- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5657a8: Display the genbank file type in upload
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5657a8b809e5938d3d996a77c826811e1176c108 https://github.com/galaxyproject/galaxy/commit/5657a8b809e5938d3d996a77c826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Display the genbank file type in upload Commit: 27d871f20edc8bc45a8b7b9d54ef88e48d3cb154 https://github.com/galaxyproject/galaxy/commit/27d871f20edc8bc45a8b7b9d54ef… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3569 from natefoo/genbank-upload Display the genbank file type in upload Compare: https://github.com/galaxyproject/galaxy/compare/6fc64f6f46f1...27d871f20edc

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[galaxyproject/galaxy] 012e26: Remove debugging warn statement.
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 012e261692a2ed8eb3e3c6ca4496b0bd48c99a84 https://github.com/galaxyproject/galaxy/commit/012e261692a2ed8eb3e3c6ca4496… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove debugging warn statement. I don't think it was meant to be here. Commit: f2e15588bfad5ad04e4f6530b9b7966e65d138ad https://github.com/galaxyproject/galaxy/commit/f2e15588bfad5ad04e4f6530b9b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #3566 from jmchilton/1701_user_warn [17.01] Remove debugging warn statement. Compare: https://github.com/galaxyproject/galaxy/compare/9feb8b3f0203...f2e15588bfad

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[galaxyproject/usegalaxy-playbook] 4254ea: Update main.
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4254ea1892437f3025aa856a821243b93fc76042 https://github.com/galaxyproject/usegalaxy-playbook/commit/4254ea1892437f30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update main.

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[galaxyproject/usegalaxy-playbook] 2bce42: Update test.
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2bce4225a8d87f21350040eaff122c79e5aec1ab https://github.com/galaxyproject/usegalaxy-playbook/commit/2bce4225a8d87f21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update test.

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[galaxyproject/galaxy] c3650d: add initial release notes
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3650d9fb6b2c422d62db1c10c4bfffe425e5f36 https://github.com/galaxyproject/galaxy/commit/c3650d9fb6b2c422d62db1c10c4b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst Log Message: ----------- add initial release notes Commit: 1fe0f2f76b67bbb034af48e0ee963da4dd176284 https://github.com/galaxyproject/galaxy/commit/1fe0f2f76b67bbb034af48e0ee96… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- bring in @nsoranzo's comments Commit: 47863ff13444b1596e12fb4903229717593bdea4 https://github.com/galaxyproject/galaxy/commit/47863ff13444b1596e12fb490322… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- more work towards reasonable release notes Commit: 21525ee25ef2b7b49733d845affe6fd9ede5b7b2 https://github.com/galaxyproject/galaxy/commit/21525ee25ef2b7b49733d845affe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify fastq compression handling Commit: e0d2f6dbc8b8bc5d96855cc74bf62fa56c731fd6 https://github.com/galaxyproject/galaxy/commit/e0d2f6dbc8b8bc5d96855cc74bf6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify how to prevent unpacking of archives Commit: 2d2e7ddc958f9908fa72caca540c333929e8b517 https://github.com/galaxyproject/galaxy/commit/2d2e7ddc958f9908fa72caca540c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Don't encourage uploads of fastq in release notes. My understanding is nearly all data now produced is fastqsanger. Commit: 32e624195b827b1e3ba607337c1b87067651b0c2 https://github.com/galaxyproject/galaxy/commit/32e624195b827b1e3ba607337c1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- Add all PRs and authors for compressed fastq support Commit: 76076dfeff8de4eb9509e60563a6cc905d2b5b22 https://github.com/galaxyproject/galaxy/commit/76076dfeff8de4eb9509e60563a6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- remove jmchilton from credits the Galaxy-lab members are explicitly omitted from RN mentions Commit: 9217889d2e23d339665a95a06d97112a28e91b2b https://github.com/galaxyproject/galaxy/commit/9217889d2e23d339665a95a06d97… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Add ashvark to author list Commit: 2f0a635e9f270007ec1da64b7ed054ff47cbb35e https://github.com/galaxyproject/galaxy/commit/2f0a635e9f270007ec1da64b7ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- Various improvements to the release notes. - Rewording things to focus on reader concerns. - Grouping things into single bullets (like testing stuff) and close to similar topics (like Conda stuff). - Eliminated some things which should have been marked #minor Commit: e3f50e90f8ab9e8313d077da2961a81bafb7c90a https://github.com/galaxyproject/galaxy/commit/e3f50e90f8ab9e8313d077da2961… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- More work on 17.01 release notes. Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix new history naming for batchmode workflow runs Commit: 639e2e5b2c4631901450a58710acbee373b498d8 https://github.com/galaxyproject/galaxy/commit/639e2e5b2c4631901450a58710ac… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- minor tweaks of RN Commit: 715e73adc97ea2c88639a50d1aaf88b9a1f3bcdc https://github.com/galaxyproject/galaxy/commit/715e73adc97ea2c88639a50d1aaf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- minor changes thanks to @nsoranzo Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0 https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Merge pull request #3532 from guerler/fix_new_history_naming [16.10] Fix new history naming for batchmode workflow runs Commit: f9edf39f58b9942b461e5238c9df60ab5765faea https://github.com/galaxyproject/galaxy/commit/f9edf39f58b9942b461e5238c9df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Migrate galaxy_utils to a wheel. Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now. xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td467… Rebased with fixes from @nsoranzo and @mvdbeek. Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8 https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Ensure toolbox conf watcher updates cached hash when config change is detected Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda439… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3558 from natefoo/toolconf-watch-hash [16.10] Ensure toolbox conf watcher updates cached hash when config change is detected Commit: 43873b8a6de5a6f1669f8364fff54c206b5f2f84 https://github.com/galaxyproject/galaxy/commit/43873b8a6de5a6f1669f8364fff5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3560 from galaxyproject/release_16.10 [17.01] Merge 16.10 into 17.01 Commit: 16a97e47c70f544d7acd30aac107a6687f01b736 https://github.com/galaxyproject/galaxy/commit/16a97e47c70f544d7acd30aac107… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #3551 from jmchilton/galaxy_utils_external [17.01] Migrate galaxy_utils to a wheel. Commit: 9feb8b3f02038c5cadad858d4b4675467ec90616 https://github.com/galaxyproject/galaxy/commit/9feb8b3f02038c5cadad858d4b46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- Merge pull request #3497 from martenson/17.01_release_notes [17.01] add release notes Commit: 440c75fe589d3c92e6837bdd244490dc29003e45 https://github.com/galaxyproject/galaxy/commit/440c75fe589d3c92e6837bdd2444… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 6fc64f6f46f16efb45450cf4597d5e86dec865b5 https://github.com/galaxyproject/galaxy/commit/6fc64f6f46f16efb45450cf4597d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #3565 from dannon/merge_1701_dev Merge 1701 to dev Compare: https://github.com/galaxyproject/galaxy/compare/ed98b1b75aac...6fc64f6f46f1

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[galaxyproject/galaxy] a391af: Remove duplicated/unused display_migration_details...
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a391af968742ab616f98edf7b889fe639302cf00 https://github.com/galaxyproject/galaxy/commit/a391af968742ab616f98edf7b889… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/model/migrate/check.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/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/0026_cloud_tables.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/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.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/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Remove duplicated/unused display_migration_details() functions Also fix import order. Commit: ed98b1b75aacc676d0f43a0a3a519132756518b7 https://github.com/galaxyproject/galaxy/commit/ed98b1b75aacc676d0f43a0a3a51… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/model/migrate/check.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/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/0026_cloud_tables.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/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.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/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Merge pull request #3564 from nsoranzo/remove_display_migration_details Remove duplicated/unused display_migration_details() functions Compare: https://github.com/galaxyproject/galaxy/compare/900c8d2dfe5e...ed98b1b75aac

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[galaxyproject/galaxy] c3650d: add initial release notes
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: c3650d9fb6b2c422d62db1c10c4bfffe425e5f36 https://github.com/galaxyproject/galaxy/commit/c3650d9fb6b2c422d62db1c10c4b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst Log Message: ----------- add initial release notes Commit: 1fe0f2f76b67bbb034af48e0ee963da4dd176284 https://github.com/galaxyproject/galaxy/commit/1fe0f2f76b67bbb034af48e0ee96… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- bring in @nsoranzo's comments Commit: 47863ff13444b1596e12fb4903229717593bdea4 https://github.com/galaxyproject/galaxy/commit/47863ff13444b1596e12fb490322… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- more work towards reasonable release notes Commit: 21525ee25ef2b7b49733d845affe6fd9ede5b7b2 https://github.com/galaxyproject/galaxy/commit/21525ee25ef2b7b49733d845affe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify fastq compression handling Commit: e0d2f6dbc8b8bc5d96855cc74bf62fa56c731fd6 https://github.com/galaxyproject/galaxy/commit/e0d2f6dbc8b8bc5d96855cc74bf6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify how to prevent unpacking of archives Commit: 2d2e7ddc958f9908fa72caca540c333929e8b517 https://github.com/galaxyproject/galaxy/commit/2d2e7ddc958f9908fa72caca540c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Don't encourage uploads of fastq in release notes. My understanding is nearly all data now produced is fastqsanger. Commit: 32e624195b827b1e3ba607337c1b87067651b0c2 https://github.com/galaxyproject/galaxy/commit/32e624195b827b1e3ba607337c1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- Add all PRs and authors for compressed fastq support Commit: 76076dfeff8de4eb9509e60563a6cc905d2b5b22 https://github.com/galaxyproject/galaxy/commit/76076dfeff8de4eb9509e60563a6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- remove jmchilton from credits the Galaxy-lab members are explicitly omitted from RN mentions Commit: 9217889d2e23d339665a95a06d97112a28e91b2b https://github.com/galaxyproject/galaxy/commit/9217889d2e23d339665a95a06d97… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Add ashvark to author list Commit: 2f0a635e9f270007ec1da64b7ed054ff47cbb35e https://github.com/galaxyproject/galaxy/commit/2f0a635e9f270007ec1da64b7ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- Various improvements to the release notes. - Rewording things to focus on reader concerns. - Grouping things into single bullets (like testing stuff) and close to similar topics (like Conda stuff). - Eliminated some things which should have been marked #minor Commit: e3f50e90f8ab9e8313d077da2961a81bafb7c90a https://github.com/galaxyproject/galaxy/commit/e3f50e90f8ab9e8313d077da2961… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- More work on 17.01 release notes. Commit: 639e2e5b2c4631901450a58710acbee373b498d8 https://github.com/galaxyproject/galaxy/commit/639e2e5b2c4631901450a58710ac… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- minor tweaks of RN Commit: 715e73adc97ea2c88639a50d1aaf88b9a1f3bcdc https://github.com/galaxyproject/galaxy/commit/715e73adc97ea2c88639a50d1aaf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- minor changes thanks to @nsoranzo Commit: 9feb8b3f02038c5cadad858d4b4675467ec90616 https://github.com/galaxyproject/galaxy/commit/9feb8b3f02038c5cadad858d4b46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- Merge pull request #3497 from martenson/17.01_release_notes [17.01] add release notes Compare: https://github.com/galaxyproject/galaxy/compare/16a97e47c70f...9feb8b3f0203

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[galaxyproject/galaxy] 5ee67b: Implement automatic tool_data_table reload
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ee67b0f2d586f6af9416d27a839a900b3864a0f https://github.com/galaxyproject/galaxy/commit/5ee67b0f2d586f6af9416d27a839… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Implement automatic tool_data_table reload if *.loc files have been modified. Commit: 732e2966329b77c61da4a992750aeeba326fca81 https://github.com/galaxyproject/galaxy/commit/732e2966329b77c61da4a992750a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Replace all LocDir and loc_dir related variable names with ToolDataDir or tool_data_dir (thanks @nsoranzo) Commit: a48f97ae1bb4bd4c9515e85c59afc7f5b1cc1ba7 https://github.com/galaxyproject/galaxy/commit/a48f97ae1bb4bd4c9515e85c59af… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Activate recursive watching for tool datat dir since toolshed datamanager tables are in subdirectory Commit: 900c8d2dfe5ee687b8926c55a6d1a701c5049113 https://github.com/galaxyproject/galaxy/commit/900c8d2dfe5ee687b8926c55a6d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3533 from mvdbeek/tdt_reload Watch tool data table *.loc files, and reload if modified. Compare: https://github.com/galaxyproject/galaxy/compare/d62824892ccf...900c8d2dfe5e

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[galaxyproject/galaxy] ea013f: add a task to protect the release branch in github
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea013fefa82ea6454168feda71be7e589e3b162d https://github.com/galaxyproject/galaxy/commit/ea013fefa82ea6454168feda71be… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- add a task to protect the release branch in github to the release process should prevent https://github.com/galaxyproject/galaxy/pull/3560#issuecomment-277520315 thanks @nsoranzo Commit: 2392bb90624273a6288b720819a6816c945a0cc1 https://github.com/galaxyproject/galaxy/commit/2392bb90624273a6288b720819a6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A 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tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py R tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/pasteWrapper.xml M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.py M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.py M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.py M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.py M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.py M tools/maf/vcf_to_maf_customtrack.xml M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.py M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/fastq_gen_conv.xml M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'dev' into protect-release-branch Commit: 9c4587969ec71a0759e9a46053ffaf13e98944da https://github.com/galaxyproject/galaxy/commit/9c4587969ec71a0759e9a46053ff… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- typo spotted by @nsoranzo Commit: d62824892ccfbdd20b5ff6af46b8af61eca3c8b9 https://github.com/galaxyproject/galaxy/commit/d62824892ccfbdd20b5ff6af46b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3562 from martenson/protect-release-branch add a task to protect the release branch in github Compare: https://github.com/galaxyproject/galaxy/compare/c952f1be3360...d62824892ccf

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[galaxyproject/galaxy] f9edf3: Migrate galaxy_utils to a wheel.
by GitHub 05 Feb '17

05 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f9edf39f58b9942b461e5238c9df60ab5765faea https://github.com/galaxyproject/galaxy/commit/f9edf39f58b9942b461e5238c9df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Migrate galaxy_utils to a wheel. Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now. xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td467… Rebased with fixes from @nsoranzo and @mvdbeek. Commit: 16a97e47c70f544d7acd30aac107a6687f01b736 https://github.com/galaxyproject/galaxy/commit/16a97e47c70f544d7acd30aac107… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #3551 from jmchilton/galaxy_utils_external [17.01] Migrate galaxy_utils to a wheel. Compare: https://github.com/galaxyproject/galaxy/compare/43873b8a6de5...16a97e47c70f

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[galaxyproject/galaxy]
by GitHub 05 Feb '17

05 Feb '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy]
by GitHub 04 Feb '17

04 Feb '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] f985b6: Fix new history naming for batchmode workflow runs
by GitHub 04 Feb '17

04 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix new history naming for batchmode workflow runs Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0 https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Merge pull request #3532 from guerler/fix_new_history_naming [16.10] Fix new history naming for batchmode workflow runs Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8 https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Ensure toolbox conf watcher updates cached hash when config change is detected Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda439… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3558 from natefoo/toolconf-watch-hash [16.10] Ensure toolbox conf watcher updates cached hash when config change is detected Commit: 43873b8a6de5a6f1669f8364fff54c206b5f2f84 https://github.com/galaxyproject/galaxy/commit/43873b8a6de5a6f1669f8364fff5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3560 from galaxyproject/release_16.10 [17.01] Merge 16.10 into 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/49970e786fcf...43873b8a6de5

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[galaxyproject/galaxy] 934bf6: Ensure toolbox conf watcher updates cached hash wh...
by GitHub 04 Feb '17

04 Feb '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8 https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Ensure toolbox conf watcher updates cached hash when config change is detected Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda439… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3558 from natefoo/toolconf-watch-hash [16.10] Ensure toolbox conf watcher updates cached hash when config change is detected Compare: https://github.com/galaxyproject/galaxy/compare/4df803a930c1...b41b8e305bac

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[galaxyproject/galaxy] e16266: Add missing decompress attribute to tool XSD.
by GitHub 03 Feb '17

03 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e16266508087712f7dae5dc2eae06070fa2084df https://github.com/galaxyproject/galaxy/commit/e16266508087712f7dae5dc2eae0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add missing decompress attribute to tool XSD. Missed this in #3550. Thanks to @mvdbeek for the catch https://github.com/galaxyproject/tools-devteam/pull/449#issuecomment-277195…. Commit: c952f1be33602fe23d0107c351e3305bf310fceb https://github.com/galaxyproject/galaxy/commit/c952f1be33602fe23d0107c351e3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3553 from jmchilton/decompress_test_outputs Add missing decompress attribute to tool XSD. Compare: https://github.com/galaxyproject/galaxy/compare/0b074f3fa55e...c952f1be3360

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[galaxyproject/galaxy] dd77cd: Add API test for converters after toolbox reload
by GitHub 03 Feb '17

03 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 https://github.com/galaxyproject/galaxy/commit/dd77cdb62576a62ea7e8ce8e31d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Add API test for converters after toolbox reload Commit: 78b4f8f7627a63be7ba593109c1ffd36891168ba https://github.com/galaxyproject/galaxy/commit/78b4f8f7627a63be7ba593109c1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py Log Message: ----------- Reload converter tools after toolbox reload Commit: 36ecf28adaa3328cac3248dc7e8c3ef79211c204 https://github.com/galaxyproject/galaxy/commit/36ecf28adaa3328cac3248dc7e8c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/api/test_datatypes.py Log Message: ----------- Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton) Commit: e4999510ee2bc44802b4891a1a09b00489b01a9c https://github.com/galaxyproject/galaxy/commit/e4999510ee2bc44802b4891a1a09… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3486 from mvdbeek/converter_reload [16.10] BUG: Reload converter tools after toolbox reload Commit: cc40b9d45514e1388e2d98e676fe5b75b28d6a3e https://github.com/galaxyproject/galaxy/commit/cc40b9d45514e1388e2d98e676fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- This enforces serial workflow scheduling within the context of a particular history. Commit: 749a503534033d3260681b75ad829a640d1c4a3b https://github.com/galaxyproject/galaxy/commit/749a503534033d3260681b75ad82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Minor typo in sample. Commit: 8be1429dda7e158601371331494501fd6043a5e0 https://github.com/galaxyproject/galaxy/commit/8be1429dda7e1586013713314945… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Add configuration for history_local_serial_workflow_scheduling Commit: 2b55fc75ebad92183e78a80b3240f7b978bd448d https://github.com/galaxyproject/galaxy/commit/2b55fc75ebad92183e78a80b3240… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Might be more palatable if this is defaulted to false. Commit: 9a7066c4b4c9f3824257cc00695b87ef9a065c0f https://github.com/galaxyproject/galaxy/commit/9a7066c4b4c9f3824257cc00695b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py Log Message: ----------- fix <is_valid_xml> output test assert check Commit: 58241e8dcb71500d399dbe2089f5b20f1eb89b53 https://github.com/galaxyproject/galaxy/commit/58241e8dcb71500d399dbe2089f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Rebuild client for 17.01 with latest node. Commit: 9dc1bbd3bc4697f5fbf1e183883aba9277058706 https://github.com/galaxyproject/galaxy/commit/9dc1bbd3bc4697f5fbf1e183883a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #3535 from dannon/minor_fix [17.01] Rebuild client for 17.01 with latest node. Commit: 31725972ef9342145effa6ad24d912022afb278c https://github.com/galaxyproject/galaxy/commit/31725972ef9342145effa6ad24d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix conda resolver when conda_auto_init = True and install = False Conda dependencies were being prematurely installed during installation of repositories from the ToolShed (at the point where we are just trying to list already installed dependencies). Commit: a121b889ef584086c96c6b9230198b3e2a04d6f6 https://github.com/galaxyproject/galaxy/commit/a121b889ef584086c96c6b923019… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Only read 6 bytes. Fixes #3529 Commit: c602336cc82fe60c54d10834c26fb8b0eafe81b0 https://github.com/galaxyproject/galaxy/commit/c602336cc82fe60c54d10834c26f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix for rerunning a job when the tool does not exist. Commit: 3858528d90c1380ae33c7e6087ee3ee1a9bb85f9 https://github.com/galaxyproject/galaxy/commit/3858528d90c1380ae33c7e6087ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3537 from jmchilton/backport_genbank_fix [17.01] Backport of fix unbounded readline in genbank datatype Commit: da7fed47445d8d1483eb456f32af19a0b0ff5412 https://github.com/galaxyproject/galaxy/commit/da7fed47445d8d1483eb456f32af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix wiggle to wiggle2simple1 for Python path changes in #3364. Fixes #3539. #minor Commit: 840c3b0fd846ea5fb58fb34378717aeadea7e81a https://github.com/galaxyproject/galaxy/commit/840c3b0fd846ea5fb58fb3437871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Fix integration test for default Conda mapping. It worked locally simply because I had R already installed on my system globally. Commit: a7cc18d616a2fe020d1946eac91ab248f9a1c995 https://github.com/galaxyproject/galaxy/commit/a7cc18d616a2fe020d1946eac91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tools that use Galaxy sequence utilities for #3364. Thanks to @peterjc for reporting and @martenson for grepping. xref #minor #3364 Commit: bb15a431f006dfbe0d9777529300b8e1981fc988 https://github.com/galaxyproject/galaxy/commit/bb15a431f006dfbe0d9777529300… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3540 from jmchilton/wiggle_fix_1701 [17.01] Fix wiggle to wiggle2simple1 for Python path changes in #3364. Commit: da0affd45d4fb5479d0e0adcc4efa147bee41e63 https://github.com/galaxyproject/galaxy/commit/da0affd45d4fb5479d0e0adcc4ef… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3542 from jmchilton/more_python_preservation [17.01] Fix tools that use Galaxy sequence utilities for #3364. Commit: 105557ba35317120af7f241aebec99f43c4c8553 https://github.com/galaxyproject/galaxy/commit/105557ba35317120af7f241aebec… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- added functional test for <is_valid_xml> Commit: 2322bc1ff59e85fb4f9db281d04b96e124dd73aa https://github.com/galaxyproject/galaxy/commit/2322bc1ff59e85fb4f9db281d04b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3541 from jmchilton/backport_3508 [17.01] Fix integration test for default Conda mapping. Commit: f1062afa55c486a0b35418bf7e7e988136c78cb6 https://github.com/galaxyproject/galaxy/commit/f1062afa55c486a0b35418bf7e7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #3538 from blankenberg/fix-rerun-no-tool [17.01] Fix for rerunning a job when the tool does not exist. Commit: 0ce7f6897fe7a037ae9ff9a79c082c56fec0e929 https://github.com/galaxyproject/galaxy/commit/0ce7f6897fe7a037ae9ff9a79c08… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add comments from @mvdbeek Commit: 961efb4d9af9ea17fbd0f80b7f07158f2cb971ad https://github.com/galaxyproject/galaxy/commit/961efb4d9af9ea17fbd0f80b7f07… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3536 from blankenberg/17.01-conda-fix [17.01] Fix conda resolver when conda_auto_install = True and install = False Commit: f6919651f8225c2d48c7b2ecb667e365d7be7bf7 https://github.com/galaxyproject/galaxy/commit/f6919651f8225c2d48c7b2ecb667… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3530 from jvolkening/release_17.01 fix <is_valid_xml> output test assert check Commit: b6cd80a5b35938847d4b306501a4e1fc7030c441 https://github.com/galaxyproject/galaxy/commit/b6cd80a5b35938847d4b306501a4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 62e6639d4716462dc4c6d5292c362a4ce0ba8a31 https://github.com/galaxyproject/galaxy/commit/62e6639d4716462dc4c6d5292c36… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Fix import order Broken in commit dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 . Need to remove the file from .ci/flake8_lint_include_list.txt because 'base' is not in application-import-names Commit: 409ca0a3c7eec50aaaec15215d380ec098ce4ec1 https://github.com/galaxyproject/galaxy/commit/409ca0a3c7eec50aaaec15215d38… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #3520 from dannon/history_serial_workflow_scheduling [17.01] History-local serial workflow scheduling. Commit: 49970e786fcf2d885b6a81aa61786cba7912f3fe https://github.com/galaxyproject/galaxy/commit/49970e786fcf2d885b6a81aa6178… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3549 from nsoranzo/release_17.01_fix_import_order [17.01] Fix import order Commit: 0b074f3fa55e5e831d761cefe9dadbf2129706a7 https://github.com/galaxyproject/galaxy/commit/0b074f3fa55e5e831d761cefe9da… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/simple.xml M test/api/test_datatypes.py A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/0219e26085e7...0b074f3fa55e

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[galaxyproject/galaxy] f985b6: Fix new history naming for batchmode workflow runs
by GitHub 03 Feb '17

03 Feb '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix new history naming for batchmode workflow runs Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0 https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Merge pull request #3532 from guerler/fix_new_history_naming [16.10] Fix new history naming for batchmode workflow runs Compare: https://github.com/galaxyproject/galaxy/compare/e4999510ee2b...4df803a930c1

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[galaxyproject/galaxy] 62e663: Fix import order
by GitHub 03 Feb '17

03 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 62e6639d4716462dc4c6d5292c362a4ce0ba8a31 https://github.com/galaxyproject/galaxy/commit/62e6639d4716462dc4c6d5292c36… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Fix import order Broken in commit dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 . Need to remove the file from .ci/flake8_lint_include_list.txt because 'base' is not in application-import-names Commit: 49970e786fcf2d885b6a81aa61786cba7912f3fe https://github.com/galaxyproject/galaxy/commit/49970e786fcf2d885b6a81aa6178… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3549 from nsoranzo/release_17.01_fix_import_order [17.01] Fix import order Compare: https://github.com/galaxyproject/galaxy/compare/409ca0a3c7ee...49970e786fcf

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[galaxyproject/galaxy] 5b135f: Allow decompressing test outputs.
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b135fdd39466e8cdcad68f481e5489719c6e75a https://github.com/galaxyproject/galaxy/commit/5b135fdd39466e8cdcad68f481e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Allow decompressing test outputs. This seems to be needed to test fastq outputs from tools. Gzipped files seem to depend on the file name before compression - so diff compares (even binary ones) do not work. This allows comparing compressed outputs (and it will magically work if the expected file in test-data is compressed or not). Builds on the awesome work from @mvdbeek in #3512. Commit: 0219e26085e79a2b4117d84519a3caae7482e9ef https://github.com/galaxyproject/galaxy/commit/0219e26085e79a2b4117d84519a3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #3550 from jmchilton/decompress_test_outputs Allow decompressing tool test outputs. Compare: https://github.com/galaxyproject/galaxy/compare/1dbe75ff1d80...0219e26085e7

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[galaxyproject/galaxy] 55aaf3: Allow to get a peek for gzip/bz2/zip compressed fi...
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55aaf32c4bb334bf4d2011ef2258348a24f02407 https://github.com/galaxyproject/galaxy/commit/55aaf32c4bb334bf4d2011ef2258… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Allow to get a peek for gzip/bz2/zip compressed files Commit: dc5d568437024ffef89ae9ada6a71479a3a352ce https://github.com/galaxyproject/galaxy/commit/dc5d568437024ffef89ae9ada6a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Allow text preview of compressed Fastq files Commit: 6ca39b4bcf2eec4bae594f43fa36d465df57ead1 https://github.com/galaxyproject/galaxy/commit/6ca39b4bcf2eec4bae594f43fa36… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: A lib/galaxy/util/compression_utils.py Log Message: ----------- Add get_fileobj function that opens compressed files if necessary Commit: f9cbe55d14886b7daa32768a0d16db627cbb538f https://github.com/galaxyproject/galaxy/commit/f9cbe55d14886b7daa32768a0d16… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Use compression_utils.get_fileobj where possible Commit: 7075d79e6f4e656c0398aa6a339b880c08d73f2e https://github.com/galaxyproject/galaxy/commit/7075d79e6f4e656c0398aa6a339b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Remove unused import Commit: 1dbe75ff1d80420b8edcc9b0762cc1c32f5e1e65 https://github.com/galaxyproject/galaxy/commit/1dbe75ff1d80420b8edcc9b0762c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #3512 from mvdbeek/add_compressed_fastq_peek_and_preview Add compressed fastq peek and preview Compare: https://github.com/galaxyproject/galaxy/compare/de509a81a1c0...1dbe75ff1d80

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[galaxyproject/galaxy] cc40b9: This enforces serial workflow scheduling within th...
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: cc40b9d45514e1388e2d98e676fe5b75b28d6a3e https://github.com/galaxyproject/galaxy/commit/cc40b9d45514e1388e2d98e676fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- This enforces serial workflow scheduling within the context of a particular history. Commit: 749a503534033d3260681b75ad829a640d1c4a3b https://github.com/galaxyproject/galaxy/commit/749a503534033d3260681b75ad82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Minor typo in sample. Commit: 8be1429dda7e158601371331494501fd6043a5e0 https://github.com/galaxyproject/galaxy/commit/8be1429dda7e1586013713314945… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Add configuration for history_local_serial_workflow_scheduling Commit: 2b55fc75ebad92183e78a80b3240f7b978bd448d https://github.com/galaxyproject/galaxy/commit/2b55fc75ebad92183e78a80b3240… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Might be more palatable if this is defaulted to false. Commit: 409ca0a3c7eec50aaaec15215d380ec098ce4ec1 https://github.com/galaxyproject/galaxy/commit/409ca0a3c7eec50aaaec15215d38… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #3520 from dannon/history_serial_workflow_scheduling [17.01] History-local serial workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/b6cd80a5b359...409ca0a3c7ee

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[galaxyproject/galaxy] dd77cd: Add API test for converters after toolbox reload
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 https://github.com/galaxyproject/galaxy/commit/dd77cdb62576a62ea7e8ce8e31d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Add API test for converters after toolbox reload Commit: 78b4f8f7627a63be7ba593109c1ffd36891168ba https://github.com/galaxyproject/galaxy/commit/78b4f8f7627a63be7ba593109c1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py Log Message: ----------- Reload converter tools after toolbox reload Commit: 36ecf28adaa3328cac3248dc7e8c3ef79211c204 https://github.com/galaxyproject/galaxy/commit/36ecf28adaa3328cac3248dc7e8c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/api/test_datatypes.py Log Message: ----------- Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton) Commit: e4999510ee2bc44802b4891a1a09b00489b01a9c https://github.com/galaxyproject/galaxy/commit/e4999510ee2bc44802b4891a1a09… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3486 from mvdbeek/converter_reload [16.10] BUG: Reload converter tools after toolbox reload Commit: b6cd80a5b35938847d4b306501a4e1fc7030c441 https://github.com/galaxyproject/galaxy/commit/b6cd80a5b35938847d4b306501a4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/f6919651f822...b6cd80a5b359

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[galaxyproject/galaxy] 9a7066: fix <is_valid_xml> output test assert check
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 9a7066c4b4c9f3824257cc00695b87ef9a065c0f https://github.com/galaxyproject/galaxy/commit/9a7066c4b4c9f3824257cc00695b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py Log Message: ----------- fix <is_valid_xml> output test assert check Commit: 105557ba35317120af7f241aebec99f43c4c8553 https://github.com/galaxyproject/galaxy/commit/105557ba35317120af7f241aebec… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- added functional test for <is_valid_xml> Commit: f6919651f8225c2d48c7b2ecb667e365d7be7bf7 https://github.com/galaxyproject/galaxy/commit/f6919651f8225c2d48c7b2ecb667… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3530 from jvolkening/release_17.01 fix <is_valid_xml> output test assert check Compare: https://github.com/galaxyproject/galaxy/compare/961efb4d9af9...f6919651f822

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[galaxyproject/galaxy] 317259: Fix conda resolver when conda_auto_init = True and...
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 31725972ef9342145effa6ad24d912022afb278c https://github.com/galaxyproject/galaxy/commit/31725972ef9342145effa6ad24d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix conda resolver when conda_auto_init = True and install = False Conda dependencies were being prematurely installed during installation of repositories from the ToolShed (at the point where we are just trying to list already installed dependencies). Commit: 0ce7f6897fe7a037ae9ff9a79c082c56fec0e929 https://github.com/galaxyproject/galaxy/commit/0ce7f6897fe7a037ae9ff9a79c08… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add comments from @mvdbeek Commit: 961efb4d9af9ea17fbd0f80b7f07158f2cb971ad https://github.com/galaxyproject/galaxy/commit/961efb4d9af9ea17fbd0f80b7f07… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3536 from blankenberg/17.01-conda-fix [17.01] Fix conda resolver when conda_auto_install = True and install = False Compare: https://github.com/galaxyproject/galaxy/compare/f1062afa55c4...961efb4d9af9

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[galaxyproject/galaxy] c2e029: Fix output tests for checksum example tools.
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2e0295e0232d059de9ceb87081eec74dc3188f1 https://github.com/galaxyproject/galaxy/commit/c2e0295e0232d059de9ceb87081e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/functional/tools/checksum.xml M test/functional/tools/md5sum.xml Log Message: ----------- Fix output tests for checksum example tools. Fixes #3544 - thanks to @jvolkening for the heads up. Commit: de509a81a1c019f9f2036783f8b958ee9898f321 https://github.com/galaxyproject/galaxy/commit/de509a81a1c019f9f2036783f8b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/functional/tools/checksum.xml M test/functional/tools/md5sum.xml Log Message: ----------- Merge pull request #3545 from jmchilton/fix_checksum Fix output tests for checksum example tools. Compare: https://github.com/galaxyproject/galaxy/compare/3681dae83808...de509a81a1c0

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