.com/galaxyproject/galaxy/commit/614ec9de90651945480e50792368… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/index.rst M doc/source/project/issues.rst Log Message: ----------- Add 'project' documents to the actual documentation tree. Commit: 02183910cff1776a624c5559b2d633ecd36379aa https://github.com/galaxyproject/galaxy/commit/02183910cff1776a624c5559b2d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Add major/minor 'extra' tags proposed by @jmchilton for release notes management. Commit: 1c527d37849f173e0a34125d2f1739b437f3c0cc https://github.com/galaxyproject/galaxy/commit/1c527d37849f173e0a34125d2f17… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M doc/source/index.rst A doc/source/project/issues.rst Log Message: ----------- Merge pull request #902 from dannon/issue_management New policies for bug and issue handling, and roadmap management. Compare: https://github.com/galaxyproject/galaxy/compare/53f924fbaf07...1c527d37849f

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[galaxyproject/usegalaxy-playbook] 50d310: enable enable_beta_tool_command_isolation: "True" ...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 50d3106671eb8b4d7032cc4c35293583383f2521 https://github.com/galaxyproject/usegalaxy-playbook/commit/50d3106671eb8b4d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- enable enable_beta_tool_command_isolation: "True" on Test

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