August 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 249d18: Minor cleanup of some iterators.
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 249d185d88bfdca668ca08775ef8c93bef34557c https://github.com/galaxyproject/galaxy/commit/249d185d88bfdca668ca08775ef8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Minor cleanup of some iterators. Commit: 5885ce870e4b42b94be9115180880b7e2a1c96db https://github.com/galaxyproject/galaxy/commit/5885ce870e4b42b94be911518088… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Address Nicola's concerns. Commit: db4461177162fae94b2100363d3e617c213d09df https://github.com/galaxyproject/galaxy/commit/db4461177162fae94b2100363d3e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Merge pull request #589 from davebx/cleanup_ts Minor cleanup of some iterators. Compare: https://github.com/galaxyproject/galaxy/compare/a04147dc56cc...db4461177162

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[galaxyproject/infrastructure-playbook] 7b6c08: Removed invalid flags from ssh keys.
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7b6c0858acd570c47ebdf3f16a09db0710ad3cbe https://github.com/galaxyproject/infrastructure-playbook/commit/7b6c0858acd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Removed invalid flags from ssh keys.

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[galaxyproject/infrastructure-playbook] ca2d50: Ensure debconf utils are installed for Mailman
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ca2d50b595141bce623e55ac9fbea9f94f84fa64 https://github.com/galaxyproject/infrastructure-playbook/commit/ca2d50b5951… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M roles/mailman/tasks/main.yml Log Message: ----------- Ensure debconf utils are installed for Mailman

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[galaxyproject/infrastructure-playbook] 229fea: Fix mail on SmartOS (non-GZ, anyway). As a result, ...
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 229feae52598cc3a09fbe9ac6830c05063823b6e https://github.com/galaxyproject/infrastructure-playbook/commit/229feae5259… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: A roles/mailman/files/default-spamassassin A roles/mailman/files/mm_discard_report.py A roles/mailman/handlers/main.yml A roles/mailman/meta/main.yml A roles/mailman/tasks/main.yml A roles/mailman/templates/mailman.ini.j2 A roles/mailman/templates/mm_cfg.py.j2 A roles/mailman/templates/mm_genaliases_ldap.j2 A roles/postfix/defaults/main.yml A roles/postfix/handlers/main.yml A roles/postfix/tasks/main.yml A roles/postfix/tasks/mx.yml A roles/postfix/tasks/relay.yml A roles/postfix/templates/15-content_filter_mode.j2 A roles/postfix/templates/50-user.j2 A roles/postfix/templates/ldap-aliases.cf.j2 A roles/postfix/templates/ldap-lists.cf.j2 A roles/postfix/templates/ldap-local.cf.j2 A roles/postfix/templates/local.cf.j2 A roles/postfix/templates/mailer.conf.j2 A roles/postfix/templates/main.cf.j2 A roles/postfix/templates/master.cf.j2 A roles/postfix/vars/default.yml A roles/postfix/vars/smartos.yml Log Message: ----------- Fix mail on SmartOS (non-GZ, anyway). As a result, bring the postfix and mailman roles over from the private playbook. So far, putting almost everything in a single play seems to be working out well. The only downside here is that as more stuff is added, there will be a *lot* of skipped tasks. Commit: 5f2cd8c675fa3659788f83dcd8d20689b1806b9a https://github.com/galaxyproject/infrastructure-playbook/commit/5f2cd8c675f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M galaxyenv/group_vars/all.yml A galaxyenv/group_vars/listservers.yml A galaxyenv/group_vars/mailservers.yml A galaxyenv/host_vars/chouffe.galaxyproject.org.yml A galaxyenv/host_vars/delirium.galaxyproject.org.yml M galaxyenv/inventory M playbook.yml Log Message: ----------- Data for the previously added postfix and mailman roles. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b04320d9c6…

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[galaxyproject/usegalaxy-playbook] e22a25: Update to postgresql role version 0.9.2
by GitHub 10 Aug '15

10 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e22a25d404ed6dd749c30adc4ff3da775130e7ed https://github.com/galaxyproject/usegalaxy-playbook/commit/e22a25d404ed6dd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info M roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 Log Message: ----------- Update to postgresql role version 0.9.2

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[galaxyproject/usegalaxy-playbook] 87d14f: Fix path to zfs binary for radegast backups
by GitHub 10 Aug '15

10 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 87d14ff2b9a88a384a2091a5a9a961596f098367 https://github.com/galaxyproject/usegalaxy-playbook/commit/87d14ff2b9a88a38… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml Log Message: ----------- Fix path to zfs binary for radegast backups

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[galaxyproject/galaxy] ee4f07: Per @yhoogstrate's suggestion https://github.com/g...
by GitHub 10 Aug '15

10 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee4f077c526dbda7752baef59d97b671b9effac6 https://github.com/galaxyproject/galaxy/commit/ee4f077c526dbda7752baef59d97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Per @yhoogstrate's suggestion https://github.com/galaxyproject/galaxy/commit/c0c286a9c69dcb23a50a0b9b249c…, retab .loc.samples Commit: a04147dc56cc747c67aeacc1773b5bb747347957 https://github.com/galaxyproject/galaxy/commit/a04147dc56cc747c67aeacc1773b… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge pull request #587 from dannon/retab_loc_samples Retab .loc.samples Compare: https://github.com/galaxyproject/galaxy/compare/7baab04081cb...a04147dc56cc

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[galaxyproject/galaxy] 524fd9: remove undused files
by GitHub 10 Aug '15

10 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 524fd95ca6764dfde58b1d047474b2d3afad1e9b https://github.com/galaxyproject/galaxy/commit/524fd95ca6764dfde58b1d047474… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg R static/welcome.rst Log Message: ----------- remove undused files Commit: 7baab04081cbc6a280443ff967a1f69e8ec721d8 https://github.com/galaxyproject/galaxy/commit/7baab04081cbc6a280443ff967a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg R static/welcome.rst Log Message: ----------- Merge pull request #583 from martenson/cleanup-static remove unused files in /static Compare: https://github.com/galaxyproject/galaxy/compare/fc6b965bba06...7baab04081cb

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[galaxyproject/usegalaxy-playbook] cb17ca: Update postgresql role to 0.9.1
by GitHub 10 Aug '15

10 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cb17ca4e8d09eb59399f8708f8328976ee66461c https://github.com/galaxyproject/usegalaxy-playbook/commit/cb17ca4e8d09eb59… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M roles/galaxyprojectdotorg.postgresql/README.md M roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info M roles/galaxyprojectdotorg.postgresql/tasks/backup.yml M roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2 M roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 Log Message: ----------- Update postgresql role to 0.9.1 Commit: 13d1073b01dd7c397fed208f1c815ebfa40067c9 https://github.com/galaxyproject/usegalaxy-playbook/commit/13d1073b01dd7c39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml Log Message: ----------- Fix radegast backups Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c0fd2ffbbf8c...…

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[galaxyproject/usegalaxy-playbook] c0fd2f: Update common_roles submodule
by GitHub 10 Aug '15

10 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c0fd2ffbbf8ceca457c0f6b9224db577f34d8974 https://github.com/galaxyproject/usegalaxy-playbook/commit/c0fd2ffbbf8ceca4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M common_roles Log Message: ----------- Update common_roles submodule

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