- galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] 2f4cbc: virtualenv_command is still required if `virtualen...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 2f4cbc0969fcb875727a510dd819c03bada3903e https://github.com/galaxyproject/ansible-galaxy/commit/2f4cbc0969fcb875727a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M tasks/dependencies.yml Log Message: ----------- virtualenv_command is still required if `virtualenv` isn't on $PATH, even if the venv already exists.

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[galaxyproject/usegalaxy-playbook] 499aa7: Mutable configs on Test
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 499aa77b352f08148d5c01b86bd24168c318b61c https://github.com/galaxyproject/usegalaxy-playbook/commit/499aa77b352f0814… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on Test Commit: cf2e3d17533ed5127b5d0552930e495eb143de74 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf2e3d17533ed512… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Test Commit: fbf7179def5e363a5a0011475873688b01ecf68d https://github.com/galaxyproject/usegalaxy-playbook/commit/fbf7179def5e363a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M templates/supervisor/galaxy.conf.j2 Log Message: ----------- Update supervisor Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b84b446a6cf3...…

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[galaxyproject/galaxy] b7c8a6: Rename lib/galaxy/main.py to scripts/galaxy-main s...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7c8a6d334461b0d61928e03bd112ee9344e8f2d https://github.com/galaxyproject/galaxy/commit/b7c8a6d334461b0d61928e03bd11… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M lib/galaxy/main.py A scripts/galaxy-main Log Message: ----------- Rename lib/galaxy/main.py to scripts/galaxy-main since that makes more sense and doesn't result in lib/galaxy/ being added to sys.path. Create a symlink at lib/galaxy/main.py for backward compatibility. Commit: 7010e38b6ff76014ae66ea62a7763942dacbfcd2 https://github.com/galaxyproject/galaxy/commit/7010e38b6ff76014ae66ea62a776… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M scripts/binary_compatibility.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: 3cf8fcc216f552a8dca542bc9ea3ada02c42e78c https://github.com/galaxyproject/galaxy/commit/3cf8fcc216f552a8dca542bc9ea3… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/main.py A scripts/galaxy-main Log Message: ----------- Merge pull request #994 from natefoo/smash_eggs Rename lib/galaxy/main.py to scripts/galaxy-main Compare: https://github.com/galaxyproject/galaxy/compare/f7d8bf7dbcf4...3cf8fcc216f5

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[galaxyproject/galaxy] 091128: UI, list of pairs collection creator: create regex...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 0911287df7a5d7e810d83bbcd1e4cb1f849314d7 https://github.com/galaxyproject/galaxy/commit/0911287df7a5d7e810d83bbcd1e4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: create regexp from filters for name creation Commit: 3b133d0d9206f6162494b3f5aa4c04581368480e https://github.com/galaxyproject/galaxy/commit/3b133d0d9206f6162494b3f5aa4c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #917 from carlfeberhard/release_15.10 [15.10] UI, list of pairs collection creator: create regexp from filters for … Compare: https://github.com/galaxyproject/galaxy/compare/7bcbf140936b...3b133d0d9206

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[galaxyproject/galaxy] de2bde: Fix a regression introduced during egg smashing th...
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de2bde9f69bd225f94af97b45b5682235b2ba86b https://github.com/galaxyproject/galaxy/commit/de2bde9f69bd225f94af97b45b56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix a regression introduced during egg smashing that broke the drmaa_library_path param to the drmaa runner (importing drmaa needs to be delayed until runner initialization so that the param to modify $DRMAA_LIBRARY_PATH can be evaluated). Commit: 04f5b3087a3f1a5ba78e0a7c9313b3c2c82e8b87 https://github.com/galaxyproject/galaxy/commit/04f5b3087a3f1a5ba78e0a7c9313… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M scripts/binary_compatibility.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash-eggs-bugfix2 Commit: 04a32c7864bdeb078916b90a0b70cb059cc6ab1b https://github.com/galaxyproject/galaxy/commit/04a32c7864bdeb078916b90a0b70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Add a comment explaining the strange import behavior in drmaa to guard against future regression Commit: f7d8bf7dbcf49c17273084c425e0a31e0ae3f7d8 https://github.com/galaxyproject/galaxy/commit/f7d8bf7dbcf49c17273084c425e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #996 from natefoo/smash-eggs-bugfix2 Fix a regression introduced during egg smashing that broke the drmaa_library_path param Compare: https://github.com/galaxyproject/galaxy/compare/70bd41546151...f7d8bf7dbcf4

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[galaxyproject/galaxy] c70c1a: Fix deferred dom removal
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c70c1aabd872c1aaec3742188b74ba5c972c3c4a https://github.com/galaxyproject/galaxy/commit/c70c1aabd872c1aaec3742188b74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools.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/dataset/dataset-li-edit.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Fix deferred dom removal Remove empty line Fix comments Fix log location Fix comments Commit: 70bd41546151e2ee0a464b8bafb6b6da1767080d https://github.com/galaxyproject/galaxy/commit/70bd41546151e2ee0a464b8bafb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools.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/dataset/dataset-li-edit.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Merge pull request #997 from guerler/performance_001 Fix deferred dom removal Compare: https://github.com/galaxyproject/galaxy/compare/3529ef6b6e96...70bd41546151

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[galaxyproject/usegalaxy-playbook] b84b44: Update Main
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b84b446a6cf3e285c7d4a352ef66e1609d4a4cbc https://github.com/galaxyproject/usegalaxy-playbook/commit/b84b446a6cf3e285… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main

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[galaxyproject/usegalaxy-playbook] 09bc1f: Test mutable configs
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 09bc1f1098e93ba0d03a18b091e243a2ac7e1c96 https://github.com/galaxyproject/usegalaxy-playbook/commit/09bc1f1098e93ba0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: ac7883fca092fc857e798dae8883bbc335662966 https://github.com/galaxyproject/usegalaxy-playbook/commit/ac7883fca092fc85… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: R roles/galaxyprojectdotorg.galaxy/tasks/eggs.yml Log Message: ----------- Removal missed in the galaxy role upgrade Commit: 0807be3e6d843330c3f045c64e060253d0743814 https://github.com/galaxyproject/usegalaxy-playbook/commit/0807be3e6d843330… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Disable OpenID on Test until #994 is merged Commit: 286ba22d5dc987abf30641f0c5cd25b46c8bc521 https://github.com/galaxyproject/usegalaxy-playbook/commit/286ba22d5dc987ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ee079f369c5e...…

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[galaxyproject/galaxy] dc9c2e: Fix grid batch operations. This should correctly ...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: dc9c2e4b7569726263fac8ab06cefb889c2b8af5 https://github.com/galaxyproject/galaxy/commit/dc9c2e4b7569726263fac8ab06ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. Commit: 7bcbf140936bfc9d25b8e6bed8a0bc14270b0cf2 https://github.com/galaxyproject/galaxy/commit/7bcbf140936bfc9d25b8e6bed8a0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #978 from dannon/graft_to_stable [15.10] Fix grid bulk operations Compare: https://github.com/galaxyproject/galaxy/compare/dab1ce3f03c2...7bcbf140936b

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[galaxyproject/galaxy] 9563f1: binary_compatibility.py shouldn't fail on platform...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9563f121e8d099315c75ce8d59c9b3d0d12fcbee https://github.com/galaxyproject/galaxy/commit/9563f121e8d099315c75ce8d59c9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- binary_compatibility.py shouldn't fail on platforms that don't return anything for get_specific_platform() (e.g. things other than Linux). Commit: 3529ef6b6e960ae5cbb12d415f468993e0585338 https://github.com/galaxyproject/galaxy/commit/3529ef6b6e960ae5cbb12d415f46… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #995 from natefoo/smash-eggs-bugfix1 binary_compatibility.py shouldn't fail Compare: https://github.com/galaxyproject/galaxy/compare/a71f504b1e9e...3529ef6b6e96

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[galaxyproject/galaxy] 291f4d: add google analytics tracking to newlibs, propagat...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 291f4d77d62be708bd9ead6bfc546722eb2a66cf https://github.com/galaxyproject/galaxy/commit/291f4d77d62be708bd9ead6bfc54… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- add google analytics tracking to newlibs, propagate ga_code to JS config Commit: f0fbd25526032ce35c824c8e2af7f72794327707 https://github.com/galaxyproject/galaxy/commit/f0fbd25526032ce35c824c8e2af7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M CONTRIBUTING.md 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/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.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/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less 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/command_factory.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/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.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/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M 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/libs/jquery/jquery.dynatree.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/grid/grid-view.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/maps/reports_webapp/run_stats.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/grid/grid-view.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/scripts/reports_webapp/run_stats.js M static/style/blue/base.css 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 static/style/blue/library.css 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/galaxy/root/index.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/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/functional/tools/simple_constructs.yml 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/test_objectstore.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tools/filters/cutWrapper.xml M tools/genomespace/genomespace_importer.xml M tox.ini Log Message: ----------- Merge branch 'dev' into track-newlibs Conflicts: static/maps/galaxy.library.js.map static/scripts/galaxy.library.js Commit: a71f504b1e9e1b10a188804bc2c359218d815483 https://github.com/galaxyproject/galaxy/commit/a71f504b1e9e1b10a188804bc2c3… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- Merge pull request #959 from martenson/track-newlibs add google analytics tracking to newlibs, propagate ga_code to JS config Compare: https://github.com/galaxyproject/galaxy/compare/e31ec7b0c8bc...a71f504b1e9e

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[galaxyproject/usegalaxy-playbook] ee079f: Update galaxyprojectdotorg.galaxy to 0.6
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ee079f369c5e05952b006b73512bc431837ce58d https://github.com/galaxyproject/usegalaxy-playbook/commit/ee079f369c5e0595… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) 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/meta/main.yml M roles/galaxyprojectdotorg.galaxy/tasks/clone.yml A roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml Log Message: ----------- Update galaxyprojectdotorg.galaxy to 0.6

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[galaxyproject/ansible-galaxy]
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/tags/0.6 Home: https://github.com/galaxyproject/ansible-galaxy

1 0

[galaxyproject/ansible-galaxy] c2c4af: Ensure $VIRTUAL_ENV is always set when running pip...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: c2c4afeb19d608ed381554ea943d2566ca14cd18 https://github.com/galaxyproject/ansible-galaxy/commit/c2c4afeb19d608ed3815… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M tasks/dependencies.yml Log Message: ----------- Ensure $VIRTUAL_ENV is always set when running pip (it is not activated, but reading binary-compatibility.cfg depends on it). Add a task for running Galaxy's binary_compatibility.py script so that CentOS can install RHEL wheels.

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[galaxyproject/galaxy] 9503f1: Fix the raven conditional requirement
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9503f1ddf3b6130eb9bf14cda057be21812b8ef2 https://github.com/galaxyproject/galaxy/commit/9503f1ddf3b6130eb9bf14cda057… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Fix the raven conditional requirement Commit: 1a3a594d4e397e11b3cb38a81add00b4482505ed https://github.com/galaxyproject/galaxy/commit/1a3a594d4e397e11b3cb38a81add… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: A scripts/binary_compatibility.py M scripts/common_startup.sh Log Message: ----------- Allow CentOS to install RHEL wheels. Commit: e31ec7b0c8bc6abf4346e29b9d1eed4923916f25 https://github.com/galaxyproject/galaxy/commit/e31ec7b0c8bc6abf4346e29b9d1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py A scripts/binary_compatibility.py M scripts/common_startup.sh Log Message: ----------- Merge pull request #989 from natefoo/smash_eggs Add a script for creating binary-compatibility.cfg and run it from common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/6d7be0a21868...e31ec7b0c8bc

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[galaxyproject/galaxy] f3bfa2: remove the autorefresh on Reports app
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3bfa2f56bb71f737ff8faa622271102652c7592 https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- remove the autorefresh on Reports app because of how long each page takes on Main the request for a subpage would timeout because new autorefresh request would be automatically issued Commit: ee327702d75415261085796af1e5c1ff5b1308ee https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Fix history extraction by returning value dictionary Remove previous fix Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207 https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Undo commit, wrong branch Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453 https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7 https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #967 from martenson/remove-reports-autorefresh [15.10] remove the autorefresh on Reports app homepage Commit: 3fe148dd1981b516452df9ace6db75e95879df03 https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #970 from guerler/fix_history_extract_001 [15.10] Fix workflow extraction from history Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Fix for missing included files on history export and import. Notes: If a history was exported previously, galaxy would just serve the cached version. In that case, it is better to make some changes to the history for example, by re-running the last job and then exporting it. Export of histories that haven't been exported previously should work without problems. (cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960) Commit: dfb59002ba78373dac32d8aebefd7b2de324260b https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Use object store for imported history datasets and included files (cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7) Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #973 from natefoo/composite-history-import-export [15.10] Fix for missing included files on history export and import Commit: 6d7be0a2186882c6090584a1cd58c59c18a0a519 https://github.com/galaxyproject/galaxy/commit/6d7be0a2186882c6090584a1cd58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M lib/galaxy/tools/__init__.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge branch 'release_15.10' of https://github.com/galaxyproject/galaxy into dev Compare: https://github.com/galaxyproject/galaxy/compare/5f3fbdefbeb5...6d7be0a21868

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[galaxyproject/galaxy] f3bfa2: remove the autorefresh on Reports app
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f3bfa2f56bb71f737ff8faa622271102652c7592 https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- remove the autorefresh on Reports app because of how long each page takes on Main the request for a subpage would timeout because new autorefresh request would be automatically issued Commit: ee327702d75415261085796af1e5c1ff5b1308ee https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Fix history extraction by returning value dictionary Remove previous fix Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207 https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Undo commit, wrong branch Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453 https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7 https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #967 from martenson/remove-reports-autorefresh [15.10] remove the autorefresh on Reports app homepage Commit: 3fe148dd1981b516452df9ace6db75e95879df03 https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #970 from guerler/fix_history_extract_001 [15.10] Fix workflow extraction from history Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Fix for missing included files on history export and import. Notes: If a history was exported previously, galaxy would just serve the cached version. In that case, it is better to make some changes to the history for example, by re-running the last job and then exporting it. Export of histories that haven't been exported previously should work without problems. (cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960) Commit: dfb59002ba78373dac32d8aebefd7b2de324260b https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Use object store for imported history datasets and included files (cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7) Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #973 from natefoo/composite-history-import-export [15.10] Fix for missing included files on history export and import Compare: https://github.com/galaxyproject/galaxy/compare/ab7ec7b3abbb...dab1ce3f03c2

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[galaxyproject/galaxy] d90ba8: Add a --dev-wheels arg to common_startup.sh (calle...
by GitHub 26 Oct '15

26 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d90ba82e92e65a6f5779e149663b45d18e3aecdf https://github.com/galaxyproject/galaxy/commit/d90ba82e92e65a6f5779e149663b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Add a --dev-wheels arg to common_startup.sh (called by run_tests.sh by default) that will install things in dev-requirements.txt. Commit: 5f3fbdefbeb5aa0d1eac0cd4c8ffa1ac45eec2e7 https://github.com/galaxyproject/galaxy/commit/5f3fbdefbeb5aa0d1eac0cd4c8ff… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #988 from natefoo/smash_eggs Add a --dev-wheels arg to common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/ef08ef4eadd6...5f3fbdefbeb5

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[galaxyproject/galaxy] 797579: Do not attempt to read the `load` attribute of job...
by GitHub 26 Oct '15

26 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7975798afb7975d13578ea791b3e7824641c9973 https://github.com/galaxyproject/galaxy/commit/7975798afb7975d13578ea791b3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Do not attempt to read the `load` attribute of job runner plugins that do not have a `load` attribute. `load` is an optional attrib on the <plugin> tag in job_conf.xml, used by the dynamic runner (which is always/automatically loaded) to pass plugin params. Galaxy servers using a `load`-less plugin will fail to start if using run.sh without this fix. Commit: ef08ef4eadd6f0202b317c76e5766a2feb97f921 https://github.com/galaxyproject/galaxy/commit/ef08ef4eadd6f0202b317c76e576… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Merge pull request #986 from natefoo/smash_eggs Do not attempt to read the `load` attribute of job runner plugins that do not have a `load` attribute. Compare: https://github.com/galaxyproject/galaxy/compare/e423ab624608...ef08ef4eadd6

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[galaxyproject/ansible-galaxy] 6dbcb9: Support installation of dependency via wheels.
by GitHub 26 Oct '15

26 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 6dbcb90fc1bb37a85337e5ff2d30a7b17e718b22 https://github.com/galaxyproject/ansible-galaxy/commit/6dbcb90fc1bb37a85337… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M README.md M defaults/main.yml A tasks/dependencies.yml R tasks/eggs.yml M tasks/main.yml Log Message: ----------- Support installation of dependency via wheels.

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[galaxyproject/usegalaxy-playbook] e869d2: edit Test secret vars
by GitHub 23 Oct '15

23 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e869d268c93f0f314564e5530530bd86a8a8e37f https://github.com/galaxyproject/usegalaxy-playbook/commit/e869d268c93f0f31… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-23 (Fri, 23 Oct 2015) Changed paths: M stage/secret_vars/galaxyservers.yml Log Message: ----------- edit Test secret vars

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[galaxyproject/galaxy] 633061: WIP: Stop using eggs, start using prebuilt wheels.
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 633061f3e0e95041383901378e33f8b41b83717e https://github.com/galaxyproject/galaxy/commit/633061f3e0e95041383901378e33… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/__init__.py M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py A lib/galaxy/wheels.py R lib/pkg_resources.py M run.sh R scripts/check_eggs.py M scripts/common_startup.sh R scripts/dist-scramble.py R scripts/fetch_eggs.py R scripts/make_egg_packager.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 R scripts/test_dist_egg.py Log Message: ----------- WIP: Stop using eggs, start using prebuilt wheels. Commit: a24134c447818fc8f55e0f7b7a0f33690155444b https://github.com/galaxyproject/galaxy/commit/a24134c447818fc8f55e0f7b7a0f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install modified pip for fetching Linux wheels, fetch wheels from wheels.galaxyproject.org Commit: 0de745188e28b5b53097b7cb1d69454bf681f523 https://github.com/galaxyproject/galaxy/commit/0de745188e28b5b53097b7cb1d69… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: R dist-eggs.ini R eggs.ini Log Message: ----------- Remove (dist-)eggs.ini. Commit: 33095318f777bf55fcf01cff4fe9d00910ff2868 https://github.com/galaxyproject/galaxy/commit/33095318f777bf55fcf01cff4fe9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/wheels.py Log Message: ----------- Fix problems in wheels.py found by flake8 Commit: 55019173466628c117a8a41eb068a605c1282f06 https://github.com/galaxyproject/galaxy/commit/55019173466628c117a8a41eb068… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install modified pip in develop/edit mode so it won't be reinstalled every time (courtesy @jxtx). Commit: e6446b05d35e7950675f4bcd95cf8c9e1c89ef1d https://github.com/galaxyproject/galaxy/commit/e6446b05d35e7950675f4bcd95cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M requirements.txt Log Message: ----------- Add nose to requirements.txt. Commit: 033b1e88da99b86ffbd33321374aa59d1d72484c https://github.com/galaxyproject/galaxy/commit/033b1e88da99b86ffbd33321374a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: 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/pbed_ldreduced_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/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/lwr_client/config_util.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.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/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/reports/controllers/workflows.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/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/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/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.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/galaxy_install/install_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/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.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/bootstrap_tool_shed/create_user_with_api_key.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/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove all imports of `galaxy.eggs` and all calls to `{eggs,pkg_resources}.require`. Probably broke some stuff where we were trying to be smart about whether a particular egg was available, but Galaxy does at least start. Commit: 431ebf93bd75437fb5f5c41e40791c5c9e6e9aad https://github.com/galaxyproject/galaxy/commit/431ebf93bd75437fb5f5c41e4079… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M requirements.txt Log Message: ----------- Updating requirements.txt as I get wheels ready. TODO: automate OS X wheels. Commit: 90279909209983fc620e26c6d7fabb6031d57dfd https://github.com/galaxyproject/galaxy/commit/90279909209983fc620e26c6d7fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M requirements.txt Log Message: ----------- Pin requirements Commit: 40bde6e102ae7bd66973a9f81b79fa9a08836c55 https://github.com/galaxyproject/galaxy/commit/40bde6e102ae7bd66973a9f81b79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/wheels.py M scripts/common_startup.sh Log Message: ----------- Install required dependencies from requirements.txt rather than convoluted galaxy.wheels method. Not sure why I was doing that. Hackathons are dangerous places. Commit: 97ad53f570800fc2518925555dc99f5a56356bdc https://github.com/galaxyproject/galaxy/commit/97ad53f570800fc2518925555dc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt A CODE_OF_CONDUCT.md M CONTRIBUTING.md M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.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/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/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/history/copy-dialog.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-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/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/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M 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test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample M tool_list.py M tools/data_source/data_source.py M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into smash_eggs Conflicts: eggs.ini lib/galaxy/__init__.py lib/galaxy/datatypes/binary.py lib/galaxy/datatypes/converters/bgzip.py lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py lib/galaxy/datatypes/converters/interval_to_coverage.py lib/galaxy/datatypes/converters/interval_to_fli.py lib/galaxy/datatypes/converters/interval_to_tabix_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.py lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py lib/galaxy/datatypes/coverage.py lib/galaxy/eggs/__init__.py lib/galaxy/eggs/dist.py lib/galaxy/eggs/scramble.py lib/galaxy/exceptions/__init__.py lib/galaxy/jobs/runners/pbs.py lib/galaxy/jobs/transfer_manager.py lib/galaxy/model/__init__.py lib/galaxy/model/migrate/check.py lib/galaxy/model/orm/__init__.py lib/galaxy/model/tool_shed_install/migrate/check.py lib/galaxy/web/framework/__init__.py lib/galaxy/web/framework/helpers/__init__.py lib/galaxy/web/framework/middleware/sentry.py lib/galaxy/web/framework/openid_manager.py lib/galaxy/web/framework/webapp.py lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py lib/galaxy/webapps/galaxy/controllers/dataset.py lib/galaxy/webapps/galaxy/controllers/library_common.py lib/galaxy/webapps/reports/controllers/workflows.py lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/search/repo_search.py lib/galaxy/webapps/tool_shed/search/tool_search.py lib/galaxy_ext/metadata/set_metadata.py lib/pulsar/client/config_util.py lib/tool_shed/galaxy_install/install_manager.py lib/tool_shed/galaxy_install/migrate/check.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/repository_types/repository_suite_definition.py lib/tool_shed/repository_types/tool_dependency_definition.py lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py lib/tool_shed/scripts/check_repositories_for_functional_tests.py lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py lib/tool_shed/util/basic_util.py lib/tool_shed/util/encoding_util.py lib/tool_shed/util/hg_util.py scripts/check_eggs.py scripts/dist-scramble.py scripts/fetch_eggs.py scripts/make_egg_packager.py scripts/scramble.py scripts/scramble/lib/scramble_lib.py scripts/scramble/scripts/DRMAA_python-macosx.py scripts/scramble/scripts/DRMAA_python-solaris.py scripts/scramble/scripts/DRMAA_python.py scripts/scramble/scripts/MySQL_python-solaris.py scripts/scramble/scripts/MySQL_python.py scripts/scramble/scripts/PyRods.py scripts/scramble/scripts/bx_python-solaris.py scripts/scramble/scripts/generic.py scripts/scramble/scripts/pbs_python.py scripts/scramble/scripts/psycopg2-linux.py scripts/scramble/scripts/psycopg2-macosx.py scripts/scramble/scripts/psycopg2-solaris.py scripts/scramble/scripts/psycopg2.py scripts/scramble/scripts/pysam-solaris.py scripts/scramble/scripts/pysqlite.py scripts/test_dist_egg.py Commit: 975fddeb4092097c5f6eb02f36cac65dcddf0d6a https://github.com/galaxyproject/galaxy/commit/975fddeb4092097c5f6eb02f36ca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/wheels.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py Log Message: ----------- Fix linting errors Commit: 0469ed29e064a4aed213dcc0230e8a06e711fc24 https://github.com/galaxyproject/galaxy/commit/0469ed29e064a4aed213dcc0230e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M scripts/api/common.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/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py M scripts/functional_tests.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 M scripts/summarize_timings.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 Log Message: ----------- Remove egg cruft from scripts/ Commit: b727174326292fcc713adc79471065d483ce42a8 https://github.com/galaxyproject/galaxy/commit/b727174326292fcc713adc794710… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M tox.ini Log Message: ----------- tox: Install nose and NoseHTML for unit tests. Commit: 93410ecf2538e32bdac7bed45367dbd6c993fb04 https://github.com/galaxyproject/galaxy/commit/93410ecf2538e32bdac7bed45367… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M scripts/nosetests.py M scripts/summarize_timings.py Log Message: ----------- Fix additional lint errors created by modifying stuff in scripts/ Commit: 165d6bdc9ded10c751e4eecbcca4390d231875ee https://github.com/galaxyproject/galaxy/commit/165d6bdc9ded10c751e4eecbcca4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py Log Message: ----------- Fix ctabix import errors (would these converters ever have worked?) Commit: 222bb4294a3dd9c9c58ae9f0785a10eb361c1e77 https://github.com/galaxyproject/galaxy/commit/222bb4294a3dd9c9c58ae9f0785a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/objectstore/rods.py Log Message: ----------- Conditional import for irods Commit: bf50d44ee50f5ace7d34db3e69c39779283167c7 https://github.com/galaxyproject/galaxy/commit/bf50d44ee50f5ace7d34db3e69c3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/wheels.py Log Message: ----------- Conditional imports for optional dependencies. Commit: f33476462722ec17947522d0a88661c88b688438 https://github.com/galaxyproject/galaxy/commit/f33476462722ec17947522d0a886… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: 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/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 tox.ini Log Message: ----------- Egg cleaning in test/ Commit: a44b2c2170c9c326a2d5e1fec35beb44fd9834df https://github.com/galaxyproject/galaxy/commit/a44b2c2170c9c326a2d5e1fec35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/requirements.txt R lib/galaxy/wheels.py M requirements.txt M run.sh M scripts/common_startup.sh Log Message: ----------- Rename galaxy.wheels to the more generalized galaxy.dependencies (since technically we don't care whether they are wheels), handle optional deps more correctly. Add error handling to common_startup.sh. Commit: c0cb01c2f65ccf94e96120b080eb7b5aa06bf31b https://github.com/galaxyproject/galaxy/commit/c0cb01c2f65ccf94e96120b080eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt Log Message: ----------- Fixes for job_conf.xml conditional dependencies Commit: e6337269b6fcd2b6c9d76045ff068a22d1dc39f8 https://github.com/galaxyproject/galaxy/commit/e6337269b6fcd2b6c9d76045ff06… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/users.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/template.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Remove pkg_resources.requires from lib/ Commit: 7c9c0cecdc3c31b9e86356470611ad1c7c0e87f4 https://github.com/galaxyproject/galaxy/commit/7c9c0cecdc3c31b9e86356470611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing WebError requirement Commit: 95b102371b5a2cdf617f988ab0d9e3bebcd03ebe https://github.com/galaxyproject/galaxy/commit/95b102371b5a2cdf617f988ab0d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add Pygments as a dependency of WebError and update SQLAlchemy version Commit: 02aed9c79e9f886990d2f5b747b35183f64a2cf7 https://github.com/galaxyproject/galaxy/commit/02aed9c79e9f886990d2f5b747b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Update Mercurial to 3.5 Commit: 2955ac414ac572a0c7a32c8b7ae61e0707d90524 https://github.com/galaxyproject/galaxy/commit/2955ac414ac572a0c7a32c8b7ae6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt Log Message: ----------- pysqlite is not a dependency (we expect Python's sqlite module to exist) Commit: 665c4c299d93b8a028b92ec34988371ac8171617 https://github.com/galaxyproject/galaxy/commit/665c4c299d93b8a028b92ec34988… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Handle the case where there are no conditional (heh) requirements Commit: 94a6f4c1704e30b839ba0de8abedff04155db5d2 https://github.com/galaxyproject/galaxy/commit/94a6f4c1704e30b839ba0de8abed… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- psycopg2 is not a hard requirement Commit: 4a4bfb55ec6a721f4b915ea1a7023d0ff945557d https://github.com/galaxyproject/galaxy/commit/4a4bfb55ec6a721f4b915ea1a702… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Slurm runner is a subclass of DRMAA so its use should trigger the conditional dependency code for the drmaa wheel. Commit: 5994311d8274d8b946f51d28efcca17d31a05bbc https://github.com/galaxyproject/galaxy/commit/5994311d8274d8b946f51d28efcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Pass Galaxy's virtualenv to jobs (local and remote) if a venv is not set. Can be overridden with <env file="/path/to/activate"/> on the destination. Commit: 7df95d15ab67dd5e1f22107a200913d1b874749e https://github.com/galaxyproject/galaxy/commit/7df95d15ab67dd5e1f22107a2009… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix flake8 error Commit: 6449db2a4ccc78e35193d7c14d315b4686f12532 https://github.com/galaxyproject/galaxy/commit/6449db2a4ccc78e35193d7c14d31… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M test/unit/jobs/test_runner_local.py Log Message: ----------- Fix broken unit test caused by addition of the job wrapper's galaxy_virtual_env attribute Commit: 744835bbfe8bb07041600326af2f2f5d203365f5 https://github.com/galaxyproject/galaxy/commit/744835bbfe8bb07041600326af2f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M run_tests.sh M scripts/common_startup.sh M tox.ini Log Message: ----------- Allow the use of common_startup.sh's 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config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A 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lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M 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templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako R templates/webapps/galaxy/tool_form.mako A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py M test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/docker/base/Dockerfile M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/multi_data_param.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/tool_shed/functional/test_1140_tool_help_images.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_execution.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml R tools/data_source/echo.py R tools/data_source/echo.xml R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml M tools/filters/gff/gff_filter_by_attribute.xml 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/visualization/LAJ.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: d92787557a56fbf542a488c795a33f43b54b325f https://github.com/galaxyproject/galaxy/commit/d92787557a56fbf542a488c795a3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Move vvers and vurl vars to a more relevant scope. Commit: 735e1c1bb0ea6ee857d04cd1f137c696303af5b0 https://github.com/galaxyproject/galaxy/commit/735e1c1bb0ea6ee857d04cd1f137… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/pulsar/client/config_util.py Log Message: ----------- Fix a bad merge in pulsar client lib caught (as always) by @nsoranzo Commit: 22297e3b839f1985b70944088eeb02c1bf9f26e0 https://github.com/galaxyproject/galaxy/commit/22297e3b839f1985b70944088eeb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/pulsar/client/config_util.py Log Message: ----------- Missed the rest of the bad merge in the previous commit Commit: b6fde86369bcd715c976e6d8bd3002ffa25a2136 https://github.com/galaxyproject/galaxy/commit/b6fde86369bcd715c976e6d8bd30… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/util/plugin_config.py Log Message: ----------- More graceful handling of failure to import yaml (a la Pulsar) Commit: f22ab8a60b06512596d68080b1bae4011110f4f1 https://github.com/galaxyproject/galaxy/commit/f22ab8a60b06512596d68080b1ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Conditional boto import in s3_multipart_upload.py Commit: 367ceae2560efac06e85018f9822207011240bd6 https://github.com/galaxyproject/galaxy/commit/367ceae2560efac06e85018f9822… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M create_db.sh M manage_db.sh M manage_tools.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M set_metadata.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Dockerized tests need to create and activate .venv if it does not exist. Do this by calling common_startup.sh prior to manage_db.sh in run_test_wrapper.sh. Will require a rebuild of the testing-base image. Also, have scripts in Galaxy root activate .venv if it exists. Commit: f7d0d76c509a8d468f29cb07a4fbd98ad1640d8f https://github.com/galaxyproject/galaxy/commit/f7d0d76c509a8d468f29cb07a4fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add boto as an explicit requirement (as a dependency of bioblend) Commit: c893afda008f4c47550f9bc94feb1a1256c470e7 https://github.com/galaxyproject/galaxy/commit/c893afda008f4c47550f9bc94feb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/version.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.py M test/docker/base/run_test_wrapper.sh M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'dev' into smash_eggs Commit: 26f78a5870a551630a5f4b91533b07b64bd3cb10 https://github.com/galaxyproject/galaxy/commit/26f78a5870a551630a5f4b91533b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Bump docker test image to 15.10.1 Commit: 6aea26caf307d9931c9f8349c324ed1a90c1a5d7 https://github.com/galaxyproject/galaxy/commit/6aea26caf307d9931c9f8349c324… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add requests as a dependency of bioblend Commit: 6e00db2d35be741247fbd43d154f107585bb81c3 https://github.com/galaxyproject/galaxy/commit/6e00db2d35be741247fbd43d154f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Make galaxy.dependencies env-config-var-aware. Commit: 50bfed49f55a7d9c39308f46648616906ce20eb4 https://github.com/galaxyproject/galaxy/commit/50bfed49f55a7d9c39308f466486… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Rename conditional_requirements.txt ('_' -> '-'), add dev-requirements.txt, fix a flake8 violation that doesn't violate PEP-8. =P Commit: 4a05d5ea12142046eac2d4593030f4d4dcd3c4b1 https://github.com/galaxyproject/galaxy/commit/4a05d5ea12142046eac2d4593030… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/style/less/base.less M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/library_upload_dir.py M scripts/functional_tests.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M static/style/blue/base.css M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs Commit: 2b48f5676527a83b76cb4205950670cf16c4b2cb https://github.com/galaxyproject/galaxy/commit/2b48f5676527a83b76cb42059506… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Add lxml as a dev requirement for twill Commit: 5098b7cb27f2c64603c57ee9991bd9516e0d25bb https://github.com/galaxyproject/galaxy/commit/5098b7cb27f2c64603c57ee9991b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Downgrade twill to 0.9.1 so we don't have to install lxml, which won't compile because libxml-dev isn't installed in the testing image, so we'd have to rebuild it yet again... Commit: af89922aee11a8dffbdeabbc36cf1003828f3a73 https://github.com/galaxyproject/galaxy/commit/af89922aee11a8dffbdeabbc36cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Update the BAM datatype for pysam API changes. index_file also no longer exists (the index must be filename + b".bai" or filename[:-4] + b".bai") =/. Removing it here is okay since the impact is that we can't fetch() random regions or use .pileup(), neither of which are done here. But it might be a problem for galaxy.visualization.data_providers.genome. Commit: 048f0be1bebb233edfb47a3625e8e0a9f751a696 https://github.com/galaxyproject/galaxy/commit/048f0be1bebb233edfb47a3625e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Talked to Dan, who corrected me on a few things. Also, forgot that the whole reason we use a modified pysam is for the index_filename param... Commit: 7e372d3cd0e18e3a533d2b36fadc5ab9c755d2ca https://github.com/galaxyproject/galaxy/commit/7e372d3cd0e18e3a533d2b36fadc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Updates to vis data providers for pysam API changes Commit: 0cbaf3b8c57138d694f8e1e06e353d97b211215f https://github.com/galaxyproject/galaxy/commit/0cbaf3b8c57138d694f8e1e06e35… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use proper PEP-440 local version identifiers for modified dependencies. Commit: 4a5f5f44dc09be5194c9ee4ebc6b0b6a4a057480 https://github.com/galaxyproject/galaxy/commit/4a5f5f44dc09be5194c9ee4ebc6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install our modified pip as a wheel from wheels.galaxyproject.org rather than an editable directly from github. Also, use `set -e` in scripts/common_startup.sh to fail if anything fails, rather than chaining a bunch of things with `&&` but not properly handling failure cases. Commit: 737596413f88174edc24345282aee9a1c1b53cac https://github.com/galaxyproject/galaxy/commit/737596413f88174edc24345282ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M run.sh Log Message: ----------- Pass relevant args from run.sh to common_startup.sh. Commit: 88683c3c40821581d80b3e984da486032c746c06 https://github.com/galaxyproject/galaxy/commit/88683c3c40821581d80b3e984da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is provided. Commit: e423ab6246088fec6a41c31fb67bc34c0ff40a89 https://github.com/galaxyproject/galaxy/commit/e423ab6246088fec6a41c31fb67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M create_db.sh R dist-eggs.ini 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/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M 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 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 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 tox.ini Log Message: ----------- Merge pull request #428 from natefoo/smash_eggs Replace eggs with wheels Compare: https://github.com/galaxyproject/galaxy/compare/112c0390d586...e423ab624608

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[galaxyproject/galaxy] c3db6a: Fix grid batch operations. This should correctly ...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3db6af560b86f1fcfccb52e4241f756d836cce1 https://github.com/galaxyproject/galaxy/commit/c3db6af560b86f1fcfccb52e4241… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. Commit: 6260bd1d0f370ed4fd3b7a00ba76b0efcd5e9221 https://github.com/galaxyproject/galaxy/commit/6260bd1d0f370ed4fd3b7a00ba76… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Strip whitespace in grid-view.js Commit: 112c0390d586c5d53802e8e67e8b0a98093b364e https://github.com/galaxyproject/galaxy/commit/112c0390d586c5d53802e8e67e8b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #971 from dannon/grid_batch_fixes Grid batch operation fixes Compare: https://github.com/galaxyproject/galaxy/compare/eca98ec82815...112c0390d586

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[galaxyproject/usegalaxy-playbook] 828b68: update mutable confs for Test (installed new deept...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 828b682e63b56109ecaea0c42849ac09c6d278a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/828b682e63b56109… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update mutable confs for Test (installed new deeptools)

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[galaxyproject/galaxy] bad9cc: Update dynatree to what will be the final release; ...
by GitHub 22 Oct '15

22 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bad9cce30f3f4079a6ee11e4b6ca2dbd823702de https://github.com/galaxyproject/galaxy/commit/bad9cce30f3f4079a6ee11e4b6ca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M static/maps/libs/jquery/jquery.dynatree.js.map M static/scripts/libs/jquery/jquery.dynatree.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 Log Message: ----------- Update dynatree to what will be the final release; we probably want to just replace it at some point. Commit: 54ee8cfdc0a3560f5cbffacdd121272d730d35d7 https://github.com/galaxyproject/galaxy/commit/54ee8cfdc0a3560f5cbffacdd121… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Update old dynatree usage to 1.0 standards, clean up some of the extra-chatty debugging and an invalid ajaxComplete attachment that we don't need. Commit: eca98ec828158ef30af06aac8ecee91b204f2759 https://github.com/galaxyproject/galaxy/commit/eca98ec828158ef30af06aac8ece… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M static/maps/libs/jquery/jquery.dynatree.js.map M static/scripts/libs/jquery/jquery.dynatree.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/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #856 from dannon/dynatree_upgrade Dynatree upgrade Compare: https://github.com/galaxyproject/galaxy/compare/1c527d37849f...eca98ec82815

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