galaxy-commits December 2015

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[galaxyproject/galaxy] 114808: Implement a conda dependency resolver.
by GitHub 30 Dec '15

30 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1148081435e6eb4075eb62783129299ebbd4d490 https://github.com/galaxyproject/galaxy/commit/1148081435e6eb4075eb62783129… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_job_wrapper.py A test/unit/tools/test_conda_resolution.py Log Message: ----------- Implement a conda dependency resolver. Much more information on planemo PR that I used to build a test bed for this: https://github.com/galaxyproject/planemo/pull/392 Also syncs galaxy with planemo shared library changed. Commit: 0aa1c5133e029196444ac9c0b32f43489cee3713 https://github.com/galaxyproject/galaxy/commit/0aa1c5133e029196444ac9c0b32f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_job_wrapper.py A test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #1345 from jmchilton/conda_0 Implement a conda dependency resolver. Compare: https://github.com/galaxyproject/galaxy/compare/2b2f93d393a4...0aa1c5133e02

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[galaxyproject/galaxy] d5d404: Implement special config file to dump parameters a...
by GitHub 30 Dec '15

30 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5d404c912340013aab34fe3350a2570010b0898 https://github.com/galaxyproject/galaxy/commit/d5d404c912340013aab34fe3350a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement special config file to dump parameters as json. ``` <configfiles> <inputs name="inputs" format="json" version="1" /> </configfiles> ``` Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday. Commit: de0c913b8bb3ca01fd0ab5c8286450dbef9b604d https://github.com/galaxyproject/galaxy/commit/de0c913b8bb3ca01fd0ab5c82864… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M test/functional/tools/inputs_as_json.xml Log Message: ----------- More work on converting tool inputs to json. - Drop version requirement per commends by @bgruening. - Add examples for conditionals, repeats, sections, colors, and booleans specified truevalue/falsevalue. - Various bug fixes unearthed by new test cases. Commit: cd32b91dc9f562d17349d8cc15ba1b60eba07f70 https://github.com/galaxyproject/galaxy/commit/cd32b91dc9f562d17349d8cc15ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M test/functional/tools/inputs_as_json.xml Log Message: ----------- Update inputs_as_json.xml to drop version attribute. Also add note about filename. Commit: 9a0ef0ed14893bf1dcaae67b466a8b1167571032 https://github.com/galaxyproject/galaxy/commit/9a0ef0ed14893bf1dcaae67b466a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Expose hidden parameters in inputs json. Commit: 2b2f93d393a4e66c0e466e98a945222bd54e448a https://github.com/galaxyproject/galaxy/commit/2b2f93d393a4e66c0e466e98a945… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1405 from jmchilton/json_config Implement special config file to dump parameters as json. Compare: https://github.com/galaxyproject/galaxy/compare/14a618ee3ab0...2b2f93d393a4

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[galaxyproject/galaxy] 7269f7: Remove transiently failing maxseconds.xml framewor...
by GitHub 28 Dec '15

28 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7269f76e6e8227d26c928e76cd81941498c0acd7 https://github.com/galaxyproject/galaxy/commit/7269f76e6e8227d26c928e76cd81… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Remove transiently failing maxseconds.xml framework test. Commit: 79bbc97a189bea03392bff2ab6a819aca1fad0db https://github.com/galaxyproject/galaxy/commit/79bbc97a189bea03392bff2ab6a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Attempt to fix transiently failing capsule TS test. Guess here is that a flush is not occuring on that file because it is happening as part of garbage collection and not explictly as part of an explicit close. Commit: 14a618ee3ab084e43f51f72136afd6b4c482b4cf https://github.com/galaxyproject/galaxy/commit/14a618ee3ab084e43f51f72136af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-28 (Mon, 28 Dec 2015) Changed paths: M test/functional/tools/samples_tool_conf.xml M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1401 from jmchilton/transient_tests_2 Fix and potential fix for transiently failing tests. Compare: https://github.com/galaxyproject/galaxy/compare/798c7e20c338...14a618ee3ab0

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[galaxyproject/galaxy] 47a442: Add Jupyter Interactive Environment
by GitHub 27 Dec '15

27 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47a44202673839fe1ff00408c50c533ddd823a27 https://github.com/galaxyproject/galaxy/commit/47a44202673839fe1ff00408c50c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Add Jupyter Interactive Environment Commit: 38d40e7af11525348bb54bad3a3a8496539a2a3a https://github.com/galaxyproject/galaxy/commit/38d40e7af11525348bb54bad3a3a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- move keep_alive into jupyter.js Commit: 6ac01675f3f37a6af1d498b96cad753a03a8a776 https://github.com/galaxyproject/galaxy/commit/6ac01675f3f37a6af1d498b96cad… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample Log Message: ----------- Change default image name to a versioned tagged Docker release. Commit: 798c7e20c33860ada2bb066277a3280488e25492 https://github.com/galaxyproject/galaxy/commit/798c7e20c33860ada2bb066277a3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Merge pull request #1400 from bgruening/jupyter Add Jupyter Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/4e55f7e519a0...798c7e20c338

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[galaxyproject/usegalaxy-playbook] fa5643: Dropped Barcelona slide from rotation.
by GitHub 27 Dec '15

27 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa5643bf13d5f2fb27051425aa94a55412b52074 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa5643bf13d5f2fb… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped Barcelona slide from rotation.

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[galaxyproject/galaxy] ed11f7: Offer galaxy_web_port in all scenarios, this can b...
by GitHub 27 Dec '15

27 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed11f7ab00b0ff3f414dc23736c054a655b44663 https://github.com/galaxyproject/galaxy/commit/ed11f7ab00b0ff3f414dc23736c0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Offer galaxy_web_port in all scenarios, this can be useful in some local dev settings. Commit: 7b118990d2bee4377b364373fd596b88d0275307 https://github.com/galaxyproject/galaxy/commit/7b118990d2bee4377b364373fd59… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Catch errors in some wired cases. This will prevent the proxy to crash badly if the Docker container just disappears. Commit: 1873d2c5edbb44eb0e8138612d55510b3492782b https://github.com/galaxyproject/galaxy/commit/1873d2c5edbb44eb0e8138612d55… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- update js scripts Commit: 4e55f7e519a0e03805e0f3d91ab8de47c357d040 https://github.com/galaxyproject/galaxy/commit/4e55f7e519a0e03805e0f3d91ab8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1399 from bgruening/ie Interactive Environment updates Compare: https://github.com/galaxyproject/galaxy/compare/6aa7691a637e...4e55f7e519a0

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[galaxyproject/galaxy] 355bb2: Finish swapping unencoded ids with order_index in ...
by GitHub 26 Dec '15

26 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 355bb281e21e701e05d1f671f080022de9df987b https://github.com/galaxyproject/galaxy/commit/355bb281e21e701e05d1f671f080… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Finish swapping unencoded ids with order_index in workflows API. Running a workflow or showing a workflow can both restore the previous behavior by passing legacy=True as an API parameter. By changing these two endpoints in tandem I believe backward compatiblity for most existing code should be maintained unless: - The external application saved these workflow IDs previously and re-runs workflows without refetching the workflow definition. I could imagine Refinery for instance might do this and will have to update indexed workflows or add legacy=True to workflow requests. - The external application contacted the database directly after using this API endpoint to fetch more information about the step (seems unlikely). See conversation: - http://dev.list.galaxyproject.org/workflow-API-step-order-vs-step-id-in-bio… Rebased with changes suggested by @nsoranzo. Commit: 6aa7691a637e86491a51d41a1672521f42a06bb5 https://github.com/galaxyproject/galaxy/commit/6aa7691a637e86491a51d41a1672… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Merge pull request #1137 from jmchilton/workflow_api_order_2 Finish swapping unencoded ids with order_index in workflows API. Compare: https://github.com/galaxyproject/galaxy/compare/2466b1cb6575...6aa7691a637e

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[galaxyproject/galaxy] ddaa11: Adding uuid support to directory_hash_id
by GitHub 24 Dec '15

24 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ddaa1189f75627f516926b5363398fe7e24fe992 https://github.com/galaxyproject/galaxy/commit/ddaa1189f75627f516926b536339… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Adding uuid support to directory_hash_id Commit: 8f34f2a6104ff595d411bfc5e77b488f2c86dfd9 https://github.com/galaxyproject/galaxy/commit/8f34f2a6104ff595d411bfc5e77b… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Fixing issues for PR unit testing and linting Commit: 4840a3d8b1caae9666eeebf95d4aeaebaee8260b https://github.com/galaxyproject/galaxy/commit/4840a3d8b1caae9666eeebf95d4a… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Fixing lint problem Commit: 2466b1cb65757b0157dab67a16c7bbfd7b48c710 https://github.com/galaxyproject/galaxy/commit/2466b1cb65757b0157dab67a16c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-24 (Thu, 24 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Merge pull request #1397 from kellrott/dev Adding uuid support to directory_hash_id Compare: https://github.com/galaxyproject/galaxy/compare/26d7e97ed7b4...2466b1cb6575

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[galaxyproject/usegalaxy-playbook] 80ad59: install vegan on Main
by GitHub 23 Dec '15

23 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 80ad593085d2172ce98bb9d847c38e4f54bce1ee https://github.com/galaxyproject/usegalaxy-playbook/commit/80ad593085d2172c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install vegan on Main

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[galaxyproject/usegalaxy-playbook] 70cc35: update Main mutable confs, isntall vsearch
by GitHub 23 Dec '15

23 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 70cc35cd91c02b363906ef589a3cf953396f3229 https://github.com/galaxyproject/usegalaxy-playbook/commit/70cc35cd91c02b36… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- update Main mutable confs, isntall vsearch

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galaxy-commits December 2015