October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 76da3d: Adding information to help track down remote authe...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76da3df1cc717e24b94b74e0d3f7fd217a48068e https://github.com/galaxyproject/galaxy/commit/76da3df1cc717e24b94b74e0d3f7… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adding information to help track down remote authentication issues Commit: 022b66b826bcb34407468fbc3f37de570e769606 https://github.com/galaxyproject/galaxy/commit/022b66b826bcb34407468fbc3f37… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-03 (Sat, 03 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Update remoteuser.py Commit: 1c679021b176577723335719701d093b49c266de https://github.com/galaxyproject/galaxy/commit/1c679021b176577723335719701d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Implement @blankenberg's suggestion. Remove whitespaces. Commit: 9343d189e227592bda13a1363d2ea96cf429108f https://github.com/galaxyproject/galaxy/commit/9343d189e227592bda13a1363d2e… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1 from nsoranzo/patch-3 Implement @blankenberg's suggestion. Commit: 5a9fd385fa23211e4cc616278696459224b3e8b7 https://github.com/galaxyproject/galaxy/commit/5a9fd385fa23211e4cc616278696… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #823 from golharam/patch-1 Adding information to help track down remote authentication issues Compare: https://github.com/galaxyproject/galaxy/compare/347b1596a843...5a9fd385fa23

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[galaxyproject/usegalaxy-playbook] 3e9d83: Swapped GCC2016 Training nomination for November F...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3e9d838e4d51c7094fc75078310e76cf579402a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/3e9d838e4d51c709… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: A files/galaxy/common/static/welcome_img/201511_France.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Swapped GCC2016 Training nomination for November French events slide.

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[galaxyproject/galaxy] 20579e: Add a log.warn() if extracted file does not exist ...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20579ebd50c8e11d2f0bac45d3b0f71e1d732466 https://github.com/galaxyproject/galaxy/commit/20579ebd50c8e11d2f0bac45d3b0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add a log.warn() if extracted file does not exist when changing permissions. Should help to debug issue reported in PR #792. Commit: 347b1596a843c59e1158798bc3a2d7fa54f95a2b https://github.com/galaxyproject/galaxy/commit/347b1596a843c59e1158798bc3a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #939 from nsoranzo/debug_for_792 Add a log.warn() if extracted file does not exist when changing permissions. Compare: https://github.com/galaxyproject/galaxy/compare/123bf620df33...347b1596a843

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[galaxyproject/galaxy] dde919: Add SearchGuiArchive datatype to binary
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dde91947ac3c0c5c4089dbe94999089ddf2709ce https://github.com/galaxyproject/galaxy/commit/dde91947ac3c0c5c4089dbe94999… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add SearchGuiArchive datatype to binary Commit: 54ddc983751d66d26caf448fe4b2c2d2533b4d53 https://github.com/galaxyproject/galaxy/commit/54ddc983751d66d26caf448fe4b2… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Update binary.py Commit: e88f58a3e5fae829b54eaf2dfdc5f3a088233d29 https://github.com/galaxyproject/galaxy/commit/e88f58a3e5fae829b54eaf2dfdc5… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Correct pep8 errors Commit: c869dde1e0abe964d849621b5fca2bf351ac36d4 https://github.com/galaxyproject/galaxy/commit/c869dde1e0abe964d849621b5fca… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix typo. Commit: 91e46701de52b2bcdbb4d9ce451a20d823daf269 https://github.com/galaxyproject/galaxy/commit/91e46701de52b2bcdbb4d9ce451a… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Another attempt at pep8 compliance Commit: 123bf620df332b72c23357aea0cfab97779ce680 https://github.com/galaxyproject/galaxy/commit/123bf620df332b72c23357aea0cf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #914 from jj-umn/patch-2 Add searchgui datatype Compare: https://github.com/galaxyproject/galaxy/compare/ca4a09b78c8d...123bf620df33

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[galaxyproject/galaxy] 15a8c5: fix the filter on deleted libraries to not show th...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 15a8c594bd8041c17512a719eab6185c6b478f19 https://github.com/galaxyproject/galaxy/commit/15a8c594bd8041c17512a719eab6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- fix the filter on deleted libraries to not show the public deleted libs by default Commit: 47ce939322111da71b914976170dd9ad41c0fe7d https://github.com/galaxyproject/galaxy/commit/47ce939322111da71b914976170d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- remove log Commit: b7dfeb4174183135f8ac7c858d6ce33ba69286c0 https://github.com/galaxyproject/galaxy/commit/b7dfeb4174183135f8ac7c858d6c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- Merge pull request #934 from martenson/fix-showing-deleted-libs [15.10] fix the filter on search results to not show the public deleted libs Compare: https://github.com/galaxyproject/galaxy/compare/11d17b3e7b30...b7dfeb417418

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[galaxyproject/galaxy] c9294a: Fix syntax of error parameter of tryCatch.
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9294a6ec9270490d78b79fb3a615ed30b477650 https://github.com/galaxyproject/galaxy/commit/c9294a6ec9270490d78b79fb3a61… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix syntax of error parameter of tryCatch. Commit: ca4a09b78c8db5fe5a6068362df91d91ae94b425 https://github.com/galaxyproject/galaxy/commit/ca4a09b78c8db5fe5a6068362df9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #929 from nsoranzo/R_install_fix Fix syntax of error parameter of tryCatch in setup_r_environment action. Compare: https://github.com/galaxyproject/galaxy/compare/8bd94c1fff10...ca4a09b78c8d

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[galaxyproject/galaxy] da9ebc: Run ./scripts/common_startup.sh inside docker when...
by GitHub 17 Oct '15

17 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: da9ebc17bb687fcc2156b76652f45914389c8da5 https://github.com/galaxyproject/galaxy/commit/da9ebc17bb687fcc2156b76652f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Run ./scripts/common_startup.sh inside docker when using `run_tests.sh --dockerize`. Requires a rebuild of galaxy/base-testing. Necessary for tests to run on #428 (and anything else once #428 is merged). Commit: 8bd94c1fff10b654c8e5ea139dcd60fa99516177 https://github.com/galaxyproject/galaxy/commit/8bd94c1fff10b654c8e5ea139dcd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-17 (Sat, 17 Oct 2015) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #936 from natefoo/dockerize-tests-setup common_startup.sh fixes for run_tests.sh --dockerize and wheels Compare: https://github.com/galaxyproject/galaxy/compare/ac16cb4923f4...8bd94c1fff10

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[galaxyproject/galaxy] d47579: Use a specific version of the testing-base docker ...
by GitHub 17 Oct '15

17 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d475792d2453396d337596bd5153ff5fa7b76d20 https://github.com/galaxyproject/galaxy/commit/d475792d2453396d337596bd5153… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-16 (Fri, 16 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Use a specific version of the testing-base docker image. Commit: ac16cb4923f4d7912de9027dd4e9887eef9b91ee https://github.com/galaxyproject/galaxy/commit/ac16cb4923f4d7912de9027dd4e9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-17 (Sat, 17 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #938 from natefoo/versioned-testing-docker Version the testing-base docker image Compare: https://github.com/galaxyproject/galaxy/compare/323167674963...ac16cb4923f4

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[galaxyproject/usegalaxy-playbook] ef0d22: Update Main and admin_users
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ef0d226e6e04cdade0a59285370a09e013de9723 https://github.com/galaxyproject/usegalaxy-playbook/commit/ef0d226e6e04cdad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M production/group_vars/all.yml M production/secret_vars/galaxyservers.yml Log Message: ----------- Update Main and admin_users

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[galaxyproject/galaxy] b07459: As usual, I forgot to update the version tag when ...
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b074590efc52f92fdedc3825f5762d1dcb03a474 https://github.com/galaxyproject/galaxy/commit/b074590efc52f92fdedc3825f576… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- As usual, I forgot to update the version tag when creating the release_15.10 branch. Commit: 3231676749639f8019f058e84fec0c7fa9114e13 https://github.com/galaxyproject/galaxy/commit/3231676749639f8019f058e84fec… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #923 from natefoo/dev Bump dev branch version to 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/e540c2cc7781...323167674963

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