Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a7045c8d2102d2e6188df222e5b128b8fbe7534 https://github.com/galaxyproject/galaxy/commit/4a7045c8d2102d2e6188df222e5b1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-07-24 (Mon, 24 Jul 2017)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/less/ui.less M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/compression_utils.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tours.js M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml

Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05'

Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a4... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-09-15 (Fri, 15 Sep 2017)

Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/datatypes_conf.xml.sample M create_db.sh M extract_dataset_parts.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-select-content.js

Log Message: ----------- Merge branch 'release_17.05'

Commit: 15372f7369137b964534e9ddb8e81fb150dc2677 https://github.com/galaxyproject/galaxy/commit/15372f7369137b964534e9ddb8e81... Author: Martin Cech marten@bx.psu.edu Date: 2017-10-31 (Tue, 31 Oct 2017)

Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M Makefile M README.rst A SECURITY_POLICY.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js A client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M 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config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/reports.ini.sample A config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A config/user_preferences_extra_conf.yml.sample M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M cron/updateucsc.sh.sample M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/dependency_resolvers.rst A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst A doc/source/admin/special_topics/bug_reports.rst M 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tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini

Log Message: ----------- Merge branch 'release_17.09'

Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325fd... Author: John Chilton jmchilton@gmail.com Date: 2017-12-05 (Tue, 05 Dec 2017)

Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py

Log Message: ----------- Migrate documentation for setting up a production instance to Galaxy.

This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).

This content currently includes:

- the production configuration page - the cluster configuration page - the job configuration page - the scaling information page - the ftp configuration page - the top-level nginx page (for external auth content still linking out to the hub) - the top-level apache page (for external auth content still linking out to the hub) - the job metrics configuration page

Includes small tweaks to sphinx documentation generation.

- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs. - Use AutoStructify for better Markdown integration.

Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:

- Update the job configuration page with information about XML macros. - Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore). - Updated list of dynamic job runner configuration parameters. - Mention the ``raw`` attribute for ``env`` directives in the job configuration page. - Mention the ``total_walltime`` limit added in #3217. - Drop mentions of older URL-based job conf configuration stuff. - Mention newer Local and Paramiko based shell runners in CLI section. - Mention newer slurm job styles in CLI section. - Improved Pulsar links. - Fix dataset security link in Apache display sites config. - Update job metrics page to link to a new Github issue instead of old Trello issues.

Commit: befa077cc444115e0cac738c2bd3ee786f7425d2 https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3e... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)

Changed paths: M doc/source/admin/jobs.md

Log Message: ----------- Rework headings in jobs docs.

Thanks to comment from @erasche review.

Commit: b0c03240fd96ace2b25680e753fed0237264ec98 https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fed... Author: Martin Cech marten@bx.psu.edu Date: 2017-12-06 (Wed, 06 Dec 2017)

Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py

Log Message: ----------- Merge pull request #5135 from jmchilton/17.09_admin_docs

[17.09] Migrate documentation for setting up a production instance to Galaxy.

Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43 https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba8359... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)

Log Message: ----------- Merge pull request #5141 from jmchilton/master

[17.09] Re-merge master into release_17.09.

Commit: a901264ca74594f358b4d95862cb0ccd29346fcf https://github.com/galaxyproject/galaxy/commit/a901264ca74594f358b4d95862cb0... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)

Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py

Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/4d30b4f9cc5c...a901264ca745