- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 429ef9: WIP pgcleanup improvements
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 429ef96a106d0bf094145a7fd8a65143b113e6e5 https://github.com/galaxyproject/galaxy/commit/429ef96a106d0bf094145a7fd8a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- WIP pgcleanup improvements Commit: 941d68ad358155f6577fb89f1778625b805035fe https://github.com/galaxyproject/galaxy/commit/941d68ad358155f6577fb89f1778… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- WIP pgcleanup improvements Commit: ba83310d53488ccc62dd52907746a3ca63baaf28 https://github.com/galaxyproject/galaxy/commit/ba83310d53488ccc62dd52907746… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Mostly refactored pgcleanup.py Commit: e1a197676ec3f6f35dafaa6cb58d60c7d9d44fb2 https://github.com/galaxyproject/galaxy/commit/e1a197676ec3f6f35dafaa6cb58d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Refactor repetitive HDA purging stuff and add a function to purge HDAs with null history_ids Commit: 4d0538cc4f74c183495c9df33c1055a9441766d8 https://github.com/galaxyproject/galaxy/commit/4d0538cc4f74c183495c9df33c10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py Log Message: ----------- Add a table for logging user cleanup events Commit: e72d52c6dfe9332c5cd1c3f42d4e0276e9a75008 https://github.com/galaxyproject/galaxy/commit/e72d52c6dfe9332c5cd1c3f42d4e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Lint Commit: 3759db3297b2d277ae3039f54e203dc7493cb3dc https://github.com/galaxyproject/galaxy/commit/3759db3297b2d277ae3039f54e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6877 from natefoo/pgcleanup-inactive-users Refactor pgcleanup.py and add new routines Compare: https://github.com/galaxyproject/galaxy/compare/99bc4b33d2fa...3759db3297b2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4dd2ec: Fix ``make config-validate``
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4dd2ecb13f1cac23730debd107dd150e46c47568 https://github.com/galaxyproject/galaxy/commit/4dd2ecb13f1cac23730debd107dd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix ``make config-validate`` Commit: 194358703450ff8fef553d92531fc6e6a0938612 https://github.com/galaxyproject/galaxy/commit/194358703450ff8fef553d92531f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6908 from nsoranzo/release_18.09_config_validate [18.09] Fix ``make config-validate`` Compare: https://github.com/galaxyproject/galaxy/compare/88b840d2c6cc...194358703450 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] c6a4fe: Collect Galaxy handler process stats
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6a4fe030044926479872c4a60f95216887b893b https://github.com/galaxyproject/infrastructure-playbook/commit/c6a4fe03004… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/tacc/group_vars/galaxyservers.yml Log Message: ----------- Collect Galaxy handler process stats **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] aa23d8: Configure workflow schedulers on Main
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa23d8cf0d1d857421b02c98bf278ea0d9923ba7 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa23d8cf0d1d8574… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: R env/common/templates/galaxy/config/workflow_schedulers_conf.xml.j2 A env/main/files/galaxy/config/workflow_schedulers_conf.xml M env/main/group_vars/galaxyjobservers.yml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/galaxy/config/workflow_schedulers_conf.xml M env/test/group_vars/galaxyservers/vars.yml R env/test/templates/galaxy/config/workflow_schedulers_conf.xml.j2 Log Message: ----------- Configure workflow schedulers on Main **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 796070: Rename uWSGI logs from uwsgi_zerg*.log to zerg*.lo...
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 796070ba4ffacae52de4a889b89f271866a5bec3 https://github.com/galaxyproject/usegalaxy-playbook/commit/796070ba4ffacae5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/common/templates/supervisor/galaxy.j2 M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 Log Message: ----------- Rename uWSGI logs from uwsgi_zerg*.log to zerg*.log Commit: ecce49a63dc603bb6b0f2f4e2c08312179b7e634 https://github.com/galaxyproject/usegalaxy-playbook/commit/ecce49a63dc603bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: A env/common/templates/galaxy/config/workflow_schedulers_conf.xml.j2 M env/common/templates/supervisor/galaxy_group.j2 A env/common/templates/supervisor/galaxy_workflow_scheduler.j2 M env/test/group_vars/galaxyservers/vars.yml A env/test/templates/galaxy/config/workflow_schedulers_conf.xml.j2 Log Message: ----------- Configure a workflow scheduler on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1634bc2fc07f...… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 46e564: Use hasattr instead of relying on value
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 46e56417dddfa88c9b093c612eb006c9f471579d https://github.com/galaxyproject/galaxy/commit/46e56417dddfa88c9b093c612eb0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use hasattr instead of relying on value Commit: 88b840d2c6cc18184c71772d96301a9f9a71cbdc https://github.com/galaxyproject/galaxy/commit/88b840d2c6cc18184c71772d9630… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6893 from martenson/backport-6884 [18.09] check presence of attribute in addition to value Compare: https://github.com/galaxyproject/galaxy/compare/0aca12ce96f0...88b840d2c6cc **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 1634bc: Update Main migrated_tool_conf
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1634bc2fc07f981a55f6a9302bf429d9ceccf112 https://github.com/galaxyproject/usegalaxy-playbook/commit/1634bc2fc07f981a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/migrated_tools_conf.xml Log Message: ----------- Update Main migrated_tool_conf **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 126ee5: Create composite file archives in new_file_path in...
by GitHub 21 Oct '18

21 Oct '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 126ee5fe2bb6d8c1c2874545cd5a583389d45bca https://github.com/galaxyproject/galaxy/commit/126ee5fe2bb6d8c1c2874545cd5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Create composite file archives in new_file_path instead of TMP Commit: 3411852fedf31c93ec506aa4f8f8a922d4b57ad7 https://github.com/galaxyproject/galaxy/commit/3411852fedf31c93ec506aa4f8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-21 (Sun, 21 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #6885 from mvdbeek/create_in_new_file_path [18.05] Create composite file archives in new_file_path instead of TMP Compare: https://github.com/galaxyproject/galaxy/compare/a8fa5a1d4a6c...3411852fedf3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 60d0d9: Add grooming for composite files.
by GitHub 19 Oct '18

19 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60d0d9d5ec36fb1e6a79a4f51ab919325687b10d https://github.com/galaxyproject/galaxy/commit/60d0d9d5ec36fb1e6a79a4f51ab9… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Add grooming for composite files. Add call to groom_dataset_content() for composite files. Commit: 665e11facbf0b9b86fbcde04593fcd49ebe96777 https://github.com/galaxyproject/galaxy/commit/665e11facbf0b9b86fbcde04593f… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add ISA composite data type. Add new data types isa-tab and isa-json. Add isa-rwval library (isatools Python 2 version) in requirements. Commit: 1fb63a1369e8fa75b1f7825693ef286682659a64 https://github.com/galaxyproject/galaxy/commit/1fb63a1369e8fa75b1f7825693ef… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas (#31) * [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas. * Update isa.py Commit: fe139ad8dfe6c83188c33498d8d2854b33670c04 https://github.com/galaxyproject/galaxy/commit/fe139ad8dfe6c83188c33498d8d2… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Installs isa-rwval from develop Otherwise failing currently when building in the container. Commit: 06c57810d9050ffd4c81ce8e189741f255d6eafc https://github.com/galaxyproject/galaxy/commit/06c57810d9050ffd4c81ce8e1897… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct linting issues detected by Travis-CI run. Commit: 5babb80fc24febbbbed1af5b0bf56c84f16ab8a4 https://github.com/galaxyproject/galaxy/commit/5babb80fc24febbbbed1af5b0bf5… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct again lint errors for Travis-CI. Commit: 84c002283209a5717682c31d1013034e9cfc828b https://github.com/galaxyproject/galaxy/commit/84c002283209a5717682c31d1013… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct some more lint errors for Travis-CI. Commit: b9c63df60e12b6220f088645c17bf6d8bd68ab1b https://github.com/galaxyproject/galaxy/commit/b9c63df60e12b6220f088645c17b… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Change ISA Tools web site link. Replace ISA Tools .org web site that has just been hacked, by the GitHub page of the organization. Commit: cf7034399083c77d38e29c2832339776df103983 https://github.com/galaxyproject/galaxy/commit/cf7034399083c77d38e29c283233… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Escape filename in primary file. Commit: a50537cd5a2cb1039bcc7b0fa215d523c6e97499 https://github.com/galaxyproject/galaxy/commit/a50537cd5a2cb1039bcc7b0fa215… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Escape assay information in ISA display_data(). Commit: 86de0d3bc431404d6fca26e7506ec11415411788 https://github.com/galaxyproject/galaxy/commit/86de0d3bc431404d6fca26e7506e… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove unused method _list_archive_files(). Commit: 62ff476a7c3eeaca51147b5ae0cac753b71ba9ee https://github.com/galaxyproject/galaxy/commit/62ff476a7c3eeaca51147b5ae0ca… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Use CompressedFile class. Replace unzip custom code by Galaxy call to CompressedFile class. Commit: abd22c12f22b15c010bcfe6b7dca63d1c2135d18 https://github.com/galaxyproject/galaxy/commit/abd22c12f22b15c010bcfe6b7dca… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove logger configuration. Commit: 55bae21f77c03ebb1d114e9dbe593490b3e07993 https://github.com/galaxyproject/galaxy/commit/55bae21f77c03ebb1d114e9dbe59… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Comment out raw files listing in ISA type. Commit: e9f00065ee190ebdeca5c02d21c068d815674999 https://github.com/galaxyproject/galaxy/commit/e9f00065ee190ebdeca5c02d21c0… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove dynamical setting of study name for ISA. Commit: 2be9e1f637180d04d4e085b1c91292df3e09c72e https://github.com/galaxyproject/galaxy/commit/2be9e1f637180d04d4e085b1c912… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Add new lazy table parsing for isa-tab datatype and reintroduce data files Commit: 87cdd2156d46036807134f8d91fde4fcc2ac10de https://github.com/galaxyproject/galaxy/commit/87cdd2156d46036807134f8d91fd… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A test-data/MTBLS6.zip M test/api/test_tools_upload.py Log Message: ----------- Start writing upload test for isa-tab. Do not know how to read zip file content and submit it to uploader for a composite type. Commit: 08ce54fe6e0f3cc178ad41a6fa3c00177cfbfef1 https://github.com/galaxyproject/galaxy/commit/08ce54fe6e0f3cc178ad41a6fa3c… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Introduce new table parsers to get data files back; temporarily puts dependency back to Git repo to test against (updated PyPI package for isa-rwval will be pushed soon). Commit: eac29d55f9567b68ca94b3c2e468c380a64261ba https://github.com/galaxyproject/galaxy/commit/eac29d55f9567b68ca94b3c2e468… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fix requirements again for isa-rwval==0.10.1 Commit: b4fa3d28064e1c527a3b1a3232d10873490b6825 https://github.com/galaxyproject/galaxy/commit/b4fa3d28064e1c527a3b1a3232d1… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Cleanup presentation of data files (unused rendering using datafile id) Commit: 832f51b5168cc9751eecb77a62ff7a06807f92ed https://github.com/galaxyproject/galaxy/commit/832f51b5168cc9751eecb77a62ff… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pinned requirements as a symbolic link as done in dev branch. Commit: 39d4447a97ab8fe8359d3fd2a1df2815014570ea https://github.com/galaxyproject/galaxy/commit/39d4447a97ab8fe8359d3fd2a1df… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Add check so that empty filenames not added to file list. Commit: a98cc55db25492217ff5cb6d91716122e39347fb https://github.com/galaxyproject/galaxy/commit/a98cc55db25492217ff5cb6d9171… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Fix upload test for isa-tab datatype Commit: f2176d395478fe4c4ad41ae3f03747b3967abc6d https://github.com/galaxyproject/galaxy/commit/f2176d395478fe4c4ad41ae3f037… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update isa-rwval version as new update fixes a bug Commit: efc7864cabb0f7adc65929f3bff2f56c3ef14041 https://github.com/galaxyproject/galaxy/commit/efc7864cabb0f7adc65929f3bff2… Author: Pierrick ROGER <pk.roger(a)icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M .ci/flake8_blacklist.txt A .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh A 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M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M 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A tool-data/intermine_simple_display.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample A tools/data_source/intermine.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml 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/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'dev' into feature/isa_data_type Commit: 35093e38fcfe4f9efc3a2914d694cf4a11f24ace https://github.com/galaxyproject/galaxy/commit/35093e38fcfe4f9efc3a2914d694… Author: Pierrick ROGER <pk.roger(a)icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Remove spaces in blank line. Commit: a9eb587a3e38849c5044700f9f01c47d53f55a87 https://github.com/galaxyproject/galaxy/commit/a9eb587a3e38849c5044700f9f01… Author: Pierrick ROGER <pk.roger(a)icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Various corrections for py34-lint Add second blank line. Remove useless imports. Commit: 99bc4b33d2fa14a42f9ee7f4a9afe4dcf867c851 https://github.com/galaxyproject/galaxy/commit/99bc4b33d2fa14a42f9ee7f4a9af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-19 (Fri, 19 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt A test-data/MTBLS6.zip M test/api/test_tools_upload.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5787 from phnmnl/feature/isa_data_type Feature/isa data type Compare: https://github.com/galaxyproject/galaxy/compare/81f31d1a29e1...99bc4b33d2fa **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] a7f278: Decrease squid memory on cvmfs1-tacc0 and cvmfs1-p...
by GitHub 18 Oct '18

18 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a7f278a59e8a86c8e5a87765432809d0ac2102ca https://github.com/galaxyproject/infrastructure-playbook/commit/a7f278a59e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs1-tacc0.galaxyproject.org.yml Log Message: ----------- Decrease squid memory on cvmfs1-tacc0 and cvmfs1-psu0 until their allocated memory is increased **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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