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

[galaxyproject/usegalaxy-playbook] e989ab: update MTS
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e989abf5130cfc80c69b50260ce2d5a3b5f276f1 https://github.com/galaxyproject/usegalaxy-playbook/commit/e989abf5130cfc80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

1 0

[galaxyproject/galaxy] 1383ce: flake8 lib/galaxy_utils/
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1383ced0bdf55d3355a2927db42b584d3b00b15f https://github.com/galaxyproject/galaxy/commit/1383ced0bdf55d3355a2927db42b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- flake8 lib/galaxy_utils/ Commit: cb1538588d8a7632dcb29232bbad1b299173a84c https://github.com/galaxyproject/galaxy/commit/cb1538588d8a7632dcb29232bbad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #604 from nsoranzo/flake8_fixes flake8 lib/galaxy_utils/ Compare: https://github.com/galaxyproject/galaxy/compare/4459e9411b61...cb1538588d8a

1 0

[galaxyproject/galaxy] bf8d74: UI, Histories: move unhide_datasets and delete_hid...
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf8d74da29ba02c08cc1debed38dbf63a13dd686 https://github.com/galaxyproject/galaxy/commit/bf8d74da29ba02c08cc1debed38d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: move unhide_datasets and delete_hidden_datasets to the client, remove them from the web controller Commit: d20add4ff8abe54cbc15704edc0222935631c767 https://github.com/galaxyproject/galaxy/commit/d20add4ff8abe54cbc15704edc02… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- UI, Histories: use /history/view with current to replace /history, move history_as_xml to /history/as_xml Commit: ff13fb85cc46cdf8399e3477ba8808dfc6078ed5 https://github.com/galaxyproject/galaxy/commit/ff13fb85cc46cdf8399e3477ba88… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js M config/galaxy.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_manager.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/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map A static/maps/libs/jquery.sparklines.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js A static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/display_base.mako M templates/page_base.mako M templates/search/index.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge conflicts Commit: 971b96ddd6855e0e2fd61b89499a15d9e6fb3b93 https://github.com/galaxyproject/galaxy/commit/971b96ddd6855e0e2fd61b89499a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: when calling 'Delete hidden', both delete *and* unhide the datasets (preventing them from being both deleted and hidden) Commit: 3e212507defb88e91799883754d4a1d1ae8c0876 https://github.com/galaxyproject/galaxy/commit/3e212507defb88e91799883754d4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, Histories: fix view.mako json ref, remove unused import in root Commit: b0a8c6f52bfda10244e12b08ff3143c1f4ef0d45 https://github.com/galaxyproject/galaxy/commit/b0a8c6f52bfda10244e12b08ff31… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: use renderItems for batched changes in options menu Commit: 4459e9411b610ea106fe2db74d20dfd27363aa23 https://github.com/galaxyproject/galaxy/commit/4459e9411b610ea106fe2db74d20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- Merge pull request #578 from carlfeberhard/history.s-n-d Remove more history UIController methods. Compare: https://github.com/galaxyproject/galaxy/compare/d0a053608582...4459e9411b61

1 0

[galaxyproject/galaxy] c00196: Fix StockLineage.get_versions() when reverse=True ...
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c00196fd2cb4eb7f999bd2176c570b0834c81c2d https://github.com/galaxyproject/galaxy/commit/c00196fd2cb4eb7f999bd2176c57… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/tools/toolbox/lineages/stock.py Log Message: ----------- Fix StockLineage.get_versions() when reverse=True . Commit: 4b3a34f1d25cd00c12a5ee3815f609f238f83aa5 https://github.com/galaxyproject/galaxy/commit/4b3a34f1d25cd00c12a5ee3815f6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Simplify ToolVersion.get_version_ids() . Commit: 9c318ac1f7dac48e25e8b1c315c372e36dc0323e https://github.com/galaxyproject/galaxy/commit/9c318ac1f7dac48e25e8b1c315c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: d0a0536085821e667d39cc30423d7bdcbc8e5115 https://github.com/galaxyproject/galaxy/commit/d0a0536085821e667d39cc30423d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #596 from nsoranzo/lineage_fixes Tool lineage fixes. Compare: https://github.com/galaxyproject/galaxy/compare/cafe872bfb20...d0a053608582

1 0

[galaxyproject/galaxy] c938e6: Fix output collection terminal base class
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: c938e66e98512d85120c1c06d485a13000ff82c1 https://github.com/galaxyproject/galaxy/commit/c938e66e98512d85120c1c06d485… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix output collection terminal base class Commit: 79dbff19674dbe667887b92d070165ade85ae834 https://github.com/galaxyproject/galaxy/commit/79dbff19674dbe667887b92d0701… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #602 from guerler/fix_collections_000 [15.07] Fix output collection terminal base class Compare: https://github.com/galaxyproject/galaxy/compare/98ec06c7d6e4...79dbff19674d

1 0

[galaxyproject/usegalaxy-playbook] 5db56b: update tts
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5db56b63bbf67e4625fd8b85d52a95f56bb23967 https://github.com/galaxyproject/usegalaxy-playbook/commit/5db56b63bbf67e46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update tts

1 0

[galaxyproject/galaxy] 8b2387: fix regenerating repo metadata when coming from ba...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b2387a1c1772b07473170df23bf5eea2aed0e54 https://github.com/galaxyproject/galaxy/commit/8b2387a1c1772b07473170df23bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- fix regenerating repo metadata when coming from batch interface it used to create only single instalable revision (the latest) Commit: 98ec06c7d6e4d23c1e2d35fa2d04511bae8ab90c https://github.com/galaxyproject/galaxy/commit/98ec06c7d6e4d23c1e2d35fa2d04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Merge pull request #600 from martenson/ts-metadata-batch-reset [release_15.07] fix regenerating repo metadata when coming from batch interface Commit: cafe872bfb20633de770be9b2a8c6111eed75023 https://github.com/galaxyproject/galaxy/commit/cafe872bfb20633de770be9b2a8c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Merge branch 'release_15.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/635ef189df60...cafe872bfb20

1 0

[galaxyproject/usegalaxy-playbook] f1a579: Change from ssh to https for submodule
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f1a579d197ea764eb580d00f60674148eae61c51 https://github.com/galaxyproject/usegalaxy-playbook/commit/f1a579d197ea764e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M .gitmodules Log Message: ----------- Change from ssh to https for submodule

1 0

[galaxyproject/galaxy] 303597: Remove old cloudlaunch in favor of https://github....
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 303597e48a8503aac09c33910aa5482a374f06a1 https://github.com/galaxyproject/galaxy/commit/303597e48a8503aac09c33910aa5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Remove old cloudlaunch in favor of https://github.com/galaxyproject/cloudlaunch, at launch.usegalaxy.org Commit: 635ef189df60e9a1ce6e0e8c177fdc3b136da9a1 https://github.com/galaxyproject/galaxy/commit/635ef189df60e9a1ce6e0e8c177f… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge pull request #597 from dannon/no_more_cloudlaunch Remove old cloudlaunch in favor of … Compare: https://github.com/galaxyproject/galaxy/compare/369760aabe27...635ef189df60

1 0

[galaxyproject/galaxy] 8b2387: fix regenerating repo metadata when coming from ba...
by GitHub 13 Aug '15

13 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 8b2387a1c1772b07473170df23bf5eea2aed0e54 https://github.com/galaxyproject/galaxy/commit/8b2387a1c1772b07473170df23bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- fix regenerating repo metadata when coming from batch interface it used to create only single instalable revision (the latest) Commit: 98ec06c7d6e4d23c1e2d35fa2d04511bae8ab90c https://github.com/galaxyproject/galaxy/commit/98ec06c7d6e4d23c1e2d35fa2d04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Merge pull request #600 from martenson/ts-metadata-batch-reset [release_15.07] fix regenerating repo metadata when coming from batch interface Compare: https://github.com/galaxyproject/galaxy/compare/b3da771a637a...98ec06c7d6e4

1 0