- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 54e4f0: disable hg middleware
by GitHub 19 Aug '16

19 Aug '16

Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy Commit: 54e4f0a29c72f74f17c9cb75f16c24fc829152c5 https://github.com/galaxyproject/galaxy/commit/54e4f0a29c72f74f17c9cb75f16c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- disable hg middleware Commit: bb5aab9553a0af9368d46c74e37ca89d3cfdb7c5 https://github.com/galaxyproject/galaxy/commit/bb5aab9553a0af9368d46c74e37c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/shed_functional/functional/test_0310_hg_api_features.py Log Message: ----------- remove unwanted hg middleware remove obsolete test Commit: 47fcec8102fea8f67d0b7f469eea8b6c10940c22 https://github.com/galaxyproject/galaxy/commit/47fcec8102fea8f67d0b7f469eea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- remove obsolete config option Commit: a88829e62bd0459189d6bed24fa70bb47cf73164 https://github.com/galaxyproject/galaxy/commit/a88829e62bd0459189d6bed24fa7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- remove code related to hg push Commit: 929297f5b68e7e36260e127df83292c6dd96e591 https://github.com/galaxyproject/galaxy/commit/929297f5b68e7e36260e127df832… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/hg.py Log Message: ----------- reimplement clone tracking that used to be in the middleware Commit: 980393c6ebcb614099abe0f9c13bbf9821219f91 https://github.com/galaxyproject/galaxy/commit/980393c6ebcb614099abe0f9c13b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- prevent TS from creating sessions for repo status checks this had to be done: - enable Routes middleware - redirect in the middleware before the request reaches the app - properly forward the contents of the query string - move the controller method to the API namespace and properly decorate - provide the ability to not hexlify the response (so we can dump it in future Galaxy release) I hope that this work will allow easier transition from controllers to APIs and also smoother deprecation of API endpoints. Commit: 1c4aae3040c578dbd9d05e756f44dba44471d74f https://github.com/galaxyproject/galaxy/commit/1c4aae3040c578dbd9d05e756f44… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- reorder middleware imports, explicitly store and pass routes mapper Conflicts: lib/galaxy/webapps/tool_shed/buildapp.py Commit: 12e0b9485aaf8bf4cf104fd6bb2471c11a8e653c https://github.com/galaxyproject/galaxy/commit/12e0b9485aaf8bf4cf104fd6bb24… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- amke endpoint name more RESTful Commit: 631ee7f0b23e09355b2f583536e8566b3d8d0b83 https://github.com/galaxyproject/galaxy/commit/631ee7f0b23e09355b2f583536e8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py Log Message: ----------- make routes.middleware less chatty, and reorder import Conflicts: lib/galaxy/config.py Commit: c541c023d8fd94f0ba64059500de622ea17cbced https://github.com/galaxyproject/galaxy/commit/c541c023d8fd94f0ba64059500de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- be python3 compatible, thanks EagleEyes Commit: 08a2381e1dc8e8eb7eb0dee4c9f29bef41282d38 https://github.com/galaxyproject/galaxy/commit/08a2381e1dc8e8eb7eb0dee4c9f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- create own mapper for middleware redirects Commit: 81cc44d0d0445c84a99ad05cc2236287a3712b30 https://github.com/galaxyproject/galaxy/commit/81cc44d0d0445c84a99ad05cc223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- fix pep8 Commit: 310c053e3f6dfb27a87938bf4380ffd3fe6da6ec https://github.com/galaxyproject/galaxy/commit/310c053e3f6dfb27a87938bf4380… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/webapps/tool_shed/app.py Log Message: ----------- remove unused import Commit: 201cbc91c65c9e6be8eae4a5032774daffc07d86 https://github.com/galaxyproject/galaxy/commit/201cbc91c65c9e6be8eae4a50327… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Make tool shed logging like Galaxy logging. - Reduces duplicated code. - Enables best practice of commenting out defaults in shed sample config. - Add auto_configure_logging option to tool shed to match Galaxy. Commit: b27089ed28d7826db53befc8adcf68017012e431 https://github.com/galaxyproject/galaxy/commit/b27089ed28d7826db53befc8adcf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- move the configure_logging import to the app.py where it is used remove routes.middleware chatty logging as the PR is independent on this Commit: 9351dac59794e136b1fd4780c0bacb972560d81a https://github.com/galaxyproject/galaxy/commit/9351dac59794e136b1fd4780c0ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- put routes middleware back into chatty loggers Commit: 3e65e768c8cb486c24d6dfe87365d048f470027d https://github.com/galaxyproject/galaxy/commit/3e65e768c8cb486c24d6dfe87365… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py R lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/shed_functional/functional/test_0310_hg_api_features.py Log Message: ----------- Merge pull request #2813 from martenson/master-toolshed [master-toolshed] cherrypick middleware and sessionless changes Compare: https://github.com/galaxyproject/galaxy/compare/8d512c98e237...3e65e768c8cb

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[galaxyproject/galaxy] 94b0af: Allow NodeJS proxy to do reverse proxying
by GitHub 19 Aug '16

19 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 94b0afe1d7d107c96a526dadcd7e56085d3e8ce2 https://github.com/galaxyproject/galaxy/commit/94b0afe1d7d107c96a526dadcd7e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Allow NodeJS proxy to do reverse proxying Commit: ebcd5a5a07fd9618d94737879cae184cd50b1829 https://github.com/galaxyproject/galaxy/commit/ebcd5a5a07fd9618d94737879cae… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Enable by default Commit: 4e5eca9bc8b30df00ea86a325a4bdba934199823 https://github.com/galaxyproject/galaxy/commit/4e5eca9bc8b30df00ea86a325a4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2817 from erasche/gie-nodejs-rp Allow NodeJS proxy to do reverse proxying Compare: https://github.com/galaxyproject/galaxy/compare/83e83406984a...4e5eca9bc8b3

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[galaxyproject/usegalaxy-playbook] 01f5d5: Enable uWSGI thunder-lock. See: http://uwsgi-docs....
by GitHub 19 Aug '16

19 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 01f5d5af72269378d8f333f35d6d6d0c31c15bfd https://github.com/galaxyproject/usegalaxy-playbook/commit/01f5d5af72269378… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Enable uWSGI thunder-lock. See: http://uwsgi-docs.readthedocs.io/en/latest/articles/SerializingAccept.html

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commit/galaxy-central: clements: README.rst edited online with Bitbucket
by commits-noreply＠bitbucket.org 19 Aug '16

19 Aug '16

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a843691b7f64/ Changeset: a843691b7f64 User: clements Date: 2016-08-19 15:48:14+00:00 Summary: README.rst edited online with Bitbucket Affected #: 1 file diff -r 38999c655b2095602ce6cedb7f61357cf61c082e -r a843691b7f64f782a12b02a48ff38d34b8161e75 README.rst --- a/README.rst +++ b/README.rst @@ -1,16 +1,6 @@ .. figure:: https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&t… :alt: Galaxy Logo -This repository has moved to Github and the one here is no longer updated. -========================================================================== - -Please switch to using https://github.com/galaxyproject/galaxy -============================================================== - -The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__ -================================================================================================================ - - .. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg :target: https://biostar.usegalaxy.org :alt: Ask a question @@ -26,3 +16,12 @@ .. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev :target: https://travis-ci.org/galaxyproject/galaxy :alt: Inspect the test results + +This repository has moved to Github and the one here is no longer updated. +========================================================================== + +Please switch to using https://github.com/galaxyproject/galaxy +============================================================== + +The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__ +================================================================================================================ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: clements: README.rst edited online with Bitbucket
by commits-noreply＠bitbucket.org 19 Aug '16

19 Aug '16

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/38999c655b20/ Changeset: 38999c655b20 User: clements Date: 2016-08-19 15:46:14+00:00 Summary: README.rst edited online with Bitbucket Affected #: 1 file diff -r 81b6301b85d1b4803ab3ec76ca7c65c72125b329 -r 38999c655b2095602ce6cedb7f61357cf61c082e README.rst --- a/README.rst +++ b/README.rst @@ -1,11 +1,15 @@ .. figure:: https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&t… :alt: Galaxy Logo -# This repository has moved to Github and the one here is no longer updated. # +This repository has moved to Github and the one here is no longer updated. +========================================================================== Please switch to using https://github.com/galaxyproject/galaxy +============================================================== The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__ +================================================================================================================ + .. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg :target: https://biostar.usegalaxy.org @@ -22,41 +26,3 @@ .. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev :target: https://travis-ci.org/galaxyproject/galaxy :alt: Inspect the test results - -Galaxy Quickstart -================= - -Galaxy requires Python 2.6 or 2.7. To check your python version, run: - -.. code:: console - - $ python -V - Python 2.7.3 - -Start Galaxy: - -.. code:: console - - $ sh run.sh - -Once Galaxy completes startup, you should be able to view Galaxy in your -browser at: - -http://localhost:8080 - -You may wish to make changes from the default configuration. This can be -done in the ``config/galaxy.ini`` file. Tools can be either installed -from the Tool Shed or added manually. For details please see the Galaxy -wiki: - -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial - -Not all dependencies are included for the tools provided in the sample -``tool_conf.xml``. A full list of external dependencies is available at: - -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies - -Issues and Galaxy Development -============================= - -Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ . \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: clements: README.rst edited online with Bitbucket
by commits-noreply＠bitbucket.org 19 Aug '16

19 Aug '16

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81b6301b85d1/ Changeset: 81b6301b85d1 User: clements Date: 2016-08-19 15:37:56+00:00 Summary: README.rst edited online with Bitbucket Affected #: 1 file diff -r 3f95c21b1a85af3ae1260eb957ea041d1de8bd5b -r 81b6301b85d1b4803ab3ec76ca7c65c72125b329 README.rst --- a/README.rst +++ b/README.rst @@ -1,6 +1,10 @@ .. figure:: https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&t… :alt: Galaxy Logo +# This repository has moved to Github and the one here is no longer updated. # + +Please switch to using https://github.com/galaxyproject/galaxy + The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__ .. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg @@ -55,4 +59,4 @@ Issues and Galaxy Development ============================= -Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ . +Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ . \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/galaxy] cc3149: Fix small NoneType bug in check.py.
by GitHub 19 Aug '16

19 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cc314902b411bcdadc5c1181270521ff3d6293d6 https://github.com/galaxyproject/galaxy/commit/cc314902b411bcdadc5c11812705… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Fix small NoneType bug in check.py. Causes confusing error message when error message should be something different. Commit: e6799d50809576dd91c007dcaf7696c733648d97 https://github.com/galaxyproject/galaxy/commit/e6799d50809576dd91c007dcaf76… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Document missing database_auto_migrate option in galaxy.ini.sample. Commit: 83e83406984ad82f5ddb1c89e438236b2cacdfec https://github.com/galaxyproject/galaxy/commit/83e83406984ad82f5ddb1c89e438… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/migrate/check.py Log Message: ----------- Merge pull request #2814 from jmchilton/config_tweaks Two Small Config Tweaks Compare: https://github.com/galaxyproject/galaxy/compare/079aeddde20f...83e83406984a

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