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

[galaxyproject/galaxy] 47b9eb: Add tox startup test and build matrix for travis-c...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47b9eb47ddd64d770791556f18fedceaf3a705ec https://github.com/galaxyproject/galaxy/commit/47b9eb47ddd64d770791556f18fe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M tox.ini Log Message: ----------- Add tox startup test and build matrix for travis-ci. Commit: 4176bc9115b94eba30c6ad9c7a1bf08823a3791b https://github.com/galaxyproject/galaxy/commit/4176bc9115b94eba30c6ad9c7a1b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M .travis.yml Log Message: ----------- Move first_startup to last position Commit: 3d4ddc438eb8e7e8822a2b0b05820098140ad6f3 https://github.com/galaxyproject/galaxy/commit/3d4ddc438eb8e7e8822a2b0b0582… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M .travis.yml Log Message: ----------- Add py27-unit tests on osx Commit: 84b783027d68beb4d2f83ca21311d1ee3ea64042 https://github.com/galaxyproject/galaxy/commit/84b783027d68beb4d2f83ca21311… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/base.less M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M scripts/common_startup.sh M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/style/blue/base.css M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Merge remote-tracking branch 'galaxy/dev' into HEAD Commit: faeedd6f824f5d5def7839d2e72248f6e38e4aef https://github.com/galaxyproject/galaxy/commit/faeedd6f824f5d5def7839d2e722… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M tox.ini Log Message: ----------- Merge pull request #1649 from mvdbeek/add_startup_test Add tox startup (run.sh) test and test on OS X and linux Compare: https://github.com/galaxyproject/galaxy/compare/75f1b58ecb8a...faeedd6f824f

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[galaxyproject/galaxy] ada39d: handle correctly application/json pased in POST
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ada39dea6ab68be543f53feb7a30e97167d96013 https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- handle correctly application/json pased in POST Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0 https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix setting library permissions to accept JSON correctly Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- unify api for library creation; support POST with url params Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824 https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- catch value errors from id decoding Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85 https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix updating library API to not require payload and to properly handle optional params Commit: 4b51be57d114d840112970baccb979ec1876663b https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- allow specifying DELETE params in JSON Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2 https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow creating folders with JSON payload Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2 https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folders.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- accept json as input for setting permissions; fix inconsistency by leveraging role_manager Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442 https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow PATCHing with payload in urlparams Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6 https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- remove deletion of the payload dict item it is not necessary and the key does not have to exist Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4 https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix unused imports and unused vars Commit: 134d792c1fcfba5d09e2937074c3263792bea991 https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- delete the 'payload' if it is in kwd so it is not supplied twice Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Revert "delete the 'payload' if it is in kwd so it is not supplied twice" This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991. Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6 https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- update docs of the data libraries API Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018 https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- Merge pull request #1641 from martenson/libraries-load-handle-payload [16.01] libraries: handle correctly application/json pased in POST Compare: https://github.com/galaxyproject/galaxy/compare/c693b69b3444...ef6bd90f2039

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[galaxyproject/galaxy] 1e79c8: Optionally pass dataset lists as a single file wit...
by GitHub 05 Feb '16

05 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e79c8c77e29f0aa5e6377d77ffa68d808ca4c89 https://github.com/galaxyproject/galaxy/commit/1e79c8c77e29f0aa5e6377d77ffa… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Optionally pass dataset lists as a single file within tool wrappers This change introduces an extra boolean XML attribute 'pass_as_file', that when used with an input parameter already having the 'multiple=True' attribute, passes the dataset list of files to the wrapped program as a single file containing a list of the dataset files. Commit: 27618a319d9c3bac01484bad80494f4423c04673 https://github.com/galaxyproject/galaxy/commit/27618a319d9c3bac01484bad8049… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- [Trivial] Whitespace fixes to please pylint Commit: 66350fb87100a8986a95c28f9b532564c98f0034 https://github.com/galaxyproject/galaxy/commit/66350fb87100a8986a95c28f9b53… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Modify pass_as_file to apply to all Multiple parameters and add test case Change the pass_as_file XML attribute to a cheetah method call, and apply to all paramter types that can have Multiple=True set - those given in DatasetListWrappers and DatasetCollectionWrappers. Test case and modification suggestion provided by John Chilton <jmchilton(a)gmail.com> Commit: 75f1b58ecb8a4e60fd9f3bbcbc6b9501005b903d https://github.com/galaxyproject/galaxy/commit/75f1b58ecb8a4e60fd9f3bbcbc6b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1658 from einon/pass_lists_as_file Optionally pass dataset lists as a single file within tool wrappers Compare: https://github.com/galaxyproject/galaxy/compare/dfceb5c144de...75f1b58ecb8a

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[galaxyproject/galaxy] 4b24d9: Improve documentation about binary-compatibility.c...
by GitHub 05 Feb '16

05 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4b24d95f6f95124f357b72434a29113fa9bacf73 https://github.com/galaxyproject/galaxy/commit/4b24d95f6f95124f357b72434a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Improve documentation about binary-compatibility.cfg. Resolves #1672. Commit: 9c7c75b7661989b5fe6f2e4819b04ae6e7b901a1 https://github.com/galaxyproject/galaxy/commit/9c7c75b7661989b5fe6f2e4819b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Typo Commit: c693b69b344461bd428a0ef314b3ec985e1a60d9 https://github.com/galaxyproject/galaxy/commit/c693b69b344461bd428a0ef314b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Merge pull request #1677 from natefoo/admin-docs [16.01] Improve documentation about binary-compatibility.cfg Compare: https://github.com/galaxyproject/galaxy/compare/9ead68aeca67...c693b69b3444

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[galaxyproject/galaxy] 61f168: A slightly different check for Galaxy object defin...
by GitHub 04 Feb '16

04 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61f168d34b748da0994be2d0d1c8c77af27c4520 https://github.com/galaxyproject/galaxy/commit/61f168d34b748da0994be2d0d1c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- A slightly different check for Galaxy object definition that doesn't assume a window-attached Galaxy context, only a parent. Minor cleanup. Commit: 33ebeb801d235af58a6e1152056d52e9ee5bfac6 https://github.com/galaxyproject/galaxy/commit/33ebeb801d235af58a6e1152056d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Use backbone routing for a tours URL, since there's no serverside endpoint. Commit: ab5f1536171dba6fc2f8afaae9c0154d46e1dd5b https://github.com/galaxyproject/galaxy/commit/ab5f1536171dba6fc2f8afaae9c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Clientside routing for tour kickoff, swapping from ?tour_id=foo approach. Commit: dfceb5c144de556e10659a8d876237188bd4595f https://github.com/galaxyproject/galaxy/commit/dfceb5c144de556e10659a8d8762… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/layout/menu.js.map M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #1671 from dannon/tour_fixes_and_cleanup Tour improvements and bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/d93f095c7f56...dfceb5c144de

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[galaxyproject/infrastructure-playbook] f16b24: Modify access list
by GitHub 04 Feb '16

04 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f16b24f8ff84d74da8e21de0cd2db012678801f1 https://github.com/galaxyproject/infrastructure-playbook/commit/f16b24f8ff8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml Log Message: ----------- Modify access list

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[galaxyproject/galaxy] 8cee21: Fixes <param argument="--set" /> not working when ...
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cee212708f4de75c4bf066ac1dec0752bea0a5d https://github.com/galaxyproject/galaxy/commit/8cee212708f4de75c4bf066ac1de… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fixes <param argument="--set" /> not working when help="" is not set Commit: 09911084f3b424d4822d4b5baed7fa3ca1a0a3b9 https://github.com/galaxyproject/galaxy/commit/09911084f3b424d4822d4b5baed7… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fixes <param argument="--set" /> not working when help="" is not set (indentation) Commit: d7dd9f9040be7a66e414322a67e15bea1b93a9f6 https://github.com/galaxyproject/galaxy/commit/d7dd9f9040be7a66e414322a67e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Rebuild client stuff for #1650. Commit: d93f095c7f56c85c871ef82f532c68e12d3a3318 https://github.com/galaxyproject/galaxy/commit/d93f095c7f56c85c871ef82f532c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/param_argument_fix' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/d97e8bbbbce8...d93f095c7f56

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[galaxyproject/galaxy] 9551fc: Add the `scientific` platform (Scientific Linux) a...
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9551fc07b475b4095b7d002315cbc05bdf0925b5 https://github.com/galaxyproject/galaxy/commit/9551fc07b475b4095b7d002315cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL. Commit: 9ead68aeca6722f62d3d6fabae6484aa00246615 https://github.com/galaxyproject/galaxy/commit/9ead68aeca6722f62d3d6fabae64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1669 from natefoo/scientificlinux-tag-compat [16.01] Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL Compare: https://github.com/galaxyproject/galaxy/compare/bb95a65b2201...9ead68aeca67

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[galaxyproject/galaxy] 17a168: Warn on optional select test parameter.
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17a1683a383d7f375b77371548ff7d349a561a96 https://github.com/galaxyproject/galaxy/commit/17a1683a383d7f375b77371548ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Warn on optional select test parameter. Commit: ccdb027d38428a38d79b4272fadb076b7f428825 https://github.com/galaxyproject/galaxy/commit/ccdb027d38428a38d79b4272fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Prevent optional test parameters in conditionals Commit: 6fa7f1e1edda25ec36f2373148af223493924803 https://github.com/galaxyproject/galaxy/commit/6fa7f1e1edda25ec36f2373148af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam to new 0.8.4+gx1. Commit: 508ebea63f2376b5a3b452148e4a6d3c18366b3b https://github.com/galaxyproject/galaxy/commit/508ebea63f2376b5a3b452148e4a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #8 from jmchilton/fix_optional_001 Warn on optional select test parameter. Commit: ba9ad97c40bd994e0dc51888ef235cf3b434168a https://github.com/galaxyproject/galaxy/commit/ba9ad97c40bd994e0dc51888ef23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details. Commit: 39eb262219beca9ec6b849b49c0430d834cfd2ae https://github.com/galaxyproject/galaxy/commit/39eb262219beca9ec6b849b49c04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16 Commit: 66f20e7df91074e07cbade57b20deb68cb840a55 https://github.com/galaxyproject/galaxy/commit/66f20e7df91074e07cbade57b20d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix method signature of bam.set_meta to include a positional argument which is now required. Commit: d6325c5039f28062a2cf49d00c091d83a92865c3 https://github.com/galaxyproject/galaxy/commit/d6325c5039f28062a2cf49d00c09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Update data providers pysam.AlignmentFile usage Commit: a95827751f463f35c67e76f84127f850972244c5 https://github.com/galaxyproject/galaxy/commit/a95827751f463f35c67e76f84127… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1637 from guerler/fix_optional_001 [16.01] Prevent optional test parameters in conditionals Commit: 45f523f9229f6d943e3a65042b8cad0276a0a7d7 https://github.com/galaxyproject/galaxy/commit/45f523f9229f6d943e3a65042b8c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- fix show_welcome_with_login = True Commit: b5d1c7721ee2f8ad1095e52d4e710b998f92945d https://github.com/galaxyproject/galaxy/commit/b5d1c7721ee2f8ad1095e52d4e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1664 from bgruening/release_16.01 fix `show_welcome_with_login = True` Commit: cd3f3b330db34e294e78374e8e8b32300c66f36e https://github.com/galaxyproject/galaxy/commit/cd3f3b330db34e294e78374e8e8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py M test-data/3.bam Log Message: ----------- Merge pull request #1638 from dannon/pysam_84_update Pysam 84 update [16.01] Commit: 246870c459cffd48a0fe7b4963e674638298e620 https://github.com/galaxyproject/galaxy/commit/246870c459cffd48a0fe7b4963e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/data_providers/genome.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M test-data/3.bam Log Message: ----------- Merge branch 'release_16.01' into dev Commit: d97e8bbbbce862eb6b4f8f5732cd0baa029e9e20 https://github.com/galaxyproject/galaxy/commit/d97e8bbbbce862eb6b4f8f5732cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/data_providers/genome.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M test-data/3.bam Log Message: ----------- Merge pull request #1667 from natefoo/dev Merge release_16.01 to dev Compare: https://github.com/galaxyproject/galaxy/compare/b82efd937504...d97e8bbbbce8

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[galaxyproject/galaxy] bf989f: correct typo in text datatype
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1 https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- correct typo in text datatype Commit: bb95a65b2201509ce950d6c3c578f8d417f83cc4 https://github.com/galaxyproject/galaxy/commit/bb95a65b2201509ce950d6c3c578… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1666 from martenson/correct-datatype-typo [16.01] correct typo in text datatype Compare: https://github.com/galaxyproject/galaxy/compare/2641f0af9ac8...bb95a65b2201

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