- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6e13c3: Cherry-picked changes from pull request #1392.
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e13c3999a6d54b40b2910d5ce95da724f133122 https://github.com/galaxyproject/galaxy/commit/6e13c3999a6d54b40b2910d5ce95… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Cherry-picked changes from pull request #1392. Commit: 3ec58fd1da5f7122752627eef581d5826190bc13 https://github.com/galaxyproject/galaxy/commit/3ec58fd1da5f7122752627eef581… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Update API endpoint names in code comments. Commit: b15a7ff06df23d7004f670f34638fe9ee5d33f92 https://github.com/galaxyproject/galaxy/commit/b15a7ff06df23d7004f670f34638… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Include repository metadata when browsing repositories in a category. Commit: 02ed07ca82e19e20b37e50e9f6294069240d9ed1 https://github.com/galaxyproject/galaxy/commit/02ed07ca82e19e20b37e50e9f629… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Merge pull request #1821 from davebx/toolshed_decouple_api Cherry-picked changes from pull request #1392. Compare: https://github.com/galaxyproject/galaxy/compare/779793810d1f...02ed07ca82e1

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[galaxyproject/galaxy] e0ce68: Fix lack of output when discovering large collecti...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e0ce68cc58a6d6eeb306f5c0445563e71bcc1d12 https://github.com/galaxyproject/galaxy/commit/e0ce68cc58a6d6eeb306f5c04455… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix lack of output when discovering large collections... Example log statement collected for each dataset: ``` galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output]. ``` Commit: 0fbd22c9a30686afe62de1e1f23ff309dd6374a8 https://github.com/galaxyproject/galaxy/commit/0fbd22c9a30686afe62de1e1f23f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1852 from jmchilton/dataset_collection_log [16.01] Fix lack of log output when discovering large collections... Compare: https://github.com/galaxyproject/galaxy/compare/de70306407c0...0fbd22c9a306

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[galaxyproject/usegalaxy-playbook] 2841ee: remove border around carousel so it matches twitte...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2841ee2db805198cb43356c92f75bf5090761919 https://github.com/galaxyproject/usegalaxy-playbook/commit/2841ee2db805198c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- remove border around carousel so it matches twitter borderless widget

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[galaxyproject/galaxy] 159e5f: Do not create text values for failed inputs
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 159e5fd5d55dac24541189bea24e6f977c10a1d6 https://github.com/galaxyproject/galaxy/commit/159e5fd5d55dac24541189bea24e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not create text values for failed inputs Commit: 779793810d1f742dd1fd161c3eec1695df152d4d https://github.com/galaxyproject/galaxy/commit/779793810d1f742dd1fd161c3eec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1844 from guerler/fix_text_value_handling_000 Do not create text values for failed inputs Compare: https://github.com/galaxyproject/galaxy/compare/80bcb987c84a...779793810d1f

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[galaxyproject/galaxy] 1220e2: Prevent tours from kicking off within iframes, cau...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1220e2e9788026af7b7047720d03f7bb097f5762 https://github.com/galaxyproject/galaxy/commit/1220e2e9788026af7b7047720d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Prevent tours from kicking off within iframes, causing duplicate tour step display. Commit: 80bcb987c84a8331c84db864a557f326594afd91 https://github.com/galaxyproject/galaxy/commit/80bcb987c84a8331c84db864a557… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #1846 from dannon/tour_iframe_bug Prevent tours from kicking off within iframes Compare: https://github.com/galaxyproject/galaxy/compare/9b0c491729de...80bcb987c84a

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[galaxyproject/galaxy] 6968cf: Using node 5.7, 'grunt style' fails with the error...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6968cf0158f6b14ebbeaac3655151b5f67c393de https://github.com/galaxyproject/galaxy/commit/6968cf0158f6b14ebbeaac365515… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Using node 5.7, 'grunt style' fails with the error: "ERROR Warning: Cannot delete files outside the current working directory. Use --force to continue. " This re-enables deletion of the temporary file. Commit: 9b0c491729de2945dc78b1766f520160c846c5d3 https://github.com/galaxyproject/galaxy/commit/9b0c491729de2945dc78b1766f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Merge pull request #1841 from dannon/grunt_style Using node 5.7, 'grunt style' fails with the error: Compare: https://github.com/galaxyproject/galaxy/compare/158732edb6ce...9b0c491729de

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[galaxyproject/usegalaxy-playbook] 5aea44: mutable confs for Main; add labels
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5aea4451d1e354f1d0783d24cffe4a70bcf5ba91 https://github.com/galaxyproject/usegalaxy-playbook/commit/5aea4451d1e354f1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- mutable confs for Main; add labels

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[galaxyproject/galaxy] 499268: Hide tools that have been replaced.
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4992684d1fc58d4774e5d6a6c1df9c193218c460 https://github.com/galaxyproject/galaxy/commit/4992684d1fc58d4774e5d6a6c1df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Hide tools that have been replaced. Commit: de70306407c0682834814c479c91f8b8adc615ce https://github.com/galaxyproject/galaxy/commit/de70306407c0682834814c479c91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #1837 from davebx/release_16.01 [16.01] Hide tools that have been replaced. Compare: https://github.com/galaxyproject/galaxy/compare/dfef64db75c4...de70306407c0

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[galaxyproject/infrastructure-playbook] 66421a: Change access list on leeroy
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 66421a2b51af676da937f5608b8200fdfd0bf8b1 https://github.com/galaxyproject/infrastructure-playbook/commit/66421a2b51a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Change access list on leeroy

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[galaxyproject/galaxy] a49401: Improve dataset error log message
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: a49401189735daa55e44dec7af6b84a646e8bbc9 https://github.com/galaxyproject/galaxy/commit/a49401189735daa55e44dec7af6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve dataset error log message Commit: dfef64db75c43cd4001a67cf48143e28df3efe60 https://github.com/galaxyproject/galaxy/commit/dfef64db75c43cd4001a67cf4814… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1836 from natefoo/dataset-error-log [16.01] Improve dataset error log message Compare: https://github.com/galaxyproject/galaxy/compare/0051cab4f352...dfef64db75c4

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