- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] dcb302: Fix copypasta.
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dcb3023ba8390105c1eca869c3be4958fd40036d https://github.com/galaxyproject/usegalaxy-playbook/commit/dcb3023ba8390105… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Fix copypasta.

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[galaxyproject/usegalaxy-playbook] 818b92: Add sanitize_whitelist files to mutable configs.
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 818b9203aced5ea74568b6c00c39f79abda2c7cb https://github.com/galaxyproject/usegalaxy-playbook/commit/818b9203aced5ea7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Add sanitize_whitelist files to mutable configs.

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[galaxyproject/infrastructure-playbook] 910371: Update common_roles
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 910371e63e950a4c737c0a6ddb67af72786556a9 https://github.com/galaxyproject/infrastructure-playbook/commit/910371e63e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: 9ccfe62f803c62f03fe66cbda8fbb7356133a91d https://github.com/galaxyproject/infrastructure-playbook/commit/9ccfe62f803… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: A galaxyenv/host_vars/mjolnir0.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml M playbook.yml Log Message: ----------- Add mjolnir0, a starforge builder Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/cf8a746f22…

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[galaxyproject/galaxy] 4fc500: Fixes broken env-var declarations for tools with w...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fc500a5c9eaddbb1cb1ae420fe2b2c19d206446 https://github.com/galaxyproject/galaxy/commit/4fc500a5c9eaddbb1cb1ae420fe2… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fixes broken env-var declarations for tools with weird chars in their name Commit: 8c0b9468a20ad20530ad290136fab351fca306d3 https://github.com/galaxyproject/galaxy/commit/8c0b9468a20ad20530ad290136fa… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Replacement of dots Commit: afa65f4d9a3684f4870815709e852927e34bfdb9 https://github.com/galaxyproject/galaxy/commit/afa65f4d9a3684f4870815709e85… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1028 from yhoogstrate/step_handler_fix Fixes broken env-var declarations for tools with weird chars in their… Compare: https://github.com/galaxyproject/galaxy/compare/1649570e7806...afa65f4d9a36

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[galaxyproject/galaxy] 0fe684: Fix upload button style
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fe684c688a86a0f8398191e66794f22adf5cf5d https://github.com/galaxyproject/galaxy/commit/0fe684c688a86a0f8398191e6679… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-button.js.map M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css Log Message: ----------- Fix upload button style More fixes Commit: 1649570e7806315a235b4e9799a74e6e3e16887f https://github.com/galaxyproject/galaxy/commit/1649570e7806315a235b4e9799a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-button.js.map M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css Log Message: ----------- Rebuild client styles, merge. Compare: https://github.com/galaxyproject/galaxy/compare/4d05a5a3ed02...1649570e7806

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[galaxyproject/galaxy] 5c56ec: Fix style of labels in grids
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c56ec8bc7ef580259982d5b775b468622464e57 https://github.com/galaxyproject/galaxy/commit/5c56ec8bc7ef580259982d5b775b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/less/base.less M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js M static/style/blue/base.css Log Message: ----------- Fix style of labels in grids Fix styles Pack styles Commit: 4d05a5a3ed029abca962288ca997823c52a46bcc https://github.com/galaxyproject/galaxy/commit/4d05a5a3ed029abca962288ca997… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/less/base.less M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1027 from guerler/fix_grids_000 Fix style of menu button labels in grids Compare: https://github.com/galaxyproject/galaxy/compare/53ee0f0a8913...4d05a5a3ed02

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[galaxyproject/galaxy] 5c7dd7: Refactor test dataset populator for reuse on jobs ...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c7dd75fd0d8ee6edce98e277e7ef6215f85f92c https://github.com/galaxyproject/galaxy/commit/5c7dd75fd0d8ee6edce98e277e7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Refactor test dataset populator for reuse on jobs without outputs. Commit: ac0cfbd2e32944d0f71eda877d1e8767a86d7cb3 https://github.com/galaxyproject/galaxy/commit/ac0cfbd2e32944d0f71eda877d1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M run.sh Log Message: ----------- Add a quick shortcut for starting Galaxy with development tools. Start Galaxy using GALAXY_RUN_WITH_TEST_TOOLS=1 run.sh Enables beta tool formats (e.g. YAML, and CWL downstream), beta workflow modules, and the suite of Galaxy test tools used by testing framework. Commit: 53ee0f0a8913585e54d6ca59da79130196d31164 https://github.com/galaxyproject/galaxy/commit/53ee0f0a8913585e54d6ca59da79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M run.sh M test/api/helpers.py Log Message: ----------- Merge pull request #1014 from jmchilton/cwl_util Two Small Tweaks from CWL Branch Compare: https://github.com/galaxyproject/galaxy/compare/593cb4074b5f...53ee0f0a8913

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[galaxyproject/galaxy] 2e21e0: Insert promises
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e21e027b0b47b18ca7b1aac68d89ccbd16f2d2c https://github.com/galaxyproject/galaxy/commit/2e21e027b0b47b18ca7b1aac68d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/tools/tools-form-base.js.map M static/maps/utils/deferred.js.map M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Insert promises Revision Revise deferred class to use promises Update charts Fix comment Use resolve and reject properly Fix comments Fix comments Fix comments Fix comment Improve naming/comments Remove unnecessary queue handler Fix naming Commit: f1f5efe703cc25a63426fa5cf709ab410e19652f https://github.com/galaxyproject/galaxy/commit/f1f5efe703cc25a63426fa5cf709… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix display call Fix config Fix naming Commit: cc4e8e4a34aa8ffdaa6fc357c226164571fd384d https://github.com/galaxyproject/galaxy/commit/cc4e8e4a34aa8ffdaa6fc357c226… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst 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/managers/configuration.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.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 M lib/galaxy/web/framework/webapp.py M lib/pulsar/client/transport/curl.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 scripts/tools/maf/check_loc_file.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M static/welcome.html.sample M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_promise_000 Commit: 142db64fb3ba6d694007485da8b64803db762309 https://github.com/galaxyproject/galaxy/commit/142db64fb3ba6d694007485da8b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Use remove instead of empty if iframe is shown Commit: 593cb4074b5fc2d58685bae8831c621c16831e53 https://github.com/galaxyproject/galaxy/commit/593cb4074b5fc2d58685bae8831c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/utils/deferred.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Merge pull request #1018 from guerler/revise_promise_000 Revise deferred queue, use jQuery promises Compare: https://github.com/galaxyproject/galaxy/compare/86648d23e2fe...593cb4074b5f

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[galaxyproject/galaxy] a9ac91: Client logging: adapt metrics logger for optional ...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9ac9193c1bda03d45df7afd9aefec9898cf684b https://github.com/galaxyproject/galaxy/commit/a9ac9193c1bda03d45df7afd9aef… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/utils/add-logging.js M static/maps/galaxy-app-base.js.map M static/maps/utils/add-logging.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/utils/add-logging.js M templates/galaxy_client_app.mako Log Message: ----------- Client logging: adapt metrics logger for optional debug logging Commit: d96fc60e1f84606a33f5b86a915bc9768a2eaa4e https://github.com/galaxyproject/galaxy/commit/d96fc60e1f84606a33f5b86a915b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/utils/metrics-logger.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/base-mvc.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/utils/metrics-logger.js Log Message: ----------- Client logging: allow focusing on one or more namespaces, add function to more easily namespace loggers Commit: 945f3690038fbe744465eb34074447c307aa467e https://github.com/galaxyproject/galaxy/commit/945f3690038fbe744465eb340744… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.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 M client/galaxy/scripts/mvc/collection/collection-panel.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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-content-model.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.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-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/tags.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Client logging: namespace current loggables Commit: b75150ade7aad1a3e8e3b120e1f4a6d9f0929a23 https://github.com/galaxyproject/galaxy/commit/b75150ade7aad1a3e8e3b120e1f4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/metrics-logger.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/utils/add-logging.js M static/scripts/utils/metrics-logger.js Log Message: ----------- Client logging: remove 'namespaced', allow 'log' to be added in the standard way (now that browsers are compat with this), simplify interface in the Galaxy object Commit: 0a8ea970030f9d7e106f9e55405af5d40929edd2 https://github.com/galaxyproject/galaxy/commit/0a8ea970030f9d7e106f9e55405a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into logging: attempting to fix qunit failures Commit: b67601f74c9a0fa1dd07764dc8a4c4b0f70f512b https://github.com/galaxyproject/galaxy/commit/b67601f74c9a0fa1dd07764dc8a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/utils/add-logging.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/utils/add-logging.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/utils/add-logging.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Client logging: move logger assignment into Galaxy object, both Galaxy.user and all LoggableMixins will now respond to debugging, properly localize error messages Commit: 86648d23e2fe34893728c859c2559836eb55c752 https://github.com/galaxyproject/galaxy/commit/86648d23e2fe34893728c859c255… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.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 M client/galaxy/scripts/mvc/collection/collection-panel.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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-content-model.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.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-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/tags.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/metrics-logger.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/utils/add-logging.js M static/scripts/utils/metrics-logger.js M templates/galaxy_client_app.mako M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Merge pull request #1011 from carlfeberhard/logging Client side logging Compare: https://github.com/galaxyproject/galaxy/compare/9fd0bd1cc112...86648d23e2fe

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[galaxyproject/galaxy] 9e0973: Labels for individual tools in tool panel.
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e0973d7203ba36d5f3f37357d6cea6e603ba465 https://github.com/galaxyproject/galaxy/commit/9e0973d7203ba36d5f3f37357d6c… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-10-31 (Sat, 31 Oct 2015) Changed paths: M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/galaxy.library.js.map M static/maps/templates/compiled/tool_link.js.map M static/scripts/galaxy.library.js M static/scripts/templates/compiled/tool_link.js M static/style/blue/base.css Log Message: ----------- Labels for individual tools in tool panel. Allow one or more labels to be attached to a tool in the tool panel. These will be rendered to the right of the tool's link using the boostrap label style. Styles for specific labels can be defined in CSS, specific colored labels for "new" and "beta" are defined. Commit: f920dec0c277e8301bf8392d638757a70a441dc7 https://github.com/galaxyproject/galaxy/commit/f920dec0c277e8301bf8392d6387… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-10-31 (Sat, 31 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/search/__init__.py Log Message: ----------- Make toolbox searchable by tool labels. Commit: 9fd0bd1cc112811b10a9a16ae47bf76eef6eaaff https://github.com/galaxyproject/galaxy/commit/9fd0bd1cc112811b10a9a16ae47b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/templates/compiled/tool_link.js.map M static/scripts/templates/compiled/tool_link.js M static/style/blue/base.css Log Message: ----------- Manual merge and rebuild due to conflict. Compare: https://github.com/galaxyproject/galaxy/compare/269ed53fcdc6...9fd0bd1cc112

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[galaxyproject/galaxy] a0f65d: Apply stricter flake8 rules for the directories sh...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0f65d02866a463f9bdbf94919208212a9e441d0 https://github.com/galaxyproject/galaxy/commit/a0f65d02866a463f9bdbf9491920… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Apply stricter flake8 rules for the directories shared with Pulsar Commit: 269ed53fcdc68854a35a995c6793435d45f9d0e3 https://github.com/galaxyproject/galaxy/commit/269ed53fcdc68854a35a995c6793… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Merge pull request #1010 from nsoranzo/flake8_fixes Apply stricter flake8 rules for the directories shared with Pulsar Compare: https://github.com/galaxyproject/galaxy/compare/c78898932dac...269ed53fcdc6

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[galaxyproject/galaxy] 0e6033: Replace remaining print statements with log.*
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e60332f449609a43a49b7d33ec64bf53663befd https://github.com/galaxyproject/galaxy/commit/0e60332f449609a43a49b7d33ec6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Replace remaining print statements with log.* Commit: 5396426609b334c4fb68eb1a04baf3426e957033 https://github.com/galaxyproject/galaxy/commit/5396426609b334c4fb68eb1a04ba… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/tool_shed/app.py M lib/tool_shed/galaxy_install/tool_migration_manager.py Log Message: ----------- Fix flake8 errors, @nsoranzo Commit: c78898932dac835f07515cd291aeab37b4eb1b0c https://github.com/galaxyproject/galaxy/commit/c78898932dac835f07515cd291ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #1009 from erasche/print-logging Replace remaining print statements with log.* Compare: https://github.com/galaxyproject/galaxy/compare/99319f59c887...c78898932dac

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[galaxyproject/galaxy] d20677: Fix Remote User failures due to apache null header...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: d20677bb640de726574ae7f3e8d86739a8702cb5 https://github.com/galaxyproject/galaxy/commit/d20677bb640de726574ae7f3e8d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix Remote User failures due to apache null headers. Commit: 3b8edf6aebfb10d1b52b57701eb4cb07558e9c9e https://github.com/galaxyproject/galaxy/commit/3b8edf6aebfb10d1b52b57701eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #1003 from dannon/remote_user_apache_fix [15.10] Fix Remote User failures due to apache null headers. Compare: https://github.com/galaxyproject/galaxy/compare/3b133d0d9206...3b8edf6aebfb

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[galaxyproject/usegalaxy-playbook] 58fab7: Add Dan to reserved node users
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 58fab7545f5b61a23f61dbd0788379f04ba9bbf3 https://github.com/galaxyproject/usegalaxy-playbook/commit/58fab7545f5b61a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Add Dan to reserved node users

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[galaxyproject/usegalaxy-playbook] f2cff9: Updated slide rotation.
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f2cff9c9f1700c23e2280bde7b1b0578386df261 https://github.com/galaxyproject/usegalaxy-playbook/commit/f2cff9c9f1700c23… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016TrVote.png A files/galaxy/common/static/welcome_img/MississippiGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation.

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[galaxyproject/infrastructure-playbook] 01cd5c: Update common roles.
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 01cd5c650d6be4c6f75934de976e157826d74279 https://github.com/galaxyproject/infrastructure-playbook/commit/01cd5c650d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M common_roles Log Message: ----------- Update common roles. Commit: cf8a746f22e3596590a675729df9575f541cf504 https://github.com/galaxyproject/infrastructure-playbook/commit/cf8a746f22e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M common_roles A galaxyenv/group_vars/baseenv.yml M galaxyenv/host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- depot stuff I forgot to commit + add Dannon to sites@orval Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/577c599fa6…

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[galaxyproject/galaxy] 8b630d: Update galaxy.jobs.runners.util from pulsar.manage...
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b630d6d6c121659c1f93f9b51df8ccc8871b83a https://github.com/galaxyproject/galaxy/commit/8b630d6d6c121659c1f93f9b51df… Author: Nate Coraor <nate(a)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/c46c7e082768ecd1c11fe20d3639… Author: Nate Coraor <nate(a)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 client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.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-annotated.js M client/galaxy/scripts/mvc/history/history-panel-edit-current.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/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.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/library/library-library-view.js M 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 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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/1e2863dd1c7db1020ceba0a0cffb… Author: Nate Coraor <nate(a)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/36eb1142c4c9bae876185d79f5d7… Author: Nate Coraor <nate(a)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/a9d79b34e65c914e569bc1713ee8… Author: Nate Coraor <nate(a)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/12fdd3f9d5758f8957d57591c4bb… Author: Nate Coraor <nate(a)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/a1726d205d167a8eb30de427d56b… Author: Nate Coraor <nate(a)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/aefc35ae0309d7a9a4418cdf4798… Author: John Chilton <jmchilton(a)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/45e3257f04b3a3858f0a4f629807… Author: John Chilton <jmchilton(a)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/4e9e9a17d1dfd322ffbcb2ecebc1… Author: Nate Coraor <nate(a)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/99319f59c88715e74290267d9301… Author: John Chilton <jmchilton(a)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

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[galaxyproject/galaxy] 602d05: Log TS installation commands with repository name
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 602d05408465bb69e2594d95c5a0d479bc7f5ce1 https://github.com/galaxyproject/galaxy/commit/602d05408465bb69e2594d95c5a0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Log TS installation commands with repository name Fixes #436 Commit: 7813148d9a09198d1d00d4326403adf0aa1f2250 https://github.com/galaxyproject/galaxy/commit/7813148d9a09198d1d00d4326403… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix review comments Commit: cbc8c44f60b45c8cefb0c34fa9abc9c5aa067af9 https://github.com/galaxyproject/galaxy/commit/cbc8c44f60b45c8cefb0c34fa9ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1008 from erasche/installation_logging Log TS installation commands with repository name Compare: https://github.com/galaxyproject/galaxy/compare/f406cdefc79e...cbc8c44f60b4

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[galaxyproject/galaxy] 9c2a07: Add run_framework_tests.html to .gitignore .
by GitHub 02 Nov '15

02 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c2a07d4242110642da7ca7f28eca772e8342acb https://github.com/galaxyproject/galaxy/commit/9c2a07d4242110642da7ca7f28ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M .gitignore Log Message: ----------- Add run_framework_tests.html to .gitignore . Commit: 3c7082c64a31fa8a0296d5655039ed772d4de3b0 https://github.com/galaxyproject/galaxy/commit/3c7082c64a31fa8a0296d5655039… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst Log Message: ----------- Fix doc/source/lib using "sphinx-apidoc -M -f -o doc/source/lib/ lib/" Commit: 69cda4869051edce338e3e585345a500015b80ac https://github.com/galaxyproject/galaxy/commit/69cda4869051edce338e3e585345… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/pulsar/client/transport/curl.py M scripts/tools/maf/check_loc_file.py M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Remove remaining references to galaxy.eggs . flake8 some files in tools/ . Commit: f406cdefc79e6ecf7801b7da0dd98dad9dc43955 https://github.com/galaxyproject/galaxy/commit/f406cdefc79e6ecf7801b7da0dd9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/pulsar/client/transport/curl.py M scripts/tools/maf/check_loc_file.py M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #990 from nsoranzo/post_eggs_smash Remove remaining references to galaxy.eggs . flake8 some tools. Compare: https://github.com/galaxyproject/galaxy/compare/d9d746675a60...f406cdefc79e

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[galaxyproject/galaxy] bd95d7: Updates to default welcome page.
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd95d7672d0cf9f164abd9bcb43485c946150fa7 https://github.com/galaxyproject/galaxy/commit/bd95d7672d0cf9f164abd9bcb434… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- Updates to default welcome page. Reference CONTRIBUTORS.md, update institution references, update to HTML5, use some standard classes for formatting, include links for configuring and installling tools. Commit: 12b6d43c81c2d1dadd24248ea329b662465633fb https://github.com/galaxyproject/galaxy/commit/12b6d43c81c2d1dadd24248ea329… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- Change a.btn style, fix welcome link targets. "a" elements styled with .btn will have no underline by default. Commit: 2d60665ab503878731a4aacd8bd9873fc938281c https://github.com/galaxyproject/galaxy/commit/2d60665ab503878731a4aacd8bd9… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- Fix link target in welcome Commit: d9d746675a6072701197b2b3123b7eb51c3618f3 https://github.com/galaxyproject/galaxy/commit/d9d746675a6072701197b2b3123b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- Merge pull request #1013 from jxtx/fix-default-welcome-references Updates to default welcome page. Compare: https://github.com/galaxyproject/galaxy/compare/6b0898c32785...d9d746675a60

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[galaxyproject/galaxy] 4cbeba: Show masthead if login is required, add login page...
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cbeba4d601d16755c334c713df44370c0553600 https://github.com/galaxyproject/galaxy/commit/4cbeba4d601d16755c334c713df4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/app/app-view.js M lib/galaxy/managers/configuration.py M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Show masthead if login is required, add login page to front end Style fix Commit: 66d3289b383e34093bf14c4dc3e696c9b66b6f48 https://github.com/galaxyproject/galaxy/commit/66d3289b383e34093bf14c4dc3e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M 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-panel.js M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less M lib/galaxy/objectstore/s3.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-panel.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/root/index.mako M tools/filters/cutWrapper.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_require_login_003 Conflicts: static/maps/mvc/app/app-analysis.js.map static/scripts/mvc/app/app-analysis.js Commit: 27bde1bb1de8bf0fbd873b7dc8db215235b2126e https://github.com/galaxyproject/galaxy/commit/27bde1bb1de8bf0fbd873b7dc8db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/utils/deferred.js M create_db.sh R dist-eggs.ini M doc/source/index.rst A doc/source/project/issues.rst 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/configuration.py M lib/galaxy/managers/histories.py M 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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 A scripts/binary_compatibility.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 static/maps/galaxy.library.js.map M static/maps/libs/jquery/jquery.dynatree.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/utils/deferred.js.map M static/scripts/galaxy.library.js M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/reports_webapp/run_stats.js M static/scripts/utils/deferred.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/base/base_panels.mako M templates/webapps/tool_shed/repository/common.mako 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 tools/genomespace/genomespace_importer.xml M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_require_login_003 Conflicts: static/maps/mvc/app/app-analysis.js.map static/scripts/mvc/app/app-analysis.js Commit: f5a57b5f6ebf414fecfa2a6c325a5596fe11dd2b https://github.com/galaxyproject/galaxy/commit/f5a57b5f6ebf414fecfa2a6c325a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Undo 965 for dev Commit: bd383cc518f2f4335f3be97d50f33d66a081887f https://github.com/galaxyproject/galaxy/commit/bd383cc518f2f4335f3be97d50f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Repack scripts Commit: 6b0898c3278504f3bcac4493f7724b8e4862613e https://github.com/galaxyproject/galaxy/commit/6b0898c3278504f3bcac4493f772… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/app/app-view.js M lib/galaxy/managers/configuration.py M lib/galaxy/web/framework/webapp.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js Log Message: ----------- Merge pull request #968 from guerler/fix_require_login_003 Show masthead if login is required, add login page to front end Compare: https://github.com/galaxyproject/galaxy/compare/c8c2f96b041a...6b0898c32785

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[galaxyproject/usegalaxy-playbook] 165139: include more info at the Main's homepage
by GitHub 01 Nov '15

01 Nov '15

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 16513900e12388563df3d577c5a79c3fbc44e2bb https://github.com/galaxyproject/usegalaxy-playbook/commit/16513900e1238856… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-01 (Sun, 01 Nov 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- include more info at the Main's homepage Please reword as proper but this message is really missing and I think we should highlight it as much as possible. This is a first step. I have met so many people at #GI2015 that knew Galaxy but did not understand any of these two concepts and it would benefit them very much.

1 0

[galaxyproject/galaxy] efecf4: Change user preference datatype to text instead of...
by GitHub 30 Oct '15

30 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: efecf4e459f8bc16f3f8f51f7c55ca6e945c2a61 https://github.com/galaxyproject/galaxy/commit/efecf4e459f8bc16f3f8f51f7c55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py Log Message: ----------- Change user preference datatype to text instead of an arbitrarily limited varchar Commit: 303ee4153775e2de2109ceccd6b2dd6181de099b https://github.com/galaxyproject/galaxy/commit/303ee4153775e2de2109ceccd6b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Forgot the other commit. Commit: fb754751d99ec2d8db87a51d53b1375bef42135c https://github.com/galaxyproject/galaxy/commit/fb754751d99ec2d8db87a51d53b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Use the more abstract Text type, corresponding to what was used in the migration script. Commit: c8c2f96b041a0083a3f817e7cf716946df9ef98f https://github.com/galaxyproject/galaxy/commit/c8c2f96b041a0083a3f817e7cf71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py Log Message: ----------- Merge pull request #916 from dannon/pref_bump Change user preference datatype to text Compare: https://github.com/galaxyproject/galaxy/compare/3cf8fcc216f5...c8c2f96b041a

1 0

[galaxyproject/usegalaxy-playbook] 3d85c7: Update galaxyprojectdotorg.galaxy role to 0.6.1
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3d85c7126b951850e321d150d9379c2f8d06e429 https://github.com/galaxyproject/usegalaxy-playbook/commit/3d85c7126b951850… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml Log Message: ----------- Update galaxyprojectdotorg.galaxy role to 0.6.1

1 0

[galaxyproject/ansible-galaxy]
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/tags/0.6.1 Home: https://github.com/galaxyproject/ansible-galaxy

1 0