March 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f0b7a3: Apply patch from Fabien Mareuil to resolve json se...
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f0b7a34dd3ea5b3b10494c7e186fb10fda30441f https://github.com/galaxyproject/galaxy/commit/f0b7a34dd3ea5b3b10494c7e186f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html Commit: 3abd2c213ae508bd3547d08729c96bbff4a5b740 https://github.com/galaxyproject/galaxy/commit/3abd2c213ae508bd3547d08729c9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge pull request #1898 from dannon/quota_api_fix_fabien [16.01] Quota API issue with serialization to JSON of Decimal Compare: https://github.com/galaxyproject/galaxy/compare/afb4e9c8f40d...3abd2c213ae5

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[galaxyproject/galaxy] 50f108: Slight tweaks to our tabix usage. This fixes trac...
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 50f1089c72ff46397e525d4aa99dc80569081509 https://github.com/galaxyproject/galaxy/commit/50f1089c72ff46397e525d4aa99d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. Commit: c6f3e9b5b28268cba1ef8d7be5f1bed90b6ecc00 https://github.com/galaxyproject/galaxy/commit/c6f3e9b5b28268cba1ef8d7be5f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight cleanup, remove outdated comment regarding tabixfile.close() Commit: a351c75687921bb8d2487577c5c4c0a64bee5e5f https://github.com/galaxyproject/galaxy/commit/a351c75687921bb8d2487577c5c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Extra documentation for @mvdbeek Commit: afb4e9c8f40da5331412c2a8f83ece814fb54b05 https://github.com/galaxyproject/galaxy/commit/afb4e9c8f40da5331412c2a8f83e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1897 from dannon/pysam_compat [16.01] Slight tweaks to our tabix usage. Compare: https://github.com/galaxyproject/galaxy/compare/0c34d5bd3ff4...afb4e9c8f40d

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[galaxyproject/usegalaxy-playbook] e8e310: Updated slide rotation.
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e8e31070269b56b05c88d61174d4e411dca1a9c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/e8e31070269b56b0… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstracts.png A files/galaxy/common/static/welcome_img/GCC2016ScholarshipsInternational.png A files/galaxy/common/static/welcome_img/RDF2GraphGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation. Dropped PIA server; added RDF2Graph server. Added 2 GCC2016 deadline slides

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[galaxyproject/galaxy] 3f15d5: UI, histories: rework update system to check conte...
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f15d5af213d4ba59e75f51c11b1aef4ed101428 https://github.com/galaxyproject/galaxy/commit/3f15d5af213d4ba59e75f51c11b1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: 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-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: rework update system to check contents based on update times of contents and only stop checking when history has no more running jobs Commit: 7855e0009d21dad14b998bae974d0978ff43c6c9 https://github.com/galaxyproject/galaxy/commit/7855e0009d21dad14b998bae974d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M 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lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.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/interactive_environments.py M lib/galaxy/web/form_builder.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/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.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_common.py M lib/galaxy/webapps/galaxy/controllers/page.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/tag.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.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/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M 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lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/empty_output.xml M test/functional/tools/output_format.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_render.py M tox.ini Log Message: ----------- (merge conflicts) Commit: 8078306d9af4ce4ebff5b85f20290ee11c98177a https://github.com/galaxyproject/galaxy/commit/8078306d9af4ce4ebff5b85f2029… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- History manager: remove unused import Commit: c15e5db2eca3e177febe2da43bfa41b9bcbd4455 https://github.com/galaxyproject/galaxy/commit/c15e5db2eca3e177febe2da43bfa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tours.js M config/tool_conf.xml.main M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.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/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_tools.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tours.js M templates/webapps/tool_shed/repository/view_repository.mako M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M tools/data_source/upload.py Log Message: ----------- (manually merge conflicts) Commit: d9fc71510a4ce1c7829457f518f672859d372ed9 https://github.com/galaxyproject/galaxy/commit/d9fc71510a4ce1c7829457f518f6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/workflow/workflow-canvas.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/unit/workflows/test_modules.py Log Message: ----------- (merge conflicts) Commit: 4fd5df6d58ac4ddab59006c5251bdf3ef723de68 https://github.com/galaxyproject/galaxy/commit/4fd5df6d58ac4ddab59006c5251b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client, bundles had unresolved conflicts committed previously. Commit: effdc314da3f05908eee4770354b457505bfffb4 https://github.com/galaxyproject/galaxy/commit/effdc314da3f05908eee4770354b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: 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-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge branch 'history.updating' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6b96f7d5abce...effdc314da3f

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[galaxyproject/galaxy] f91796: Swap unpinned requirements.txt and conda-environme...
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f91796d7a652d93d2fbcaafc16a7b0654ce4af2e https://github.com/galaxyproject/galaxy/commit/f91796d7a652d93d2fbcaafc16a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Swap unpinned requirements.txt and conda-environment.txt svgfig->svgwrite Commit: a7b1ce76700b99de782fd3c031cc456b4090599f https://github.com/galaxyproject/galaxy/commit/a7b1ce76700b99de782fd3c031cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Update doc Commit: 6b96f7d5abce39ccb58c947b81daaeb5744bab2b https://github.com/galaxyproject/galaxy/commit/6b96f7d5abce39ccb58c947b81da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1896 from dannon/svgwrite_svgfig_deps svgfig->svgwrite in unpinned requirements Compare: https://github.com/galaxyproject/galaxy/compare/8311b7233f15...6b96f7d5abce

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[galaxyproject/usegalaxy-playbook] 4c874c: Update galaxyprojectdotorg.galaxy role
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4c874c3cdf1cbf6e1a3d687cafc5ee324dc7402d https://github.com/galaxyproject/usegalaxy-playbook/commit/4c874c3cdf1cbf6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml Log Message: ----------- Update galaxyprojectdotorg.galaxy role

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[galaxyproject/ansible-galaxy]
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/tags/0.6.3 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] e2393a: Use pinned-requirements.txt when fetching.
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: e2393aff87eb91dd283d09723a6eba2ea95780a4 https://github.com/galaxyproject/ansible-galaxy/commit/e2393aff87eb91dd283d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M README.md M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Use pinned-requirements.txt when fetching.

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[galaxyproject/usegalaxy-playbook] aa43ac: Update Main
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa43ac5e18e08358cb98ffa20cd643ad85845434 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa43ac5e18e08358… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Commit: c24f864205e9b58998befe56ff245eacac0ed5d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/c24f864205e9b589… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Update IE versions Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/14427de5dd47...…

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[galaxyproject/galaxy] 9b251e: Tones down the warning message about tool changes
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b251e567b0a1d5c7600d6aae7df7f22c7831700 https://github.com/galaxyproject/galaxy/commit/9b251e567b0a1d5c7600d6aae7df… Author: Brad Langhorst <brad(a)langhorst.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Tones down the warning message about tool changes This looked like an error to people here. I think this proposed language is a bit softer, but still conveys the message that users can proceed but should review the changes first to make sure their results will not be affected. Commit: 079d645bebad8b531d926f08703c5a2ae180b9d5 https://github.com/galaxyproject/galaxy/commit/079d645bebad8b531d926f08703c… Author: Brad Langhorst <brad(a)langhorst.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- typo fix Commit: 7955a2b769d02e57ed609b636621cd76d27bc3a8 https://github.com/galaxyproject/galaxy/commit/7955a2b769d02e57ed609b636621… Author: Brad Langhorst <brad(a)langhorst.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Update run.mako Commit: 8311b7233f15c04596322db57ca232e8f368d318 https://github.com/galaxyproject/galaxy/commit/8311b7233f15c04596322db57ca2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1893 from bwlang/patch-1 Tones down the warning message about tool changes Compare: https://github.com/galaxyproject/galaxy/compare/cd26a567e84b...8311b7233f15

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