November 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 880605: change join two dataset output format to auto
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 880605f17d9bd337789b783840c0fb4d35ddbe9d https://github.com/galaxyproject/galaxy/commit/880605f17d9bd337789b783840c0… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- change join two dataset output format to auto Commit: d2f01b3d000d68378e456aa46e5ec32a9fea506c https://github.com/galaxyproject/galaxy/commit/d2f01b3d000d68378e456aa46e5e… Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Update joiner.xml Commit: aaf49d6d067e84dbf31b52a45dbe7d7156dd59f3 https://github.com/galaxyproject/galaxy/commit/aaf49d6d067e84dbf31b52a45dbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Update tools/filters/joiner.xml Co-Authored-By: qiagu <36086881+qiagu(a)users.noreply.github.com> Commit: cf86049c0c46908fa6fd87c7b1221e86b1faf13f https://github.com/galaxyproject/galaxy/commit/cf86049c0c46908fa6fd87c7b122… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- update help of joiner two datasets tool Commit: 7a10f5ce0ed809ba1ab836f6a295c4fca9a637de https://github.com/galaxyproject/galaxy/commit/7a10f5ce0ed809ba1ab836f6a295… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Merge pull request #6998 from qiagu/join1 Change join two dataset output format to tabular Compare: https://github.com/galaxyproject/galaxy/compare/265a43507ebd...7a10f5ce0ed8 **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] 649d8b: Added support for overriding the rules module per ...
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 649d8bad5280174c2f9a74bd847a44ba7158ec3f https://github.com/galaxyproject/galaxy/commit/649d8bad5280174c2f9a74bd847a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py Log Message: ----------- Added support for overriding the rules module per destination Commit: 65979e473c5623a5116819bd93c182744117e6f0 https://github.com/galaxyproject/galaxy/commit/65979e473c5623a5116819bd93c1… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M test/unit/jobs/test_mapper.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py Log Message: ----------- Added test for rules module overriding Commit: 33b7f0f9d1e105dfbcbdab0a92081a9302cfe7eb https://github.com/galaxyproject/galaxy/commit/33b7f0f9d1e105dfbcbdab0a9208… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py Log Message: ----------- Refactor to use importlib Commit: 4b5312fe80fe4d8bc0a429229d84366b630d8eac https://github.com/galaxyproject/galaxy/commit/4b5312fe80fe4d8bc0a429229d84… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Updated watchers to reload rule module overrides Commit: bf1f2fe0ab5248acd86d646f1c80314561c0cdc2 https://github.com/galaxyproject/galaxy/commit/bf1f2fe0ab5248acd86d646f1c80… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/tools/lint.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/jobs/test_mapper.py Log Message: ----------- Refactor submodule imports Commit: 265a43507ebda1bac9bc5dbe2ac601912bef66d8 https://github.com/galaxyproject/galaxy/commit/265a43507ebda1bac9bc5dbe2ac6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/lint.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/jobs/test_mapper.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6993 from nuwang/allow_rules_module_override Allow rules module override and refactor submodule imports Compare: https://github.com/galaxyproject/galaxy/compare/17299356f011...265a43507ebd **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] 5385ca: Fix handling of forgotten LSF jobs in cli
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5385ca0473be64f4cde24fef07b5a38f47e9444f https://github.com/galaxyproject/galaxy/commit/5385ca0473be64f4cde24fef07b5… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Fix handling of forgotten LSF jobs in cli Previous case assumed that "is not found" was part of the STDOUT when in fact is in the STDERR (and STDOUT is empty). Commit: bfa7b200526bccf4dc0ffe888972ffe879f688bc https://github.com/galaxyproject/galaxy/commit/bfa7b200526bccf4dc0ffe888972… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Add log warning for missing LSF jobs. Co-Authored-By: pcm32 <pcm32(a)users.noreply.github.com> Commit: 17299356f011b80dcf575399be5d6803a1f31cc7 https://github.com/galaxyproject/galaxy/commit/17299356f011b80dcf575399be5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Merge pull request #7007 from pcm32/patch-2 Fix handling of forgotten LSF jobs in cli Compare: https://github.com/galaxyproject/galaxy/compare/eaacc5bc9f35...17299356f011 **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] 6ab7c3: Set downtime banner
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6ab7c39a5db5d8a6dcedf94e2dfad1f2bcd37526 https://github.com/galaxyproject/usegalaxy-playbook/commit/6ab7c39a5db5d8a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Set downtime banner **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] 2299e0: Add StoredWorkflow.show_in_tool_panel function
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2299e06a6937328f36485a8baa136c1138461144 https://github.com/galaxyproject/galaxy/commit/2299e06a6937328f36485a8baa13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add StoredWorkflow.show_in_tool_panel function This is more DRY and fixes https://github.com/galaxyproject/galaxy/issues/6889#issuecomment-438991091. The bug itself was due to comparing the id of a StoredWorkflowUserShareAssociation instead of StoredWorkflow when checking if a stored workflow should be in the tool panel. Commit: b5ce8d0dcf5affd462e33902126d4dd5c5921be6 https://github.com/galaxyproject/galaxy/commit/b5ce8d0dcf5affd462e33902126d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7014 from mvdbeek/fix_inability_to_remove_workflow_from_panel [18.01] Fix display_in_tool_panel status for shared workflows Compare: https://github.com/galaxyproject/galaxy/compare/baa992d21703...b5ce8d0dcf5a **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] 4760a0: Fix recursion issue in gff_filter_by_feature_count
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4760a0ac0f48b106f9a1cee348deeccc223eb64a https://github.com/galaxyproject/galaxy/commit/4760a0ac0f48b106f9a1cee348de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 45e475e19aa1988db2461c1d7fdf6135c02294d0 https://github.com/galaxyproject/galaxy/commit/45e475e19aa1988db2461c1d7fdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 [18.05] Backport commit 2d36e8955e020958334088d6ba5853c1027d8b75 Commit: f85afad9655b970f3af895a8dfafc0b8e301c705 https://github.com/galaxyproject/galaxy/commit/f85afad9655b970f3af895a8dfaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: fbd2284e5d355e8698360b5744538eb5f0a693ab https://github.com/galaxyproject/galaxy/commit/fbd2284e5d355e8698360b574453… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix PID file handling for gunicorn gunicorn uses `--pid`, not `--pid-file`. Commit: a1277b0e43b24594e25cc612ad844b501c7fb39b https://github.com/galaxyproject/galaxy/commit/a1277b0e43b24594e25cc612ad84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7013 from nsoranzo/release_18.09_fix_gunicorn_pid [18.09] Fix PID file handling for gunicorn Commit: 1ae8eb577db9d786f69b89226019a3ad8b437e58 https://github.com/galaxyproject/galaxy/commit/1ae8eb577db9d786f69b89226019… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/51498fc994f1...1ae8eb577db9 **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] fbd228: Fix PID file handling for gunicorn
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fbd2284e5d355e8698360b5744538eb5f0a693ab https://github.com/galaxyproject/galaxy/commit/fbd2284e5d355e8698360b574453… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix PID file handling for gunicorn gunicorn uses `--pid`, not `--pid-file`. Commit: a1277b0e43b24594e25cc612ad844b501c7fb39b https://github.com/galaxyproject/galaxy/commit/a1277b0e43b24594e25cc612ad84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7013 from nsoranzo/release_18.09_fix_gunicorn_pid [18.09] Fix PID file handling for gunicorn Commit: eaacc5bc9f351b8a01281ffa3462e1c653db3826 https://github.com/galaxyproject/galaxy/commit/eaacc5bc9f351b8a01281ffa3462… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d88f2b63daa9...eaacc5bc9f35 **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] fbd228: Fix PID file handling for gunicorn
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: fbd2284e5d355e8698360b5744538eb5f0a693ab https://github.com/galaxyproject/galaxy/commit/fbd2284e5d355e8698360b574453… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix PID file handling for gunicorn gunicorn uses `--pid`, not `--pid-file`. Commit: a1277b0e43b24594e25cc612ad844b501c7fb39b https://github.com/galaxyproject/galaxy/commit/a1277b0e43b24594e25cc612ad84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7013 from nsoranzo/release_18.09_fix_gunicorn_pid [18.09] Fix PID file handling for gunicorn Compare: https://github.com/galaxyproject/galaxy/compare/f85afad9655b...a1277b0e43b2 **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] ab75fe: Update pysam to v0.15.1
by GitHub 13 Nov '18

13 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab75fe8a37c4aaef2724bb1746f0fb7bb32c6fab https://github.com/galaxyproject/galaxy/commit/ab75fe8a37c4aaef2724bb1746f0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-12 (Mon, 12 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update pysam to v0.15.1 For Python 3.7 compatibility. Reported by @wm75. Commit: a53629ebae992e685020676f72cbcb55c954b677 https://github.com/galaxyproject/galaxy/commit/a53629ebae992e685020676f72cb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Update virtualenv installation to v16.1.0 which bundles `wheel` 0.32.2. The old virtualenv 13.1.2 included wheel 0.24.0, where tagging is broken for Python >=3.5, producing tracebacks like: ``` Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-c53eutpg/uwsgi/setup.py", line 138, in <module> 'Programming Language :: Python :: 3.6', File "/tmp/wheel_venv/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 213, in run archive_basename = self.get_archive_basename() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 161, in get_archive_basename impl_tag, abi_tag, plat_tag = self.get_tag() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 155, in get_tag assert tag == supported_tags[0] AssertionError ``` This was fixed in wheel 0.25.0. Reported by @wm75. Also update `urlretrieve` import for Python 3. Commit: d88f2b63daa91f1fce1ca161f9a9192ce20a5cd5 https://github.com/galaxyproject/galaxy/commit/d88f2b63daa91f1fce1ca161f9a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #7008 from nsoranzo/python3.7 Fixes for Python 3.7 Compare: https://github.com/galaxyproject/galaxy/compare/0395fcabf083...d88f2b63daa9 **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] 688bf3: Fix getAppRoot in layout/data.js
by GitHub 13 Nov '18

13 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 688bf3d524f7495afaf9c202a3601101baffb760 https://github.com/galaxyproject/galaxy/commit/688bf3d524f7495afaf9c202a360… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Fix getAppRoot in layout/data.js Commit: 0395fcabf083525beb1155c631a27046fa02d3a6 https://github.com/galaxyproject/galaxy/commit/0395fcabf083525beb1155c631a2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Merge pull request #7009 from dannon/app_singleton_cleaned Fix getAppRoot in layout/data.js Compare: https://github.com/galaxyproject/galaxy/compare/4ea20bc95915...0395fcabf083 **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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