galaxy-commits July 2016

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[galaxyproject/galaxy] 4ea881: Fix old bug in non-allowed_images.yml GIEs
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ea881caa21602c5562224fa268ff87788eee0dd https://github.com/galaxyproject/galaxy/commit/4ea881caa21602c5562224fa268f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix old bug in non-allowed_images.yml GIEs Commit: 1069a69ae08a4a2db609aebb03c4a8fa53162777 https://github.com/galaxyproject/galaxy/commit/1069a69ae08a4a2db609aebb03c4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2550 from erasche/asdf [16.04] Fix old bug in non-allowed_images.yml GIEs Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix tag_autocomplete issue. When we swapped to tag manager the signature changed and some of these were missed. Commit: 1507bd37fe8cb872975e46a6e7be468e984db0d8 https://github.com/galaxyproject/galaxy/commit/1507bd37fe8cb872975e46a6e7be… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- More defensive proxying Commit: f8e40bb5951cc38dce118cebcc09a5cc3ca96930 https://github.com/galaxyproject/galaxy/commit/f8e40bb5951cc38dce118cebcc09… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2585 from erasche/backport-proxy-fix [16.04] Backport proxy fixes Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: acdfd2423f3e8764375d0b7a23dad3c919db47fc https://github.com/galaxyproject/galaxy/commit/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: 84d152082009418f2fd5dfe0e9001e8924a678fc https://github.com/galaxyproject/galaxy/commit/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Absolute positioning for tabular dataset chunking, vs abstract chunk. Ships a minimum of one line regardless of size, and relies on client to know position. Commit: ca4b51b390d14077188b5226e4c83ed0991dcbb5 https://github.com/galaxyproject/galaxy/commit/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Make client with new tabular display. Commit: a65faa961ca434901baaaeffe2e5926d4ac523c1 https://github.com/galaxyproject/galaxy/commit/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix tabular chunked display offset=0 request, pass through ck_size to allow client specification of chunk size overriding the app defaults (neither of these are used by the js client currently though) Commit: d7cdf74bdf2690ab1d83cb262021251ae3e28d14 https://github.com/galaxyproject/galaxy/commit/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Handle the case when the last character of the initial read is a newline. Commit: b7718a0f9ae3a626ab88080e0798a451597984c8 https://github.com/galaxyproject/galaxy/commit/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Swap ck_size default from 0 to None to indicate unset. This does not change any behavior at all, but @nsoranzo requested the change to make usage more clear. Commit: 1d8f39d987217c09048e05e1d5443173eb02a9f2 https://github.com/galaxyproject/galaxy/commit/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove old, unused arguments from some display_dataset methods, minor argument tweaks. Commit: 4da2119c2560c68cb716270933959eb8cf3d48ed https://github.com/galaxyproject/galaxy/commit/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Remove explicit 'chunk' parameter passthrough in datasets API Commit: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #2569 from dannon/workflow_tag_fixes [16.04] Fix tag_autocomplete issue in workflow editor. Commit: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes Commit: a74a23764cc1aa0a481d0e2ea65ac26a8f151865 https://github.com/galaxyproject/galaxy/commit/a74a23764cc1aa0a481d0e2ea65a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/77f547ed89a9...a74a23764cc1

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[galaxyproject/galaxy] 7c2c2c: Tabular dataset chunking fix which should prevent ...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: acdfd2423f3e8764375d0b7a23dad3c919db47fc https://github.com/galaxyproject/galaxy/commit/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: 84d152082009418f2fd5dfe0e9001e8924a678fc https://github.com/galaxyproject/galaxy/commit/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Absolute positioning for tabular dataset chunking, vs abstract chunk. Ships a minimum of one line regardless of size, and relies on client to know position. Commit: ca4b51b390d14077188b5226e4c83ed0991dcbb5 https://github.com/galaxyproject/galaxy/commit/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Make client with new tabular display. Commit: a65faa961ca434901baaaeffe2e5926d4ac523c1 https://github.com/galaxyproject/galaxy/commit/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix tabular chunked display offset=0 request, pass through ck_size to allow client specification of chunk size overriding the app defaults (neither of these are used by the js client currently though) Commit: d7cdf74bdf2690ab1d83cb262021251ae3e28d14 https://github.com/galaxyproject/galaxy/commit/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Handle the case when the last character of the initial read is a newline. Commit: b7718a0f9ae3a626ab88080e0798a451597984c8 https://github.com/galaxyproject/galaxy/commit/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Swap ck_size default from 0 to None to indicate unset. This does not change any behavior at all, but @nsoranzo requested the change to make usage more clear. Commit: 1d8f39d987217c09048e05e1d5443173eb02a9f2 https://github.com/galaxyproject/galaxy/commit/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove old, unused arguments from some display_dataset methods, minor argument tweaks. Commit: 4da2119c2560c68cb716270933959eb8cf3d48ed https://github.com/galaxyproject/galaxy/commit/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Remove explicit 'chunk' parameter passthrough in datasets API Commit: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes Compare: https://github.com/galaxyproject/galaxy/compare/ab2e48bae739...05c063b13a3f

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[galaxyproject/galaxy] 61a113: When CONDA_ALREADY_INSTALLED is undefined there's ...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61a11341f9eb5f18ac33bd88e6acefc37a6f46af https://github.com/galaxyproject/galaxy/commit/61a11341f9eb5f18ac33bd88e6ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- When CONDA_ALREADY_INSTALLED is undefined there's an error due to the number of arguments in the boolean expression (we actually *do* always want a 1 or 0 there, never empty) Commit: 77f547ed89a90e31df6e388e311bef29d18f2e65 https://github.com/galaxyproject/galaxy/commit/77f547ed89a90e31df6e388e311b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2599 from dannon/fix_startup_condaskip When CONDA_ALREADY_INSTALLED is undefined there's an error due to the… Compare: https://github.com/galaxyproject/galaxy/compare/c0101e011fc3...77f547ed89a9

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[galaxyproject/galaxy] c3bf89: Fix tag_autocomplete issue. When we swapped to ta...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix tag_autocomplete issue. When we swapped to tag manager the signature changed and some of these were missed. Commit: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #2569 from dannon/workflow_tag_fixes [16.04] Fix tag_autocomplete issue in workflow editor. Compare: https://github.com/galaxyproject/galaxy/compare/f8e40bb5951c...ab2e48bae739

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[galaxyproject/galaxy] b53a92: Add Warning when Conda is installed because we ski...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b53a9275d54d8ed0373a11a4e95c500619a3d5b0 https://github.com/galaxyproject/galaxy/commit/b53a9275d54d8ed0373a11a4e95c… Author: remimarenco <remi.marenco(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add Warning when Conda is installed because we skip the virtualenv creation Fix the case where we could have conda not installed but not setting VirtualEnv still (and have this non relevant warning Commit: de702db55d8f1ca397b4ab926085e006cd39a490 https://github.com/galaxyproject/galaxy/commit/de702db55d8f1ca397b4ab926085… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- s/creation/activation. Thx @nsoranzo Commit: c0101e011fc3aacad1533d1bb80fdf4588c6bdb6 https://github.com/galaxyproject/galaxy/commit/c0101e011fc3aacad1533d1bb80f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2596 from remimarenco/conda_virtualenv_warning Add Warning when Conda is installed Compare: https://github.com/galaxyproject/galaxy/compare/83f1b07687a5...c0101e011fc3

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[galaxyproject/galaxy] 89b838: Add controller consistent workflow api endpoint
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89b83885a79c58e28b305450ca33e08343d421cb https://github.com/galaxyproject/galaxy/commit/89b83885a79c58e28b305450ca33… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Add controller consistent workflow api endpoint Commit: 83f1b07687a5397bec60d4d57a2e0c9bcb44deda https://github.com/galaxyproject/galaxy/commit/83f1b07687a5397bec60d4d57a2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Merge pull request #2077 from guerler/revise_workflow_run_004 Run workflow form revision Compare: https://github.com/galaxyproject/galaxy/compare/834c97a81da6...83f1b07687a5

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[galaxyproject/galaxy] a074af: Ignore W503 as PEP 8 has reversed its position on ...
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a074af5668bc37685649a245e48f2f6e60613591 https://github.com/galaxyproject/galaxy/commit/a074af5668bc37685649a245e48f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M setup.cfg Log Message: ----------- Ignore W503 as PEP 8 has reversed its position on this. Commit: 834c97a81da6cef6cfab0a14e86318fcc7cb38fe https://github.com/galaxyproject/galaxy/commit/834c97a81da6cef6cfab0a14e863… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M setup.cfg Log Message: ----------- Merge pull request #2594 from natefoo/ignore-w503 Ignore W503 (line break before binary operator) as PEP 8 has reversed its position on this. Compare: https://github.com/galaxyproject/galaxy/compare/05eebac85ded...834c97a81da6

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[galaxyproject/galaxy] d2d2b4: fix UnboundLocalError
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d2d2b437372f7d96329c24f74ac2b2c4ccdef96d https://github.com/galaxyproject/galaxy/commit/d2d2b437372f7d96329c24f74ac2… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- fix UnboundLocalError Commit: 1d228d9a5c79f90e4b015c768f3841b132a4482b https://github.com/galaxyproject/galaxy/commit/1d228d9a5c79f90e4b015c768f38… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_multiple_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- add test case for galaxyproject/tools-iuc/issues/857 Commit: fb116f5715d9cd291d2fdf956b5a3a91b3e84296 https://github.com/galaxyproject/galaxy/commit/fb116f5715d9cd291d2fdf956b5a… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_conditional.xml R test/functional/tools/identifier_multiple_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- fix missing element_identifier with data_collection input parama Commit: cf29b1dcd60c8dcc39cfc7e507572f08ff86347d https://github.com/galaxyproject/galaxy/commit/cf29b1dcd60c8dcc39cfc7e50757… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- apply comments Commit: 706a9bfb237679658d57cb5c20592ac25b91f364 https://github.com/galaxyproject/galaxy/commit/706a9bfb237679658d57cb5c2059… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_collection.xml R test/functional/tools/identifier_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- cleanup test tool Commit: 05eebac85deda173bea8e22e19d1cb2fe3327901 https://github.com/galaxyproject/galaxy/commit/05eebac85deda173bea8e22e19d1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2570 from abretaud/identifier_bug Fix element_identifier unavailable with data_collection input param Compare: https://github.com/galaxyproject/galaxy/compare/a630c92df447...05eebac85ded

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[galaxyproject/usegalaxy-playbook] 2bdea6: Updated slide rotation. GCC2016 -> GCC2017, Erasm...
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2bdea6e237ac04a8f6647121c2137235f1489441 https://github.com/galaxyproject/usegalaxy-playbook/commit/2bdea6e237ac04a8… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: A files/galaxy/common/static/welcome_img/CPTGalaxy.png A files/galaxy/common/static/welcome_img/GCC2017.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation. GCC2016 -> GCC2017, Erasmuc MC Server -> CPT Server

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[galaxyproject/usegalaxy-playbook] b1b0c7: Update Main
by GitHub 06 Jul '16

06 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b1b0c73b3a91a13a4d9a97e2a098402046d07683 https://github.com/galaxyproject/usegalaxy-playbook/commit/b1b0c73b3a91a13a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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galaxy-commits July 2016