- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c1fe8a: Fix inconsistency in update state handling for too...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1fe8aac0a646b2bed0b3dbfbf0cd75b595f1690 https://github.com/galaxyproject/galaxy/commit/c1fe8aac0a646b2bed0b3dbfbf0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix inconsistency in update state handling for tool modules Commit: eaf8f4ed5056317f19950fef5e5340217fd0e809 https://github.com/galaxyproject/galaxy/commit/eaf8f4ed5056317f19950fef5e53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Extend doc tests for parameter handling Commit: 86d2b29026fc4176070d3ef5150a4f0f0ff86829 https://github.com/galaxyproject/galaxy/commit/86d2b29026fc4176070d3ef5150a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1993 from guerler/revise_parameters_000 Fix inconsistency in update state handling for tool modules Compare: https://github.com/galaxyproject/galaxy/compare/0a77851b9b9d...86d2b29026fc

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[galaxyproject/galaxy] ab31bd: move text out of icon spans for library dataset vi...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab31bd9f4865c3544a8bb8a4be8c77d41360bbed https://github.com/galaxyproject/galaxy/commit/ab31bd9f4865c3544a8bb8a4be8c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js Log Message: ----------- move text out of icon spans for library dataset view also re-touch the html to be better readable Commit: 0a77851b9b9dba237b529c06d7fcbe3b97ab2b47 https://github.com/galaxyproject/galaxy/commit/0a77851b9b9dba237b529c06d7fc… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js Log Message: ----------- Merge pull request #2008 from martenson/libtext-from-span libraries: move text out of icon spans for library dataset view Compare: https://github.com/galaxyproject/galaxy/compare/909a5491e505...0a77851b9b9d

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[galaxyproject/galaxy] cfd937: Repack scripts
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfd937a46e8795c4d06deb3325e18d7439390d65 https://github.com/galaxyproject/galaxy/commit/cfd937a46e8795c4d06deb3325e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: 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 Log Message: ----------- Repack scripts Commit: 909a5491e50521c7374ef4e939e89015afe0ddde https://github.com/galaxyproject/galaxy/commit/909a5491e50521c7374ef4e939e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: 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 Log Message: ----------- Merge pull request #2004 from guerler/repack_000 Repack js-scripts Compare: https://github.com/galaxyproject/galaxy/compare/3b0743fab272...909a5491e505

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[galaxyproject/galaxy] 93b747: remove deprecated user-facing lib link;
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93b7473be87813454753c9c8e58bca297a59ca2e https://github.com/galaxyproject/galaxy/commit/93b7473be87813454753c9c8e58b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- remove deprecated user-facing lib link; remove 'published' from the menu items for shared elements Commit: 3b0743fab27220824ad14a0579b960ce79b20f0c https://github.com/galaxyproject/galaxy/commit/3b0743fab27220824ad14a0579b9… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1996 from martenson/remove-liblink alter 'shared data' menu Compare: https://github.com/galaxyproject/galaxy/compare/fb549c80d49c...3b0743fab272

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[galaxyproject/galaxy] b51bdd: Basepanels don't have Galaxy object, causing failu...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b51bdd06b189baccab235def65d15a69c761ac28 https://github.com/galaxyproject/galaxy/commit/b51bdd06b189baccab235def65d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly Commit: dede9459b019ceb1212f4f152b4108632f892384 https://github.com/galaxyproject/galaxy/commit/dede9459b019ceb1212f4f152b41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2003 from dannon/trackster_debugging [16.01] Fix shared viz (and other base_panels.mako displays) early URL generation. Compare: https://github.com/galaxyproject/galaxy/compare/21e71a9b46b9...dede9459b019

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[galaxyproject/usegalaxy-playbook] 8af4f9: Add a 32 GB destination, increase the BWA-MEM DM t...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8af4f9b38a8b14d898700befa0856acecca8c77b https://github.com/galaxyproject/usegalaxy-playbook/commit/8af4f9b38a8b14d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M files/galaxy/common/dynamic_rules/reserved.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add a 32 GB destination, increase the BWA-MEM DM to 64GB

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[galaxyproject/galaxy] 7186fb: Add page layout test cases
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7186fbba9259ff9381c9253632a0269a6359cd6b https://github.com/galaxyproject/galaxy/commit/7186fbba9259ff9381c9253632a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js Log Message: ----------- Add page layout test cases Commit: fb549c80d49c9c89bcb94634a0ee4cafc4a6f116 https://github.com/galaxyproject/galaxy/commit/fb549c80d49c9c89bcb94634a0ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js Log Message: ----------- Merge pull request #1991 from guerler/fix_panel_003 Add page layout test cases Compare: https://github.com/galaxyproject/galaxy/compare/033241c99f8b...fb549c80d49c

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[galaxyproject/usegalaxy-playbook] c3d761: Mutable configs from Test
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3d761d62cd9a544c7f17bd80c3dcadfd4bce856 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3d761d62cd9a544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Test

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[galaxyproject/usegalaxy-playbook] d7e78c: Update Jupyter image, admin users
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d7e78ce06b34857da60d6eaa1820d9ba5e75fbcd https://github.com/galaxyproject/usegalaxy-playbook/commit/d7e78ce06b34857d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Jupyter image, admin users

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[galaxyproject/galaxy] 62b5f2: Remove unnecessary encoding in remote_files. This...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries Commit: 033241c99f8bb80e4ecac2504a4bdc1f3a4dd657 https://github.com/galaxyproject/galaxy/commit/033241c99f8bb80e4ecac2504a4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/layout/masthead.js.map 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/masthead.js M static/scripts/layout/page.js M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge 16.01, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/c171fd168d69...033241c99f8b

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