- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] b787af: Use autofs for mounting Jetstream scratch on nodes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b787af633f4b3431e536b34e2080917cc4b96b95 https://github.com/galaxyproject/infrastructure-playbook/commit/b787af633f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/slurmclients.yml A roles/jetstream_nfs/tasks/client.yml M roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/templates/auto.jetstream.j2 Log Message: ----------- Use autofs for mounting Jetstream scratch on nodes

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[galaxyproject/infrastructure-playbook] 938fd7: Use autofs for mounting Jetstream scratch on nodes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 938fd7d2c7c645277c46e63a618d597010040f36 https://github.com/galaxyproject/infrastructure-playbook/commit/938fd7d2c7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml A roles/jetstream_nfs/tasks/client.yml M roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/templates/auto.jetstream.j2 Log Message: ----------- Use autofs for mounting Jetstream scratch on nodes

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[galaxyproject/infrastructure-playbook] df05c3: Use autofs for mounting Jetstream scratch on nodes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: df05c32750ea5a0da4b8160fa34bea293922e636 https://github.com/galaxyproject/infrastructure-playbook/commit/df05c32750e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M jetstreamtaccenv/group_vars/galaxynodes.yml A roles/jetstream_nfs/tasks/client.yml M roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/templates/auto.jetstream.j2 Log Message: ----------- Use autofs for mounting Jetstream scratch on nodes

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[galaxyproject/galaxy] 10ef0a: HTCondor and Docker documentation
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10ef0a3b00681dbab09119cc057a3ebe47e3d4f9 https://github.com/galaxyproject/galaxy/commit/10ef0a3b00681dbab09119cc057a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- HTCondor and Docker documentation Commit: ba409e75181224c80f0acf02530cac31fe28461c https://github.com/galaxyproject/galaxy/commit/ba409e75181224c80f0acf02530c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- enable HTCondor Docker integration Commit: 3ab43e38f5b2d63c300e99635234051956905f94 https://github.com/galaxyproject/galaxy/commit/3ab43e38f5b2d63c300e99635234… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M test/functional/tools/catDocker.xml Log Message: ----------- add new Docker Image. We need to have bash inside of Docker. Commit: ead96a55a9d05602a7b241d2d8b8acf557ce9425 https://github.com/galaxyproject/galaxy/commit/ead96a55a9d05602a7b241d2d8b8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-01 (Sun, 01 May 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add the ability to set the default handler and destination via environment variables. Commit: 7bd595b8f1caf4ea5085a41ba8129653d48f83a7 https://github.com/galaxyproject/galaxy/commit/7bd595b8f1caf4ea5085a41ba812… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M test/functional/tools/catDocker.xml Log Message: ----------- Revert "add new Docker Image. We need to have bash inside of Docker." This reverts commit 3ab43e38f5b2d63c300e99635234051956905f94. Commit: 917c882255ff1261bb99bb4bfc8bd1e165e26b96 https://github.com/galaxyproject/galaxy/commit/917c882255ff1261bb99bb4bfc8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Revise HTCondor Docker image resolution. Bring inline with the rest of the job runner's Docker image resolution stuff. Order of reosolution is: - Use destination specified override if found: docker_container_id_override - Use the tool specified container if not found and no override: see tool - Else - use docker_default_container_id. This adjusts the documentation to reflect this and make the the parameters more consistent throughout. I've modified this so docker_image (the old name introduced by the Docker Condor PR) still works - but I have left it undocumented intentionally for consistency. Commit: 8e6211aeb1bc3ffa696d61be89954d6e68215be4 https://github.com/galaxyproject/galaxy/commit/8e6211aeb1bc3ffa696d61be8995… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #10 from jmchilton/htcondor_docker Revise HTCondor Docker image resolution. Commit: c2ea4ee5266370ef1378df922af5a0c96d0f835c https://github.com/galaxyproject/galaxy/commit/c2ea4ee5266370ef1378df922af5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2278 from bgruening/htcondor_docker HTCondor Docker Integration Compare: https://github.com/galaxyproject/galaxy/compare/6fc2ae42cd4f...c2ea4ee52663

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[galaxyproject/usegalaxy-playbook] 2f7c3b: Main mutable config changes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2f7c3b4a674701fc1a1bc7577351f210d3986c9c https://github.com/galaxyproject/usegalaxy-playbook/commit/2f7c3b4a674701fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable config changes

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[galaxyproject/usegalaxy-playbook] ca7935: Store Main mutable configs in NFS so they don't ha...
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ca793528240877fe9d2b09099adce6722be9c43f https://github.com/galaxyproject/usegalaxy-playbook/commit/ca793528240877fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M production/group_vars/galaxyservers.yml M roles/usegalaxy/tasks/main.yml M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Store Main mutable configs in NFS so they don't have to be distributed.

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[galaxyproject/usegalaxy-playbook] 4bd600: Add extra headers for web-02->web-01 proxy for lau...
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4bd6000817455d34514161e718e06481a77e9ef0 https://github.com/galaxyproject/usegalaxy-playbook/commit/4bd6000817455d34… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M templates/nginx/usegalaxy.j2 Log Message: ----------- Add extra headers for web-02->web-01 proxy for launching Jupyter (this is necessary for the returned page to have the correct host in the IE links).

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[galaxyproject/galaxy] 90c48f: update check for Conda env.
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90c48ff6e314c77da75deab8ca716bf14065d089 https://github.com/galaxyproject/galaxy/commit/90c48ff6e314c77da75deab8ca71… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- update check for Conda env. Commit: ea2e9163d6827de2e1eb4208db205017c0d94dc4 https://github.com/galaxyproject/galaxy/commit/ea2e9163d6827de2e1eb4208db20… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- changed grep statement to match 2 patterns Now matches both "anaconda" and "continuum analytics" Commit: 6fc2ae42cd4fb20daa7c3927fb52834ca5771580 https://github.com/galaxyproject/galaxy/commit/6fc2ae42cd4fb20daa7c3927fb52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2295 from matthdsm/patch-4 update check for Conda env. Compare: https://github.com/galaxyproject/galaxy/compare/df2a068a3bc0...6fc2ae42cd4f

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[galaxyproject/galaxy] 1a6f1a: Update README to remove 2.6
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a6f1a36f4a157d0e5109189f982df1a5083dbbb https://github.com/galaxyproject/galaxy/commit/1a6f1a36f4a157d0e5109189f982… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M README.rst Log Message: ----------- Update README to remove 2.6 Hi :), Galaxy is not compatible with Python 2.6 since 16.01, right? What do we think about removing it from this README? We could also say 2.6 for Galaxy version under 16.01, and 2.7 for upper. Commit: df2a068a3bc0e86a0895e85b9ee5a5700eb8e22e https://github.com/galaxyproject/galaxy/commit/df2a068a3bc0e86a0895e85b9ee5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M README.rst Log Message: ----------- Merge pull request #2367 from remimarenco/patch-6 Update README to remove 2.6 Compare: https://github.com/galaxyproject/galaxy/compare/180eeeafe338...df2a068a3bc0

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[galaxyproject/galaxy] c749e1: Revise portlet view
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c749e13973ee8a5f46a486411fbfd14fdda578bd https://github.com/galaxyproject/galaxy/commit/c749e13973ee8a5f46a486411fbf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Revise portlet view Commit: 180eeeafe3385777861d06241c97633145fd4f82 https://github.com/galaxyproject/galaxy/commit/180eeeafe3385777861d06241c97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Merge branch 'revise_portlet_000' into dev Compare: https://github.com/galaxyproject/galaxy/compare/665809f25cb0...180eeeafe338

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[galaxyproject/galaxy] 384be8: Cleanup of E203 primarily, and some other misc for...
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 384be8c66116dda9e979128ff2fdb60216c70a40 https://github.com/galaxyproject/galaxy/commit/384be8c66116dda9e979128ff2fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/inflection.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py Log Message: ----------- Cleanup of E203 primarily, and some other misc formatting encountered during it. Commit: aba34eecda840d6f468dfe8ec3031ccf0353dce3 https://github.com/galaxyproject/galaxy/commit/aba34eecda840d6f468dfe8ec303… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.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 lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M 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lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Update to 'new' except style. Commit: ec9423f0867e548a326e5c2fe2dc9d80f2f98f44 https://github.com/galaxyproject/galaxy/commit/ec9423f0867e548a326e5c2fe2dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- dos2unix of molecules datatype module. 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M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.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/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/galaxy_utils/sequence/fastq.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.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/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.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/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/galaxy_install/utility_containers/__init__.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Merge pull request #2364 from dannon/fix_comma_usage Cleanup of E203 primarily, and some other misc formatting encountered… Compare: https://github.com/galaxyproject/galaxy/compare/a5f6195c3d4f...665809f25cb0

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[galaxyproject/galaxy] 996933: Revise form data visitor
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99693306e6c41aa011c559e98b137c67c92f0255 https://github.com/galaxyproject/galaxy/commit/99693306e6c41aa011c559e98b13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.html Log Message: ----------- Revise form data visitor Commit: a5f6195c3d4f9a08bbf0b26b2d9225e55da0fbad https://github.com/galaxyproject/galaxy/commit/a5f6195c3d4f9a08bbf0b26b2d92… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.html Log Message: ----------- Merge branch 'revise_visit_000' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0c78c2726f71...a5f6195c3d4f

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[galaxyproject/galaxy] 2390da: Fix for slurm's complete_terminal_job where if una...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 2390da54aec143358767e7977cffc70d040b04b5 https://github.com/galaxyproject/galaxy/commit/2390da54aec143358767e7977cff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. Commit: cc86096c83b5835e40e034611ad64bf3827e5c6d https://github.com/galaxyproject/galaxy/commit/cc86096c83b5835e40e034611ad6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2362 from dannon/slurm_complete_job_fix [16.04] Fix for slurm's complete_terminal_job where if unable to inspect the … Compare: https://github.com/galaxyproject/galaxy/compare/38209bbbac70...cc86096c83b5

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[galaxyproject/galaxy] 661e00: fix problems in bootstrap_history probably due to ...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 661e008f1d0bda5f9c0de18a46fe018286c8ae79 https://github.com/galaxyproject/galaxy/commit/661e008f1d0bda5f9c0de18a46fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- fix problems in bootstrap_history probably due to refactoring should work out of the box now, also minor rewording Commit: 70c65f6bd26207de001d01f7827255d5368ca18d https://github.com/galaxyproject/galaxy/commit/70c65f6bd26207de001d01f78272… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- remove prints Commit: 0c78c2726f719811b1d2be94fd9ea87664fbecbc https://github.com/galaxyproject/galaxy/commit/0c78c2726f719811b1d2be94fd9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2366 from martenson/fix-bootstrapping Fix release notes generator Compare: https://github.com/galaxyproject/galaxy/compare/ddc2412e60d4...0c78c2726f71

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[galaxyproject/galaxy] d76d92: API, sharable: serialize users_shared_with
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d76d92d3a0c8a053f17b7bdb9f988c4ab9be322a https://github.com/galaxyproject/galaxy/commit/d76d92d3a0c8a053f17b7bdb9f98… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, sharable: serialize users_shared_with - Changes sharable serializers so that, when requested with `keys=users_shared_with`, they return a list of encoded user ids for each user that the item has been shared with - Adds tests in test_HistoryManager Commit: dc1924bcdf780949df2614f6c721b48780da9d16 https://github.com/galaxyproject/galaxy/commit/dc1924bcdf780949df2614f6c721… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Testing: fixes galaxy_mock set_datatypes_registry - Add the datatypes_registry to the mock app using an empty registry Commit: 7ffa8aac676cf4f2ea8051a0ddd4056135935752 https://github.com/galaxyproject/galaxy/commit/7ffa8aac676cf4f2ea8051a0ddd4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, sharable: deserialize users_shared_with - Adds a deserializer for users_shared_with. PUT a list of user ids to update who an item is shared with. - Invalid users are skipped, bad ids error - (Only affects histories ATM) - Tests added to test_HistoryManager Commit: 133d8c65556ef1e709500dcce8707914cf2293a8 https://github.com/galaxyproject/galaxy/commit/133d8c65556ef1e709500dcce870… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history.sharing-api Commit: 4baa3377ed7809278d224ee1af90577e1dbd7627 https://github.com/galaxyproject/galaxy/commit/4baa3377ed7809278d224ee1af90… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Tests: load_datatypes in galaxy_mock Commit: e2f34f7a25d3c6ee081dfa7126b15f2585803df9 https://github.com/galaxyproject/galaxy/commit/e2f34f7a25d3c6ee081dfa7126b1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- API, history: skip users_shared_with for non-owner - If the requesting user is not the owner, don't return users_shared_with even when requested - add tests Commit: ddc2412e60d4a651e629262ff8e74b00a5838bcf https://github.com/galaxyproject/galaxy/commit/ddc2412e60d4a651e629262ff8e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/managers/sharable.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #2340 from carlfeberhard/history.sharing-api History/Sharable model user sharing API Compare: https://github.com/galaxyproject/galaxy/compare/a0291c61426c...ddc2412e60d4

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[galaxyproject/galaxy] 45ba2b: API, history: add DCE count to HDCA serializer
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45ba2b4e101c7e73494fa6237bc27f6b34f44210 https://github.com/galaxyproject/galaxy/commit/45ba2b4e101c7e73494fa6237bc2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/managers/hdcas.py Log Message: ----------- API, history: add DCE count to HDCA serializer Commit: a16ba6c615558ddcd8847e236575f155638a7064 https://github.com/galaxyproject/galaxy/commit/a16ba6c615558ddcd8847e236575… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js Log Message: ----------- UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Commit: f9afb7bcdca49add9d0112e4b46e61c423665202 https://github.com/galaxyproject/galaxy/commit/f9afb7bcdca49add9d0112e4b46e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/managers/hdcas.py M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI & API, history: return element_count by default - Adds element_count to summary serialization for hdcas through history/{:id}/contents - Implements a HistoryContents fetch method to decorate the hdcas after loading if necessary Commit: 8ce93d7fed04163ae524c829bac12f54068e3ee0 https://github.com/galaxyproject/galaxy/commit/8ce93d7fed04163ae524c829bac1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, history: doc updates Commit: 3aaccdac7b626f58303602dd9cf4728c9b0c7796 https://github.com/galaxyproject/galaxy/commit/3aaccdac7b626f58303602dd9cf4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M lib/galaxy/managers/hdcas.py M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: get element_counts after history load - Waits 2s after history contents loading and fetches element_count for all dataset collections in the history - Removes element_count as a default summary field for HDCAs Commit: ab60901cdc678bd57dd11caaa8ba49b557a439ff https://github.com/galaxyproject/galaxy/commit/ab60901cdc678bd57dd11caaa8ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako Log Message: ----------- (merge conflicts) Commit: a0291c61426cda865e0a2535fc7fa0a8acccaaf9 https://github.com/galaxyproject/galaxy/commit/a0291c61426cda865e0a2535fc7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M lib/galaxy/managers/hdcas.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- Merge branch 'show-dce-count' into dev Compare: https://github.com/galaxyproject/galaxy/compare/28acca5276b5...a0291c61426c

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[galaxyproject/galaxy] 1ba740: Improve composite output tool test.
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ba74094a35b5e59a8404d71300a0355d6aeb9d5 https://github.com/galaxyproject/galaxy/commit/1ba74094a35b5e59a8404d71300a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: A test-data/composite_output_expected_log M test/functional/tools/composite_output.xml Log Message: ----------- Improve composite output tool test. - Rename expected output Log from input Log. This relieves a concern I had that the tests were just working because the inputs and outputs match. - Add another "unregistered" output file to the output directory and add a test for it. This verifies that such files are infact tested. - Add a nested "unregistered" output file to the output directory and add a test for it. This verifies that nested files are tested. Commit: 28acca5276b5a4ceb125bafff5d107f062d04166 https://github.com/galaxyproject/galaxy/commit/28acca5276b5a4ceb125bafff5d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: A test-data/composite_output_expected_log M test/functional/tools/composite_output.xml Log Message: ----------- Merge pull request #2363 from jmchilton/test_composite Improve composite output tool test. Compare: https://github.com/galaxyproject/galaxy/compare/d9c0f4fa4444...28acca5276b5

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[galaxyproject/galaxy] 889ed2: UI & API: fix display of inaccessible datasets
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 889ed2547a2b6a94a5a357792eb69349b63f8232 https://github.com/galaxyproject/galaxy/commit/889ed2547a2b6a94a5a357792eb6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-model.js M test/unit/managers/test_HDAManager.py Log Message: ----------- UI & API: fix display of inaccessible datasets - Uses contexts in serializers to restore inaccessible field of hdas - Overrides serialize to return only the inaccessible view of inaccessible hdas (no other keys are returned): 'accessible', 'id', 'name', 'history_id', 'hid', 'history_content_type', 'state', 'deleted', 'visible' - If a DatasetAssociation Backbone Model is inaccessible, considers it to have details preventing the (failing) GET for more details Should be revisited if/when thread local contexts (user/session) are working. Commit: d9c0f4fa4444747bfd08ec021102d5a2b66d3cd3 https://github.com/galaxyproject/galaxy/commit/d9c0f4fa4444747bfd08ec021102… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/managers/hdas.py M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-model.js M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge branch 'datasets.show-inaccessible' into dev Compare: https://github.com/galaxyproject/galaxy/compare/65c57c5d52bc...d9c0f4fa4444

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[galaxyproject/galaxy] 7ab406: Update to latest galaxy-lib.
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ab4065d670ddc82e9e033db34a5f19c1ec80d9d https://github.com/galaxyproject/galaxy/commit/7ab4065d670ddc82e9e033db34a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Update to latest galaxy-lib. An assortment of tweaks and fixes to tool parsing and cwltool handling used by planemo and down stream CWL fork of Galaxy. Commit: b76889f4cac559d6cc2579272a66955b3195a3b3 https://github.com/galaxyproject/galaxy/commit/b76889f4cac559d6cc2579272a66… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py Log Message: ----------- Spelling fix thanks to @nsoranzo. Commit: 65c57c5d52bc1500b2c9ed8502b7bd2203d13eb2 https://github.com/galaxyproject/galaxy/commit/65c57c5d52bc1500b2c9ed8502b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Merge pull request #2354 from jmchilton/galaxy-lib-update Update to latest galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/aaff453a9031...65c57c5d52bc

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[galaxyproject/galaxy] cd96a5: Fix an issue about not-lowercasing extensions in l...
by GitHub 16 May '16

16 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd96a504bb83ecf5a4d19675f76e8108df9830fc https://github.com/galaxyproject/galaxy/commit/cd96a504bb83ecf5a4d19675f76e… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix an issue about not-lowercasing extensions in load_display_applications. Refactored in a function the lowercasing because DRY Commit: 5d47c7961d0826e9f5531f14e86d963c63a45eb2 https://github.com/galaxyproject/galaxy/commit/5d47c7961d0826e9f5531f14e86d… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Handle the case where extension is None Commit: aaff453a9031a1a07f2e4eddd8c8342aba71c319 https://github.com/galaxyproject/galaxy/commit/aaff453a9031a1a07f2e4eddd8c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #2361 from remimarenco/registry_uppercase Fix issue with lowercasing in datatypes/registry.py Compare: https://github.com/galaxyproject/galaxy/compare/b5ea024cd17b...aaff453a9031

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[galaxyproject/galaxy] 35a716: Not all objects added to the runner work queue are
by GitHub 14 May '16

14 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 35a716b8549bd575c96ef9cafe0e78a7e2048139 https://github.com/galaxyproject/galaxy/commit/35a716b8549bd575c96ef9cafe0e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Not all objects added to the runner work queue are JobWrappers/TaskWrappers as claimed in the comment. AsynchronousJobStates could also be added, and if the fail method was called this would result in the AttributeError of attempting to access an AJS' non-existent `get_id_tag` being logged in job.exeception as a red herring. Commit: 38209bbbac705612c11f7f3083e357e046cb5c64 https://github.com/galaxyproject/galaxy/commit/38209bbbac705612c11f7f3083e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #2350 from natefoo/fix-ajs-red-herring [16.04] Properly handle AsynchronousJobState objects in the job runner work queue Compare: https://github.com/galaxyproject/galaxy/compare/e28d305f3cda...38209bbbac70

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[galaxyproject/galaxy] 86050f: Build job success messages within tool form view
by GitHub 14 May '16

14 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86050f2b67e84c3322363d67ef457e5303ce52c9 https://github.com/galaxyproject/galaxy/commit/86050f2b67e84c3322363d67ef45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css Log Message: ----------- Build job success messages within tool form view Commit: b5ea024cd17ba60cbf96eec0cd6ba0d84e1db208 https://github.com/galaxyproject/galaxy/commit/b5ea024cd17ba60cbf96eec0cd6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css Log Message: ----------- Merge pull request #2355 from guerler/revise_template_001 Build job success messages within tool form view Compare: https://github.com/galaxyproject/galaxy/compare/db8afda49d59...b5ea024cd17b

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[galaxyproject/galaxy] 3a708a: Add filter_failed_datasets_from_collection.py scri...
by GitHub 14 May '16

14 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3a708a0089c87437bfe5336258a4a63a56a90d29 https://github.com/galaxyproject/galaxy/commit/3a708a0089c87437bfe5336258a4… Author: chambm <matt.chambers42(a)gmail.com> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: A scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Add filter_failed_datasets_from_collection.py script Commit: 384bdbfe7099bfb5360e0b43af55c99da8b179b0 https://github.com/galaxyproject/galaxy/commit/384bdbfe7099bfb5360e0b43af55… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Fix flaky "errors" Commit: db8afda49d595d5472f4346ea46c6c263b193fff https://github.com/galaxyproject/galaxy/commit/db8afda49d595d5472f4346ea46c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-14 (Sat, 14 May 2016) Changed paths: A scripts/api/filter_failed_datasets_from_collection.py Log Message: ----------- Merge pull request #2358 from chambm/feature/filter_failed_datasets_from_collection Add filter_failed_datasets_from_collection.py script Compare: https://github.com/galaxyproject/galaxy/compare/bf7996087e8b...db8afda49d59

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[galaxyproject/infrastructure-playbook] 364ce6: Install LZO on execution hosts now that we don't s...
by GitHub 13 May '16

13 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 364ce6ed84c15a09a008b2bdcafb4aa192c4b842 https://github.com/galaxyproject/infrastructure-playbook/commit/364ce6ed84c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-13 (Fri, 13 May 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M taccenv/group_vars/galaxynodes.yml Log Message: ----------- Install LZO on execution hosts now that we don't ship it (formerly an egg)

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[galaxyproject/galaxy] 8255e7: Do not pollute param_dict with a non JSONifiable d...
by GitHub 12 May '16

12 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8255e722cd21bb1cee594db3212657c6a22aa730 https://github.com/galaxyproject/galaxy/commit/8255e722cd21bb1cee594db32126… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Do not pollute param_dict with a non JSONifiable dict When running a data manager with a dataset parameter, the job fails with the following backtrace: Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job job_wrapper.prepare() File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare tool_evaluator.set_compute_environment( compute_environment, get_special=get_special ) File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment self.tool.exec_before_job( self.app, inp_data, out_data, param_dict ) File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job out.write( json.dumps( (json_params) ).encode('utf8') ) File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps return _default_encoder.encode(obj) File "/usr/lib/python2.7/json/encoder.py", line 207, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode return _iterencode(o, 0) TypeError: keys must be a string The bug was introduced in PR #2029. Commit: e28d305f3cda4377325190363057431f1f4f4d46 https://github.com/galaxyproject/galaxy/commit/e28d305f3cda4377325190363057… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029 [16.04] Do not pollute param_dict with a non JSONifiable dict Commit: bf7996087e8b3da9c40f7cd575691cf7123d760d https://github.com/galaxyproject/galaxy/commit/bf7996087e8b3da9c40f7cd57569… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/366056c0b70a...bf7996087e8b

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