April 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 2db848: Create symlinks for conda dep resolution in Pulsar
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2db8485a502ab6574f50301f62b14a2995563cb2 https://github.com/galaxyproject/infrastructure-playbook/commit/2db8485a502… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml Log Message: ----------- Create symlinks for conda dep resolution in Pulsar

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[galaxyproject/infrastructure-playbook] 4c22d7: Update GIE Docker image volume
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4c22d7e9f1d98bf8e734440cef30ad5cfe093c51 https://github.com/galaxyproject/infrastructure-playbook/commit/4c22d7e9f1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml Log Message: ----------- Update GIE Docker image volume

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[galaxyproject/usegalaxy-playbook] 448253: Enable Conda on Main Jetstream
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 448253e6cd22b4ac0bba5266aec3d4a376374810 https://github.com/galaxyproject/usegalaxy-playbook/commit/448253e6cd22b4ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A files/pulsar/usegalaxy.org/config/jetstream_dependency_resolvers_conf.xml M production/host_vars/jetstream-iu0.galaxyproject.org.yml M production/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Enable Conda on Main Jetstream

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[galaxyproject/usegalaxy-playbook] 9ff176: Use Conda on Jetstream
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9ff176d1b0f074e93da2055e29b6decd16b09ead https://github.com/galaxyproject/usegalaxy-playbook/commit/9ff176d1b0f074e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A env/common/files/pulsar/config/jetstream_dependency_resolvers_conf.xml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Use Conda on Jetstream

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[galaxyproject/galaxy] 0fc0a4: change 'user' menu to login or register for anons
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fc0a49b4bb7de0f95bdd8f594a22515243cd4a7 https://github.com/galaxyproject/galaxy/commit/0fc0a49b4bb7de0f95bdd8f594a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- change 'user' menu to login or register for anons Commit: 1fa8c837accda3d8120538da98ef200ab0250453 https://github.com/galaxyproject/galaxy/commit/1fa8c837accda3d8120538da98ef… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- improve french localization of the new menu item Commit: e842a265875909a0bead4e6e3e9f8006170067c3 https://github.com/galaxyproject/galaxy/commit/e842a265875909a0bead4e6e3e9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge pull request #3955 from martenson/user-menu-ux change 'user' menu to login or register for anons Compare: https://github.com/galaxyproject/galaxy/compare/439579298acb...e842a2658759

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[galaxyproject/galaxy] 33d662: Fix another tool (GeneBed_Maf_Fasta2) requiring th...
by GitHub 21 Apr '17

21 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33d6628dabdf75c27979925cb45b94e7ab59d725 https://github.com/galaxyproject/galaxy/commit/33d6628dabdf75c27979925cb45b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Commit: 1fe9c4d066e11b61767e22475a1392e0bbacf196 https://github.com/galaxyproject/galaxy/commit/1fe9c4d066e11b61767e22475a13… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3931 from jmchilton/maf_fix_47 [17.01] Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Commit: 439579298acbe2f85d79dd484ba1dca9cb15eee3 https://github.com/galaxyproject/galaxy/commit/439579298acbe2f85d79dd484ba1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3956 from galaxyproject/release_17.01 merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/e04ac6100378...439579298acb

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[galaxyproject/galaxy] 4adda2: Remove Google from OpenID providers in the sample....
by GitHub 21 Apr '17

21 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4adda20b0b75ba68ebc69b4aefc86adea68299d4 https://github.com/galaxyproject/galaxy/commit/4adda20b0b75ba68ebc69b4aefc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/openid_conf.xml.sample R openid/google.xml Log Message: ----------- Remove Google from OpenID providers in the sample. Google dropped OpenID support a while back. Commit: 0bc8d1f4ceb8bf3a212c5d17ddc2a1aa3e096191 https://github.com/galaxyproject/galaxy/commit/0bc8d1f4ceb8bf3a212c5d17ddc2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M config/openid_conf.xml.sample Log Message: ----------- move genomespace as the first shown provider in selection Commit: e04ac61003787ea7c99bc524017ae8afaec1decf https://github.com/galaxyproject/galaxy/commit/e04ac61003787ea7c99bc524017a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M config/openid_conf.xml.sample R openid/google.xml Log Message: ----------- Merge pull request #3953 from dannon/openid_sample_nogoogle Remove Google from OpenID providers in the sample. Compare: https://github.com/galaxyproject/galaxy/compare/386afbb4f6ac...e04ac6100378

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[galaxyproject/galaxy] 8599df: Standardize usage of log.exception in datatypes re...
by GitHub 21 Apr '17

21 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8599dff7a0098e121ddb244345a1c478f0a05cee https://github.com/galaxyproject/galaxy/commit/8599dff7a0098e121ddb244345a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Standardize usage of log.exception in datatypes registry. Commit: d303cf5ffbea29ad9d0d96b167f20606a022a488 https://github.com/galaxyproject/galaxy/commit/d303cf5ffbea29ad9d0d96b167f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Strip exception strings from being included in log.exception statements across the project. Commit: c46e36bdee354a879d2770b0ec9e22b00ec1c104 https://github.com/galaxyproject/galaxy/commit/c46e36bdee354a879d2770b0ec9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.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/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Overhaul string templating in log.exception statements -- should apply to all logs, eventually. Commit: d43d7aa140f399fbaa65308fe842c9afba8c44a3 https://github.com/galaxyproject/galaxy/commit/d43d7aa140f399fbaa65308fe842… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-14 (Fri, 14 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/tool_shed/capsule/capsule_manager.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/metadata/metadata_generator.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Fix E241, F841 from exception refactoring. Commit: 386afbb4f6ac703c60d2ffd975a1c3740f67457b https://github.com/galaxyproject/galaxy/commit/386afbb4f6ac703c60d2ffd975a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.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/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Merge pull request #3933 from dannon/exception_logging_fixes Standardize usage of log.exception Compare: https://github.com/galaxyproject/galaxy/compare/01b3eb42d88b...386afbb4f6ac

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[galaxyproject/galaxy] 9b6a9d: Start work on a relabelling collection operation.
by GitHub 20 Apr '17

20 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff https://github.com/galaxyproject/galaxy/commit/9b6a9dc0c73dfc0625e55a3db4c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_1.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Start work on a relabelling collection operation. I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is: - Validate uniqueness of identifiers and provide nice messages if they are not unique. - Validate that at least the required number of lines are present in the file and provide a nice message if not. - Add strict mode to ensure exactly the correct number of lines is added. - Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created. - Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration. - Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool. Commit: d21c14f0096b1fa7954396e7e9878b1d1e712331 https://github.com/galaxyproject/galaxy/commit/d21c14f0096b1fa7954396e7e987… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_2.txt Log Message: ----------- Add possibility to rename collection items from a tabular file Commit: 338130a979c99f60a171ba6b9ffca5db0a0e16a8 https://github.com/galaxyproject/galaxy/commit/338130a979c99f60a171ba6b9ffc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Fix failing test case in relable_from_file based on comment from @mvdbeek. Commit: 09bcdd9185e969c0eec34770faf8cb418c0f3e47 https://github.com/galaxyproject/galaxy/commit/09bcdd9185e969c0eec34770faf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_1.txt Log Message: ----------- Various improvements to relabel from file collection operation. - Better error handling (check for bad characters when creating collections). - Implement a strict mode parameter to do even more validation. - Rework tabular vs txt mode to be explicit user choice. - Mirror fix in release_17.01 for datasets not having a history, Commit: 2288a88ab793198147fdb5a1050d0325a831d9f8 https://github.com/galaxyproject/galaxy/commit/2288a88ab793198147fdb5a1050d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_2.txt Log Message: ----------- Fix relabel_from_file collection operation error handling if duplicate identifiers. Commit: 49abfced0918e2722ad0325aa7df6abbd2c5019e https://github.com/galaxyproject/galaxy/commit/49abfced0918e2722ad0325aa7df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement collection operation for filtering lists from a file. Commit: 01b3eb42d88b1900b73a8dfb9eecdbce49e531e0 https://github.com/galaxyproject/galaxy/commit/01b3eb42d88b1900b73a8dfb9eec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml A lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3940 from jmchilton/collection_op_filter_from_file Collection Operation - Filtering from a File Compare: https://github.com/galaxyproject/galaxy/compare/9f4fd7c44964...01b3eb42d88b

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[galaxyproject/galaxy] abe643: Update ethercalc GIE for readiness checking
by GitHub 20 Apr '17

20 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: abe6434916812a8236052560d58ab184b98b3ccb https://github.com/galaxyproject/galaxy/commit/abe6434916812a8236052560d58a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- Update ethercalc GIE for readiness checking Commit: a2b8b43179cbf880f1e16ab43172545e4309c058 https://github.com/galaxyproject/galaxy/commit/a2b8b43179cbf880f1e16ab43172… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Generate proper url for readiness endpoint Commit: 154530994f979070fe8c94c7730a99d11164c7fc https://github.com/galaxyproject/galaxy/commit/154530994f979070fe8c94c7730a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Error handling for GIE container readiness check Commit: 1e536e4ec7325b8d61394ea4091d8285eff24315 https://github.com/galaxyproject/galaxy/commit/1e536e4ec7325b8d61394ea4091d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add an ignore_volumes option for swarm_mode containers Commit: 9f4fd7c449646f8c3da9ba90d642a99b9cec386c https://github.com/galaxyproject/galaxy/commit/9f4fd7c449646f8c3da9ba90d642… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/containers_conf.yml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M lib/galaxy/containers/docker_swarm.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #3941 from natefoo/containers-bugfixes Containers interface and GIE bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/e9011488f2f5...9f4fd7c44964

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