- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 99000f: update rename dataset action to accept . in repeat...
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99000fbed3b6c13274a3ddf9eb58310cb40653f7 https://github.com/galaxyproject/galaxy/commit/99000fbed3b6c13274a3ddf9eb58… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- update rename dataset action to accept . in repeat input parameters, also when not using additional operations like '|basename'. e.g. for filter bam 0.0.1: #{input_bams_0.input_bam} and #{input_bams_0.input_bam|basename} work. And for filter bam 0.0.2: #{input_bams1} and #{input_bams2|basename} work. Commit: 306c64d1bc3cec871f38b522ad3f7bf8e0ca3a66 https://github.com/galaxyproject/galaxy/commit/306c64d1bc3cec871f38b522ad3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3197 from scholtalbers/workflows-rename-output-minor-update update rename dataset action to accept . in repeat input parameters Compare: https://github.com/galaxyproject/galaxy/compare/538447be76da...306c64d1bc3c

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[galaxyproject/galaxy] 96678f: More IPython to Jupyter changes
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 96678f57ccef01f322a6c6525defaa73333e56d0 https://github.com/galaxyproject/galaxy/commit/96678f57ccef01f322a6c6525def… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- More IPython to Jupyter changes Follow-up on #3294. Commit: 538447be76da011508eb4a8784eefe2b9e45b270 https://github.com/galaxyproject/galaxy/commit/538447be76da011508eb4a8784ee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #3333 from nsoranzo/followup_on_3294 More IPython to Jupyter changes Compare: https://github.com/galaxyproject/galaxy/compare/af90b42a68d1...538447be76da

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[galaxyproject/galaxy] c61be9: Prettier Job information page
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c61be93b70fd65b4bccf5f8416b58086ae98a085 https://github.com/galaxyproject/galaxy/commit/c61be93b70fd65b4bccf5f8416b5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Prettier Job information page Commit: fe2ec33d0bb67b0cbf0ef9297b737592f4f938bb https://github.com/galaxyproject/galaxy/commit/fe2ec33d0bb67b0cbf0ef9297b73… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove empty header from non-admin view Commit: dd062b5ca8de36a43b133a58b09d374ce07d63bd https://github.com/galaxyproject/galaxy/commit/dd062b5ca8de36a43b133a58b09d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako Log Message: ----------- Remove replace, just don't add in first place Commit: 1c7055fe3b974d06c8e166e39ac1a53d2f078642 https://github.com/galaxyproject/galaxy/commit/1c7055fe3b974d06c8e166e39ac1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Split metric table into sections Commit: 4756cab4cbcca729e3db66f33a8d031b796eb8d2 https://github.com/galaxyproject/galaxy/commit/4756cab4cbcca729e3db66f33a8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove visual noise Commit: 64b0d0326097f96c7637bd6355ca790c4ef8d4be https://github.com/galaxyproject/galaxy/commit/64b0d0326097f96c7637bd6355ca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- cleanup css a bit Commit: cc32dcae4be031a95c393fd4efee459d398ae9c7 https://github.com/galaxyproject/galaxy/commit/cc32dcae4be031a95c393fd4efee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Initial tool form and dataset detail selenium testing. - Test parameters and tables appear on dataset details page after running a tool. - Test a simple tool execution with an integer field. - Test re-run a tool. - Test a tool with a data drop down. - Improved select2 abstractions. Commit: 097cf7f0fbcce7bc82539e17c12f7355deeaa558 https://github.com/galaxyproject/galaxy/commit/097cf7f0fbcce7bc82539e17c12f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Job metrics: Sort metrics on displayed title not key used for database. Commit: ef1fd488241a18952df146d30852054ab27a4a63 https://github.com/galaxyproject/galaxy/commit/ef1fd488241a18952df146d30852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Fix bad merge in cc32dcae4be031a95c393fd4efee459d398ae9c7. Spotted by @erasche. Commit: a5af4d155f6e4ab549c50e51703de49ee3052d16 https://github.com/galaxyproject/galaxy/commit/a5af4d155f6e4ab549c50e51703d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix Python 3 linting error for #3340. Commit: af90b42a68d119118d3fd2845738ef4835799af1 https://github.com/galaxyproject/galaxy/commit/af90b42a68d119118d3fd2845738… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3340 from erasche/nicer_info_page Prettier Job Information Page Compare: https://github.com/galaxyproject/galaxy/compare/e407b4b2c722...af90b42a68d1

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[galaxyproject/galaxy] 9bb570: Allow admins to see API keys under REMOTE_USER
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bb570f62f8e6f135f2776808a6a92e91ec8b7cb https://github.com/galaxyproject/galaxy/commit/9bb570f62f8e6f135f2776808a6a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Allow admins to see API keys under REMOTE_USER Commit: e407b4b2c7226fc00d5cf2c42126ab83409bca7a https://github.com/galaxyproject/galaxy/commit/e407b4b2c7226fc00d5cf2c42126… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3338 from erasche/admin_see_apikeys Allow admins to see API keys under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/e1b54f60f20e...e407b4b2c722

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[galaxyproject/galaxy] 854b24: Fix linting of gff_filter_by_attribute.
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 854b24bb009c46c8e48eb799aef3bf142610bcad https://github.com/galaxyproject/galaxy/commit/854b24bb009c46c8e48eb799aef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 5eafa8bae312182a58f27e55bb93a9a471d95dd2 https://github.com/galaxyproject/galaxy/commit/5eafa8bae312182a58f27e55bb93… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 Commit: e1b54f60f20e13353d9742fb15ec4cfd2c48fd2e https://github.com/galaxyproject/galaxy/commit/e1b54f60f20e13353d9742fb15ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-20 (Tue, 20 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/43075015dd7b...e1b54f60f20e

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[galaxyproject/galaxy] 854b24: Fix linting of gff_filter_by_attribute.
by GitHub 20 Dec '16

20 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 854b24bb009c46c8e48eb799aef3bf142610bcad https://github.com/galaxyproject/galaxy/commit/854b24bb009c46c8e48eb799aef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 5eafa8bae312182a58f27e55bb93a9a471d95dd2 https://github.com/galaxyproject/galaxy/commit/5eafa8bae312182a58f27e55bb93… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 Compare: https://github.com/galaxyproject/galaxy/compare/553ec588ed11...5eafa8bae312

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[galaxyproject/galaxy] c36fbe: genbank datatype
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c36fbebb443ae5b5263ba6cad6ad36113bb52f44 https://github.com/galaxyproject/galaxy/commit/c36fbebb443ae5b5263ba6cad6ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- genbank datatype Commit: 5e2249c1b4698db4880fb74e422a903585bc3054 https://github.com/galaxyproject/galaxy/commit/5e2249c1b4698db4880fb74e422a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Address review concerns Commit: 43075015dd7bd81bef0394259f0a60721f4163df https://github.com/galaxyproject/galaxy/commit/43075015dd7bd81bef0394259f0a… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3339 from erasche/genbank Genbank datatype Compare: https://github.com/galaxyproject/galaxy/compare/415ddbb3bf8d...43075015dd7b

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[galaxyproject/infrastructure-playbook] c436aa: Run CVMFS client on cvmfs1-psu0 and serve datacach...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c436aa3d213fb7b4caa3ca0a891c03be6e3ef24f https://github.com/galaxyproject/infrastructure-playbook/commit/c436aa3d213… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M common_roles M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml Log Message: ----------- Run CVMFS client on cvmfs1-psu0 and serve datacache rsync from there

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc1299… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Allow multiple workflow parameters in a single line Commit: 733a53adcfbd90bf3a02e2e1fadbc81ba3c512ea https://github.com/galaxyproject/galaxy/commit/733a53adcfbd90bf3a02e2e1fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Replace workflow parameter values in template value string Commit: 3f07c7b52e1128ad3902ded6723eb575198de7e1 https://github.com/galaxyproject/galaxy/commit/3f07c7b52e1128ad3902ded6723e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Preserve template value if no workflow parameter value has been specified Commit: 5c3a0e1df06a1690a132498398298b742745e98f https://github.com/galaxyproject/galaxy/commit/5c3a0e1df06a1690a13249839829… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Identify workflow parameters through regex from original value Commit: 553ec588ed11effb3be665c92a3a7878914d3c1b https://github.com/galaxyproject/galaxy/commit/553ec588ed11effb3be665c92a3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling Commit: 415ddbb3bf8d44acdcabc29478544420a45fc7e4 https://github.com/galaxyproject/galaxy/commit/415ddbb3bf8d44acdcabc2947854… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f83a1bacf653...415ddbb3bf8d

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc1299… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Allow multiple workflow parameters in a single line Commit: 733a53adcfbd90bf3a02e2e1fadbc81ba3c512ea https://github.com/galaxyproject/galaxy/commit/733a53adcfbd90bf3a02e2e1fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Replace workflow parameter values in template value string Commit: 3f07c7b52e1128ad3902ded6723eb575198de7e1 https://github.com/galaxyproject/galaxy/commit/3f07c7b52e1128ad3902ded6723e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Preserve template value if no workflow parameter value has been specified Commit: 5c3a0e1df06a1690a132498398298b742745e98f https://github.com/galaxyproject/galaxy/commit/5c3a0e1df06a1690a13249839829… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Identify workflow parameters through regex from original value Commit: 553ec588ed11effb3be665c92a3a7878914d3c1b https://github.com/galaxyproject/galaxy/commit/553ec588ed11effb3be665c92a3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling Compare: https://github.com/galaxyproject/galaxy/compare/c1397908cd1f...553ec588ed11

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