August 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c6c646: Document the Chat Server
by GitHub 23 Aug '16

23 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c6c646ead407ef29a42ff6a6de7182837a97a1f7 https://github.com/galaxyproject/galaxy/commit/c6c646ead407ef29a42ff6a6de71… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png M doc/source/admin/index.rst Log Message: ----------- Document the Chat Server Commit: a1b2ec386e32f9fc357cb86836033a46084d8855 https://github.com/galaxyproject/galaxy/commit/a1b2ec386e32f9fc357cb8683603… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png M doc/source/admin/index.rst Log Message: ----------- Merge pull request #2843 from erasche/chat-docs [16.07] Document the Chat Server Compare: https://github.com/galaxyproject/galaxy/compare/c33bf2a222a0...a1b2ec386e32

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[galaxyproject/galaxy] 95113b: Skip whoami check for LDAP servers not supporting ...
by GitHub 23 Aug '16

23 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 95113b9c8473a6d33010e27910771299c25d35e0 https://github.com/galaxyproject/galaxy/commit/95113b9c8473a6d33010e2791077… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Skip whoami check for LDAP servers not supporting it Fix #2805. Commit: b16a9403de99f9b143f62fb35a9d0989987f050d https://github.com/galaxyproject/galaxy/commit/b16a9403de99f9b143f62fb35a9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #2832 from nsoranzo/fix_for_2805 Skip whoami check for LDAP servers not supporting it Compare: https://github.com/galaxyproject/galaxy/compare/ac3f8b0f5d4b...b16a9403de99

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[galaxyproject/galaxy] 873f34: Inject HOME, so that conda doens't attempt to writ...
by GitHub 23 Aug '16

23 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 873f34f07953eaf194ec0338139a736d413c30c0 https://github.com/galaxyproject/galaxy/commit/873f34f07953eaf194ec0338139a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Inject HOME, so that conda doens't attempt to write to ~/.conda Commit: c33bf2a222a09cc7707bdf621c257e1a951f969a https://github.com/galaxyproject/galaxy/commit/c33bf2a222a09cc7707bdf621c25… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2825 from mvdbeek/conda_install_fix Inject HOME, so that conda doens't attempt to write to ~/.conda Compare: https://github.com/galaxyproject/galaxy/compare/f4806e9dd4b8...c33bf2a222a0

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[galaxyproject/galaxy] a2f0bd: disable conda_auto_init
by GitHub 23 Aug '16

23 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a2f0bdbded8a0ae84567ed12107fb6b4fd294d48 https://github.com/galaxyproject/galaxy/commit/a2f0bdbded8a0ae84567ed12107f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- disable conda_auto_init Commit: ac3f8b0f5d4b4602c76e21d9a7a8cb8e59f0ee34 https://github.com/galaxyproject/galaxy/commit/ac3f8b0f5d4b4602c76e21d9a7a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2834 from martenson/disable_conda_auto_init [16.07] disable conda_auto_init Compare: https://github.com/galaxyproject/galaxy/compare/a079bc410bcf...ac3f8b0f5d4b

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[galaxyproject/galaxy] bf43b2: Remove beaker session options from reports and she...
by GitHub 23 Aug '16

23 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf43b2735e4aaf8becf776a3b99bb5f27694fecf https://github.com/galaxyproject/galaxy/commit/bf43b2735e4aaf8becf776a3b99b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample Log Message: ----------- Remove beaker session options from reports and shed. These were removed from Galaxy's config a while ago. Commit: 55d4f13d75382ad1d6186d78e2e18de1bdd3322f https://github.com/galaxyproject/galaxy/commit/55d4f13d75382ad1d6186d78e2e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Synchronize and update documentation for reports and shed. Commit: a079bc410bcfbb0bafb5d8ffa8ffc11599fa6b09 https://github.com/galaxyproject/galaxy/commit/a079bc410bcfbb0bafb5d8ffa8ff… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #2841 from jmchilton/sync_config_init Synchronize and regularize configs of shed & reports Compare: https://github.com/galaxyproject/galaxy/compare/65e8635ef38e...a079bc410bcf

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[galaxyproject/galaxy] 56914b: filter mail blacklist on the first domain level
by GitHub 23 Aug '16

23 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56914b2d203c0bb1b3835c533e7ff36ec0894721 https://github.com/galaxyproject/galaxy/commit/56914b2d203c0bb1b3835c533e7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/security/validate_user_input.py Log Message: ----------- filter mail blacklist on the first domain level Commit: 65e8635ef38ea3479fb47ccc213c48ac1b0357f4 https://github.com/galaxyproject/galaxy/commit/65e8635ef38ea3479fb47ccc213c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M lib/galaxy/security/validate_user_input.py Log Message: ----------- Merge pull request #2839 from martenson/adjust_mail_blacklist filter disposable mail blacklist on the first domain level only Compare: https://github.com/galaxyproject/galaxy/compare/49560c5dc0a7...65e8635ef38e

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[galaxyproject/ansible-galaxy] bd7a7f: Ensure shed_tools dir exists (as defined in Galaxy...
by GitHub 22 Aug '16

22 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: bd7a7f727e0747be2a631b70682a31f39b3d8728 https://github.com/galaxyproject/ansible-galaxy/commit/bd7a7f727e0747be2a63… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M defaults/main.yml M tasks/static_setup.yml Log Message: ----------- Ensure shed_tools dir exists (as defined in Galaxy's shed_tool_conf.xml) Commit: a6d62da7f8a37fe30242efbd3d4423c222b0cf78 https://github.com/galaxyproject/ansible-galaxy/commit/a6d62da7f8a37fe30242… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M defaults/main.yml M tasks/static_setup.yml Log Message: ----------- Merge pull request #16 from afgane/master Ensure shed_tools dir exists (as defined in Galaxy's shed_tool_conf.xml) Compare: https://github.com/galaxyproject/ansible-galaxy/compare/bf923e5b6c51...a6d6…

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[galaxyproject/galaxy] 0cf4f7: Fix Galaxy for if pyuwsgi is install in .venv.
by GitHub 22 Aug '16

22 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0cf4f7277e62f5f1318a0a6bba1afeacbce4ee10 https://github.com/galaxyproject/galaxy/commit/0cf4f7277e62f5f1318a0a6bba1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Fix Galaxy for if pyuwsgi is install in .venv. Commit: 49560c5dc0a7bfab5980c524948fb31871813276 https://github.com/galaxyproject/galaxy/commit/49560c5dc0a7bfab5980c524948f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge pull request #2836 from jmchilton/pyuwsgi_fix Fix Galaxy for if pyuwsgi is install in .venv. Compare: https://github.com/galaxyproject/galaxy/compare/bee9ebdbc126...49560c5dc0a7

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[galaxyproject/galaxy] bbdef2: Regularize galaxy.ini.sample.
by GitHub 19 Aug '16

19 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bbdef291e671eb0a24988ec0207c8a8eca37ed3e https://github.com/galaxyproject/galaxy/commit/bbdef291e671eb0a24988ec0207c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Regularize galaxy.ini.sample. Commit: bee9ebdbc126c15cd8a5eac4c6367e6398b8706e https://github.com/galaxyproject/galaxy/commit/bee9ebdbc126c15cd8a5eac4c636… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #2824 from jmchilton/regularize_sample Regularize galaxy.ini.sample. Compare: https://github.com/galaxyproject/galaxy/compare/41a369081268...bee9ebdbc126

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[galaxyproject/galaxy] fc450e: Make npm happier
by GitHub 19 Aug '16

19 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc450eafb6021e4766aa73afa286efb15c7784e4 https://github.com/galaxyproject/galaxy/commit/fc450eafb6021e4766aa73afa286… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Make npm happier Commit: 41a369081268a14b3bf4d20c57039ab5d4010c78 https://github.com/galaxyproject/galaxy/commit/41a369081268a14b3bf4d20c5703… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #2816 from erasche/node-proxy-license Correct license name in nodejs proxy Compare: https://github.com/galaxyproject/galaxy/compare/4e5eca9bc8b3...41a369081268

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