[galaxy-commits] [galaxyproject/galaxy] 8b630d: Update galaxy.jobs.runners.util from pulsar.manage...

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b630d6d6c121659c1f93f9b51df8ccc8871b83a https://github.com/galaxyproject/galaxy/commit/8b630d6d6c121659c1f93f9b51df8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py Log Message: ----------- Update galaxy.jobs.runners.util from pulsar.managers.util Commit: c46c7e082768ecd1c11fe20d3639ee5ada0ab61b https://github.com/galaxyproject/galaxy/commit/c46c7e082768ecd1c11fe20d3639e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: A .ci/flake8_blacklist.txt A .ci/flake8_wrapper.sh M .gitignore A .travis.yml A CODE_OF_CONDUCT.md M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js A client/README.md R client/README.txt M client/bower.json M client/galaxy/scripts/base.js M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/backbone/backbone.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/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/lunr.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/citation/citation-view.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js A client/galaxy/scripts/mvc/collection/collection-panel-edit.js M client/galaxy/scripts/mvc/collection/collection-panel.js A client/galaxy/scripts/mvc/collection/list-collection-creator.js A client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js A client/galaxy/scripts/mvc/collection/pair-collection-creator.js R client/galaxy/scripts/mvc/collection/paired-collection-creator.js M client/galaxy/scripts/mvc/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js A client/galaxy/scripts/mvc/form/form-data.js A client/galaxy/scripts/mvc/form/form-input.js A client/galaxy/scripts/mvc/form/form-parameters.js A client/galaxy/scripts/mvc/form/form-repeat.js A client/galaxy/scripts/mvc/form/form-section.js A client/galaxy/scripts/mvc/form/form-select-content.js A client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M 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client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-content.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/tools/tools-input.js M client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-parameters.js R client/galaxy/scripts/mvc/tools/tools-repeat.js R client/galaxy/scripts/mvc/tools/tools-section.js R client/galaxy/scripts/mvc/tools/tools-select-content.js M client/galaxy/scripts/mvc/tools/tools-template.js R client/galaxy/scripts/mvc/tools/tools-tree.js A client/galaxy/scripts/mvc/ui/error-modal.js R 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client/galaxy/style/less/upload.less A client/galaxy/style/source_material/circle.py A client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/galaxy_spinner.fla A client/grunt-tasks/install-libs.js A client/grunt-tasks/scripts.js A client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js A client/toolshed/scripts/toolshed.groups.js A 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/object_store_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M 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config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/circster/config/circster.xml A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/graphview/config/graphview.xml A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/reports_wsgi.ini.sample M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample M config/tool_sheds_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M create_db.sh M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml A display_applications/igv/gff.xml A display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml R dist-eggs.ini M doc/patch.py A doc/source/_static/style.css A doc/source/_templates/layout.html A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg A doc/source/admin/interactive_environments_success.png A doc/source/admin/useful_scripts.rst A doc/source/api/guidelines.rst A doc/source/api/quickstart.rst A 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 R doc/source/lib/fpconst.rst M doc/source/lib/galaxy.actions.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst A 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tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py 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/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/validation/fix_errors.xml M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge branch 'dev' into pulsar-client-update Commit: 1e2863dd1c7db1020ceba0a0cffb77c771c7e788 https://github.com/galaxyproject/galaxy/commit/1e2863dd1c7db1020ceba0a0cffb7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py A lib/galaxy/tools/linters/xsd.py A lib/galaxy/tools/linters/xsd_util.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge linting and tool loader changes from Planemo Commit: 36eb1142c4c9bae876185d79f5d7229bf08c0b8d https://github.com/galaxyproject/galaxy/commit/36eb1142c4c9bae876185d79f5d72... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/tools/linters/tests.py Log Message: ----------- PEP-8 fix for linters Commit: a9d79b34e65c914e569bc1713ee82dd8877c2d6f https://github.com/galaxyproject/galaxy/commit/a9d79b34e65c914e569bc1713ee82... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge Planemo and Galaxy tools.deps changes (and a PEP-8 fix) Commit: 12fdd3f9d5758f8957d57591c4bbd777bd1d5723 https://github.com/galaxyproject/galaxy/commit/12fdd3f9d5758f8957d57591c4bbd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py Log Message: ----------- Correct a mistakenly reformatted comment. Inline isn't possible because hanging an inline violates E113 (although PEP-8 does not explicitly say it's not allowed, but it does say "An inline comment is a comment on the same line as a statement"), so convert the comments to block. Commit: a1726d205d167a8eb30de427d56b81fdd7529397 https://github.com/galaxyproject/galaxy/commit/a1726d205d167a8eb30de427d56b8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Python 3-ify the object store (from Pulsar, for Planemo) Commit: aefc35ae0309d7a9a4418cdf479821e07e154fbd https://github.com/galaxyproject/galaxy/commit/aefc35ae0309d7a9a4418cdf47982... Author: John Chilton <jmchilton@gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: R lib/galaxy/tools/linters/xsd.py R lib/galaxy/tools/linters/xsd_util.py Log Message: ----------- Remove old XSD linting code. Commit: 45e3257f04b3a3858f0a4f6298076d1f91acc712 https://github.com/galaxyproject/galaxy/commit/45e3257f04b3a3858f0a4f6298076... Author: John Chilton <jmchilton@gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py Log Message: ----------- Restore changes to tool shed package resolver. Commit: 4e9e9a17d1dfd322ffbcb2ecebc184fe5538ec7e https://github.com/galaxyproject/galaxy/commit/4e9e9a17d1dfd322ffbcb2ecebc18... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py R lib/galaxy/tools/linters/xsd.py R lib/galaxy/tools/linters/xsd_util.py Log Message: ----------- Merge pull request #1 from jmchilton/pulsar-planemo-lib-update Remove old XSD linting code. Commit: 99319f59c88715e74290267d93018d1f172512ca https://github.com/galaxyproject/galaxy/commit/99319f59c88715e74290267d93018... Author: John Chilton <jmchilton@gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge pull request #1005 from natefoo/pulsar-planemo-lib-update Merge changes to common modules shared between Galaxy, Planemo, and Pulsar. Compare: https://github.com/galaxyproject/galaxy/compare/cbc8c44f60b4...99319f59c887