- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 577c59: Backup Biostar to westvleteren
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 577c599fa6ab496e86018e69ef98b56a85d184fd https://github.com/galaxyproject/infrastructure-playbook/commit/577c599fa6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M common_roles M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_host_vars/biostar.usegalaxy.org.yml M galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml M playbook.yml Log Message: ----------- Backup Biostar to westvleteren

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[galaxyproject/galaxy] ffc5b0: Swap naïve spaces for regex
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffc5b02db98109fd3df35a0ba7f6a7b7cfd2b3a8 https://github.com/galaxyproject/galaxy/commit/ffc5b02db98109fd3df35a0ba7f6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Swap naïve spaces for regex Commit: 6f2b43330d5334bb46c10e1ce2a5675793e76219 https://github.com/galaxyproject/galaxy/commit/6f2b43330d5334bb46c10e1ce2a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #951 from erasche/949-followup Swap naïve spaces for regex Compare: https://github.com/galaxyproject/galaxy/compare/5ae2db59049f...6f2b43330d53

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[galaxyproject/galaxy] 8c8ddb: Tools don't start with <tool_dependencies
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c8ddb9ce967bf3a47bf4cbdd2173e696228630d https://github.com/galaxyproject/galaxy/commit/8c8ddb9ce967bf3a47bf4cbdd217… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Tools don't start with <tool_dependencies Tools start with '<tool ' Commit: 5ae2db59049fb38a6fa804ec8c5c8d08dda214b4 https://github.com/galaxyproject/galaxy/commit/5ae2db59049fb38a6fa804ec8c5c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #949 from erasche/looks-like-a-bug Tools don't start with <tool_dependencies Compare: https://github.com/galaxyproject/galaxy/compare/d29283616ed8...5ae2db59049f

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[galaxyproject/galaxy] b80eb8: Fix tool url building
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b80eb8d47ce93cb4520459f59a20659d11c81e58 https://github.com/galaxyproject/galaxy/commit/b80eb8d47ce93cb4520459f59a20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Fix tool url building Commit: d29283616ed83a707012d5c5d65a9efc33ae7a0e https://github.com/galaxyproject/galaxy/commit/d29283616ed83a707012d5c5d65a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #947 from guerler/fix_tool_url_000 Revise tool url building Compare: https://github.com/galaxyproject/galaxy/compare/278c2aa399c4...d29283616ed8

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[galaxyproject/infrastructure-playbook] a15fae: Change backup cron job for Jenkins to not copy the...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a15fae8401e73bfa68e07cfe6bbb81f5850d0737 https://github.com/galaxyproject/infrastructure-playbook/commit/a15fae8401e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Change backup cron job for Jenkins to not copy the workspace.

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[galaxyproject/galaxy] 61f1cd: Added script to upload a directory to a data libra...
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61f1cdf5d7e2078569cb4c1efb3c1df3bda6d0e2 https://github.com/galaxyproject/galaxy/commit/61f1cdf5d7e2078569cb4c1efb3c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: A scripts/api/library_upload_dir.py Log Message: ----------- Added script to upload a directory to a data library Commit: a8b727791ffbdcbe70d2b638080101ec2a8a3a4d https://github.com/galaxyproject/galaxy/commit/a8b727791ffbdcbe70d2b6380801… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Correct language in galaxy dev doc Commit: decca0e96a43bf9cf23af56d09a966898018b354 https://github.com/galaxyproject/galaxy/commit/decca0e96a43bf9cf23af56d09a9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Refactor to accept output of find Commit: aec9961407717f305b4ee3a5fdd6f655f4885944 https://github.com/galaxyproject/galaxy/commit/aec9961407717f305b4ee3a5fdd6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Strip newlines Commit: 1f9be2410bb9efe8cd647e240bd45a9e99a3bdce https://github.com/galaxyproject/galaxy/commit/1f9be2410bb9efe8cd647e240bd4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst Log Message: ----------- Documented use of library upload tool Commit: 33925747b8b3b554b7b1cbb185ab4f15cfa3586b https://github.com/galaxyproject/galaxy/commit/33925747b8b3b554b7b1cbb185ab… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Allow linking only Commit: 705445a2f2605d45d31fb11ef773460f252b0afd https://github.com/galaxyproject/galaxy/commit/705445a2f2605d45d31fb11ef773… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- Correct doc script name Commit: 6be301ca8afcbc3cd1c3c7e3d74d3dee17a6a607 https://github.com/galaxyproject/galaxy/commit/6be301ca8afcbc3cd1c3c7e3d74d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Support local/non local data and paths including root Commit: 2cca823a787dfcd48b5cfb7ef685d81e9341d189 https://github.com/galaxyproject/galaxy/commit/2cca823a787dfcd48b5cfb7ef685… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Prepopulate memoization cache Commit: 8a66701d4f622e3a57e39274fb3046dc67640be5 https://github.com/galaxyproject/galaxy/commit/8a66701d4f622e3a57e39274fb30… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Don't re-upload if already there Commit: 5dd7370b845202b45b30b88c67e8ca98362935a5 https://github.com/galaxyproject/galaxy/commit/5dd7370b845202b45b30b88c67e8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- Add a line of documentation about syncing Commit: 278c2aa399c45aec0eac6e8fa66e47d83e3bace2 https://github.com/galaxyproject/galaxy/commit/278c2aa399c45aec0eac6e8fa66e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst A scripts/api/library_upload_dir.py Log Message: ----------- Merge pull request #918 from erasche/library_upload_dir_script Library upload dir script Compare: https://github.com/galaxyproject/galaxy/compare/5a9fd385fa23...278c2aa399c4

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[galaxyproject/infrastructure-playbook] a09e61: Stuff for Jenkins
by GitHub 19 Oct '15

19 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a09e61e00ca62e4de76684035c69028a1b9502eb https://github.com/galaxyproject/infrastructure-playbook/commit/a09e61e00ca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml Log Message: ----------- Stuff for Jenkins

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[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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[galaxyproject/galaxy] b6f378: remove test_map_over_two_collections_legacy as it ...
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6f3783acd03b4979448ba51395af8e1fc605d27 https://github.com/galaxyproject/galaxy/commit/b6f3783acd03b4979448ba51395a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- remove test_map_over_two_collections_legacy as it is obsolete Commit: e540c2cc7781c82d842103de1db9b1c38e7888a5 https://github.com/galaxyproject/galaxy/commit/e540c2cc7781c82d842103de1db9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #924 from martenson/remove-legacy-test remove test_map_over_two_collections_legacy as it is obsolete Compare: https://github.com/galaxyproject/galaxy/compare/6c7ebdbbcb6b...e540c2cc7781

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[galaxyproject/usegalaxy-playbook] fa5668: Update Test and admin_users
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa5668b25e5ced931dea1062c1cf7b0689083244 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa5668b25e5ced93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M stage/group_vars/all.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test and admin_users

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[galaxyproject/galaxy] 8cb894: Fix data library test case
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cb894b34a162b4082a49b3c41df8e96dfedd04b https://github.com/galaxyproject/galaxy/commit/8cb894b34a162b4082a49b3c41df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix data library test case Fix library data test case Commit: 6c7ebdbbcb6b9c93229d7586ddff133a03776271 https://github.com/galaxyproject/galaxy/commit/6c7ebdbbcb6b9c93229d7586ddff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #898 from guerler/fix_library_test_000 Fix data library test case Compare: https://github.com/galaxyproject/galaxy/compare/296dab0588ba...6c7ebdbbcb6b

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[galaxyproject/galaxy] a9c91d: reorder workflow inputs to top
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9c91d3a5606dbcdc42d2181b3085d6b41d50a31 https://github.com/galaxyproject/galaxy/commit/a9c91d3a5606dbcdc42d2181b308… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- reorder workflow inputs to top Commit: 296dab0588badfe7b9aba436988daf5e0872f384 https://github.com/galaxyproject/galaxy/commit/296dab0588badfe7b9aba436988d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #912 from scholtalbers/reorder-workflow-controls Reorder workflow inputs to top Compare: https://github.com/galaxyproject/galaxy/compare/2d01cae6b200...296dab0588ba

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[galaxyproject/galaxy] a74219: Fixes for switching history (standard as well as m...
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: a742198a36d700f299019ef8929a9dc55d58c17a https://github.com/galaxyproject/galaxy/commit/a742198a36d700f299019ef8929a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fixes for switching history (standard as well as multiview) when using IE11. Intentionally minimal fix for 15.10, more comprehensive refactoring+solution forthcoming for dev. Commit: 11d17b3e7b305a28aaa0fb8392424dbb650e70d6 https://github.com/galaxyproject/galaxy/commit/11d17b3e7b305a28aaa0fb839242… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #920 from dannon/release_15.10 [15.10] IE11 history-stuck fix Compare: https://github.com/galaxyproject/galaxy/compare/cf59e8bd3c52...11d17b3e7b30

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[galaxyproject/galaxy] 7a5e8f: Add check for HTTP_GX_SECRET
by GitHub 15 Oct '15

15 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a5e8f7749db9ac1822a00d2e77b23279b72f719 https://github.com/galaxyproject/galaxy/commit/7a5e8f7749db9ac1822a00d2e77b… 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: ----------- Add check for HTTP_GX_SECRET If not provided, safe_str_cmp crashes and present debug trace log to user. Commit: 63e30dac5d4a6b4be5176464e6f744fbb51c900f https://github.com/galaxyproject/galaxy/commit/63e30dac5d4a6b4be5176464e6f7… 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: ----------- Removed trailing white space Commit: 100ed418e8f2361b5c83ab3dee9b318bec222a2d https://github.com/galaxyproject/galaxy/commit/100ed418e8f2361b5c83ab3dee9b… 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 removed empty lines Commit: 973e70103373d49e5100fb3262aae8df4fc5bc5e https://github.com/galaxyproject/galaxy/commit/973e70103373d49e5100fb3262aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Remove trailing whitespace Commit: e54df2e6ac4337265e9aba95c6e62d8e49eb5f48 https://github.com/galaxyproject/galaxy/commit/e54df2e6ac4337265e9aba95c6e6… Author: Ryan <ngsbioinformatics(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #2 from erasche/whitespace-fix-827 Remove trailing whitespace Commit: 2d01cae6b2002d966ede39bd435c35da4f3d9764 https://github.com/galaxyproject/galaxy/commit/2d01cae6b2002d966ede39bd435c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #827 from golharam/patch-2 Add check for HTTP_GX_SECRET Compare: https://github.com/galaxyproject/galaxy/compare/005561c22a40...2d01cae6b200

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[galaxyproject/galaxy] 4cebca: Redo total disk calculation adjustments to be less...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cebca81c677a6692e22006468310d0e21195251 https://github.com/galaxyproject/galaxy/commit/4cebca81c677a6692e2200646831… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Redo total disk calculation adjustments to be less race condition-y. ... at least when finishing the job. Method should probably be used other places as well. Commit: b77496ec638e5e15f6cb8b1e83077fdf266634d2 https://github.com/galaxyproject/galaxy/commit/b77496ec638e5e15f6cb8b1e8307… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Update other quota manipulations to use the new user.adjust_quota_usage function. Commit: 3e5b91ceca04bc2ce040617a0ba17ab73d274469 https://github.com/galaxyproject/galaxy/commit/3e5b91ceca04bc2ce040617a0ba1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove duplicate func import Commit: c05315c7d38790b5de75f386fab06db0f241212d https://github.com/galaxyproject/galaxy/commit/c05315c7d38790b5de75f386fab0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Avoid overriding 'bytes' type with the local variable. Commit: 005561c22a40d74693318ccfd0c94e41bbd309e0 https://github.com/galaxyproject/galaxy/commit/005561c22a40d74693318ccfd0c9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #907 from dannon/quota_bugfix Quota bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/977ef6b7c7c0...005561c22a40

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[galaxyproject/galaxy] 4657ce: Add support for constructive solid geometry dataty...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4657ce6f34ab16d1b4ab472cf3b7faf39086e572 https://github.com/galaxyproject/galaxy/commit/4657ce6f34ab16d1b4ab472cf3b7… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Add support for constructive solid geometry datatypes ply and vtk. Commit: 977ef6b7c7c0e8dc627333dca093dce0762b2888 https://github.com/galaxyproject/galaxy/commit/977ef6b7c7c0e8dc627333dca093… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Merge pull request #905 from gregvonkuster/dev Add support for constructive solid geometry datatypes ply and vtk. Compare: https://github.com/galaxyproject/galaxy/compare/744ed8cd4c80...977ef6b7c7c0

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