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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 9f8021f1b4ecc0e072f6b0b89a457a09feea0ab1 https://github.com/galaxyproject/galaxy/commit/9f8021f1b4ecc0e072f6b0b89a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 63a3cfad30656b7fa8516e9c386f144f0f3b1fe3 https://github.com/galaxyproject/galaxy/commit/63a3cfad30656b7fa8516e9c386f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9e3cc281564a...63a3cfad3065

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 9f8021f1b4ecc0e072f6b0b89a457a09feea0ab1 https://github.com/galaxyproject/galaxy/commit/9f8021f1b4ecc0e072f6b0b89a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/2d772d74b940...9f8021f1b4ec

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/beb28d4aff2a...8e6cdd73aa4d

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[galaxyproject/galaxy] 36a182: Resort to os.path.exists() also for paths not endi...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Compare: https://github.com/galaxyproject/galaxy/compare/34421966d41a...d80e60ce74aa

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[galaxyproject/infrastructure-playbook] b2fb46: Fix stats/upgrade stats components
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b2fb46db5f10c868a15cff8676e503f5bde1570a https://github.com/galaxyproject/infrastructure-playbook/commit/b2fb46db5f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: R env/tacc/group_vars/stats/vars.yml R env/tacc/group_vars/stats/vault.yml R env/tacc/group_vars/statsservers.yml A env/tacc/group_vars/statsservers/vars.yml A env/tacc/group_vars/statsservers/vault.yml M roles/stats/defaults/main.yml M roles/stats/tasks/main.yml Log Message: ----------- Fix stats/upgrade stats components Commit: 73dc2d961db7f2ee524f41582e14c4f7fddd7b6d https://github.com/galaxyproject/infrastructure-playbook/commit/73dc2d961db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/tacc/group_vars/all.yml M env/tacc/group_vars/galaxyservers.yml M env/tacc/group_vars/statsservers/vars.yml M env/tacc/playbook.yml A env/tacc/telegraf.yml M env/tacc/templates/supervisor/stats.j2 A roles/dj-wasabi.telegraf/.gitignore A roles/dj-wasabi.telegraf/.travis.yml A roles/dj-wasabi.telegraf/CHANGELOG.md A roles/dj-wasabi.telegraf/README.md A roles/dj-wasabi.telegraf/defaults/main.yml A roles/dj-wasabi.telegraf/handlers/main.yml A roles/dj-wasabi.telegraf/meta/.galaxy_install_info A roles/dj-wasabi.telegraf/meta/main.yml A roles/dj-wasabi.telegraf/molecule/default/Dockerfile.j2 A roles/dj-wasabi.telegraf/molecule/default/INSTALL.rst A roles/dj-wasabi.telegraf/molecule/default/create.yml A roles/dj-wasabi.telegraf/molecule/default/destroy.yml A roles/dj-wasabi.telegraf/molecule/default/molecule.yml A roles/dj-wasabi.telegraf/molecule/default/playbook.yml A roles/dj-wasabi.telegraf/molecule/default/tests/test_default.py A roles/dj-wasabi.telegraf/molecule/default/tests/test_default.pyc A roles/dj-wasabi.telegraf/molecule/default/yaml-lint.yml A roles/dj-wasabi.telegraf/tasks/Debian.yml A roles/dj-wasabi.telegraf/tasks/RedHat.yml A roles/dj-wasabi.telegraf/tasks/main.yml A roles/dj-wasabi.telegraf/templates/etc-opt-telegraf-telegraf.conf.j2 A roles/dj-wasabi.telegraf/templates/telegraf-extra-plugin.conf.j2 A roles/dj-wasabi.telegraf/templates/telegraf.conf.j2 M roles/sentry/tasks/main.yml M roles/stats/tasks/main.yml R roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Run telegraf on everything, and have Galaxy log to a telegraf+statsd running host-local so these stats can be separated Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/dd951a455b…

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[galaxyproject/usegalaxy-playbook] a62d49: Use multi-manager swarm connection on Test
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a62d49033c11667e011e2e7f97f6ddddf1ef3421 https://github.com/galaxyproject/usegalaxy-playbook/commit/a62d49033c11667e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Use multi-manager swarm connection on Test Commit: 4c873738f6240db2728fed8abdcdd45c98c63558 https://github.com/galaxyproject/usegalaxy-playbook/commit/4c873738f6240db2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Log to local statsd (telegraf) rather than a centralized one, so that differences between instances can be determined Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b3f87bde2a98...…

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[galaxyproject/usegalaxy-playbook] b3f87b: update TTS
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3f87bde2a98d7c97c55b6effc2069aed4894bec https://github.com/galaxyproject/usegalaxy-playbook/commit/b3f87bde2a98d7c9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] 2fe757: Fix for running jobs in containers.
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fe7579d12c352b878bd9a9f3751ce7db1fb2bba https://github.com/galaxyproject/galaxy/commit/2fe7579d12c352b878bd9a9f3751… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix for running jobs in containers. Broken with 5861. Commit: 9e3cc281564a2f3cb91ae5c10b3ad501230228ae https://github.com/galaxyproject/galaxy/commit/9e3cc281564a2f3cb91ae5c10b3a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #5938 from jmchilton/docker_fix_containers_lib Fix for running jobs in containers. Compare: https://github.com/galaxyproject/galaxy/compare/5acb2dff792f...9e3cc281564a

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[galaxyproject/galaxy] e6d752: Fix for running in containers when job_tmp is set ...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6d752c85930bde846eb57e26de8a8716bf92b08 https://github.com/galaxyproject/galaxy/commit/e6d752c85930bde846eb57e26de8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Fix for running in containers when job_tmp is set in job_conf.xml. Commit: 5acb2dff792fbb799215537335425b820bd16d4d https://github.com/galaxyproject/galaxy/commit/5acb2dff792fbb79921553733542… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5937 from jmchilton/docker_fix_tmp Fix for running in containers when job_tmp is set in job_conf.xml. Compare: https://github.com/galaxyproject/galaxy/compare/284795b94f2f...5acb2dff792f

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[galaxyproject/galaxy] 3182df: correct signal num
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3182dfa70e4220621fe5eb85a05b2f5430a31d3d https://github.com/galaxyproject/galaxy/commit/3182dfa70e4220621fe5eb85a05b… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- correct signal num Commit: c85f07cf5fa2452122487cb66c3955fc88c6ea45 https://github.com/galaxyproject/galaxy/commit/c85f07cf5fa2452122487cb66c39… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5921 from erasche/fix-docs [18.01] correct signal num in docs Commit: fe0a4853b96ddc163ebfb09f961885b88c5577dd https://github.com/galaxyproject/galaxy/commit/fe0a4853b96ddc163ebfb09f9618… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- forgot to document github bug reporter Commit: 393f055a2307f090f71dc2c7750b8487cfafcd96 https://github.com/galaxyproject/galaxy/commit/393f055a2307f090f71dc2c7750b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- Merge pull request #5928 from erasche/document-gh-reporter [18.01] forgot to document github bug reporter Commit: 0c321cb86e8b8658de00169a1e1e675d547efe07 https://github.com/galaxyproject/galaxy/commit/0c321cb86e8b8658de00169a1e1e… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- removed config.ini parameter from cleanup scripts fixes https://github.com/galaxyproject/galaxy/issues/5941 Commit: 2d772d74b940f67f48e46f21270db0362a93276c https://github.com/galaxyproject/galaxy/commit/2d772d74b940f67f48e46f21270d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge pull request #5956 from bernt-matthias/topic/cleanup_for18.01 removed config.ini parameter from cleanup scripts Commit: 284795b94f2fa7f2a9ad4dc82990195815de1e9c https://github.com/galaxyproject/galaxy/commit/284795b94f2fa7f2a9ad4dc82990… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/feb3e5688dd6...284795b94f2f

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