- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fb30e2: Update SnpEffDb and SnpSiftDbNSFP vor SnpEff v4.1
by GitHub 13 Feb '16

13 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb30e2b06103f3fbfa3dd1238c1f4e707d04b633 https://github.com/galaxyproject/galaxy/commit/fb30e2b06103f3fbfa3dd1238c1f… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update SnpEffDb and SnpSiftDbNSFP vor SnpEff v4.1 Commit: acef6ab3f99e5420602ea06b77ac647599f80e5a https://github.com/galaxyproject/galaxy/commit/acef6ab3f99e5420602ea06b77ac… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix style errors Commit: 8fb3e461aca6f0702f45b1a5d34392893fdd2cb5 https://github.com/galaxyproject/galaxy/commit/8fb3e461aca6f0702f45b1a5d343… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1280 from jj-umn/patch-2 Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1 Compare: https://github.com/galaxyproject/galaxy/compare/063c5ad0f87c...8fb3e461aca6

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[galaxyproject/galaxy] e0ee12: Fix problem with legacy workflows and duplicate ou...
by GitHub 13 Feb '16

13 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e0ee1203c6fc176ffb56ecd717540cc6b2f0b0e7 https://github.com/galaxyproject/galaxy/commit/e0ee1203c6fc176ffb56ecd71754… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix problem with legacy workflows and duplicate output labels. Fixes #1704 - many thanks to @tzk and @mvdbeek. Commit: ff29b263630614b96c617eb9468afcec9d04d72f https://github.com/galaxyproject/galaxy/commit/ff29b263630614b96c617eb9468a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1718 from jmchilton/workflow_fixes [16.01] Fix problem with legacy workflows and duplicate output labels. Compare: https://github.com/galaxyproject/galaxy/compare/65d9ec9cab2b...ff29b2636306

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[galaxyproject/galaxy] 3e3bc1: Wrap conditional test parameters
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e3bc132d89d97fc9daac5115c63ce5c08eb0aef https://github.com/galaxyproject/galaxy/commit/3e3bc132d89d97fc9daac5115c63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Wrap conditional test parameters Commit: 749fa90a4a67c4bd6b5b3ff24468f9b300dfb9fa https://github.com/galaxyproject/galaxy/commit/749fa90a4a67c4bd6b5b3ff24468… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Attempt to handle backward compatibility for previously unwrapped conditional test parameters Commit: 063c5ad0f87c6d7ef753608e715b64b1852745ad https://github.com/galaxyproject/galaxy/commit/063c5ad0f87c6d7ef753608e715b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #1714 from guerler/fix_conditional_wrapper_000 Wrap conditional test parameters Compare: https://github.com/galaxyproject/galaxy/compare/f8a6ee335407...063c5ad0f87c

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[galaxyproject/ansible-galaxy] 01b070: tags static setup
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 01b070656c76f3a6b425cf5c4c06d324db4e0791 https://github.com/galaxyproject/ansible-galaxy/commit/01b070656c76f3a6b425… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M tasks/main.yml Log Message: ----------- tags static setup Commit: 81856d319353f57642d3b74f3ea54a1baf9d3884 https://github.com/galaxyproject/ansible-galaxy/commit/81856d319353f57642d3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M tasks/main.yml Log Message: ----------- Merge pull request #10 from mvdbeek/add_tag tag static_setup Compare: https://github.com/galaxyproject/ansible-galaxy/compare/6209af56b96b...8185…

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[galaxyproject/usegalaxy-playbook] 997e3a: commit Test mutable confs
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 997e3abfb0f0a9db4c5c1832f4bb1c8b47f2c201 https://github.com/galaxyproject/usegalaxy-playbook/commit/997e3abfb0f0a9db… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- commit Test mutable confs uploaded the backup version from PB to Test because of accidental overwrite and playbook reordered it

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[galaxyproject/usegalaxy-playbook] 5f5599: update Main's mutable confs
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5f5599998c9d8a379f31e0dd5e39d49a62c060cb https://github.com/galaxyproject/usegalaxy-playbook/commit/5f5599998c9d8a37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 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: ----------- update Main's mutable confs

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[galaxyproject/galaxy] 2ddf6e: Remove broken and hidden fix_errors tool.
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ddf6eed639957369e3891d8766fa9f5c3d48c32 https://github.com/galaxyproject/galaxy/commit/2ddf6eed639957369e3891d8766f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M config/tool_conf.xml.sample R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py Log Message: ----------- Remove broken and hidden fix_errors tool. Commit: 8703f3bd9ef595fb3b77a7021c85174f8502efa5 https://github.com/galaxyproject/galaxy/commit/8703f3bd9ef595fb3b77a7021c85… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: R tools/plotting/plot_filter.py R tools/plotting/plotter.py Log Message: ----------- Remove unused files. Commit: 39da6c327857a028d3540ec7e7c3b9aa101ff132 https://github.com/galaxyproject/galaxy/commit/39da6c327857a028d3540ec7e7c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix the remaining 2180 flake8 errors in tools/ . Commit: f8a6ee3354072d6edc8f7bf002d81e96285f17f0 https://github.com/galaxyproject/galaxy/commit/f8a6ee3354072d6edc8f7bf002d8… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M config/tool_conf.xml.sample M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #1713 from nsoranzo/flake8_fixes Fix the remaining 2180 flake8 errors in tools/ . Compare: https://github.com/galaxyproject/galaxy/compare/1e46198becdb...f8a6ee335407

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[galaxyproject/galaxy] a4a104: API: allow filtering by date using string format Y...
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4a104dcc2f020ed4100ed7edda75dd1d2857578 https://github.com/galaxyproject/galaxy/commit/a4a104dcc2f020ed4100ed7edda7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API: allow filtering by date using string format YYYY-MM-DDTHH:MM (by removing the 'T' from when parsing the filter), allow filtering by hybrid properties and not just columns; API, history contents: allow filtering, order, and limit/offset of contents (in the same format as histories) Commit: 1cb1c48975e915ab98a0776a6a37dca914c542d4 https://github.com/galaxyproject/galaxy/commit/1cb1c48975e915ab98a0776a6a37… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Managers, history contents: use text fn to wrap history_content_type filters; API, history contents: correct default order Commit: d4374bd0617d162db1a7b2803f1cc42880e0a9c7 https://github.com/galaxyproject/galaxy/commit/d4374bd0617d162db1a7b2803f1c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- Managers, history contents: remove model_class column, remove content_type from allowed filters (does not work on postgres), general cleanup Commit: 31e252743e633ffb48c655a3a12f4640a90c155e https://github.com/galaxyproject/galaxy/commit/31e252743e633ffb48c655a3a12f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: provide support for deleted and visible filters as bare keywords (e.g. 'deleted=True') Commit: 81b4eb484d55c30b386cce0af3141d6e5d4ee565 https://github.com/galaxyproject/galaxy/commit/81b4eb484d55c30b386cce0af314… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: remove unreadable preceding binary operator, add blank line Commit: 120fef8cd09c4b158e5577833d89db60e7da3caf https://github.com/galaxyproject/galaxy/commit/120fef8cd09c4b158e5577833d89… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- API, History contents: allow filtering by state, history_content_type Commit: d95c7c9d2b25d8b27d342f94c28d5c967c4af47a https://github.com/galaxyproject/galaxy/commit/d95c7c9d2b25d8b27d342f94c28d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: split code path in index to prevent backwards incompatibility Commit: c423f1eaa5f17190bf79f5f97b4f8a41903f5e3b https://github.com/galaxyproject/galaxy/commit/c423f1eaa5f17190bf79f5f97b4f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- API, history_contents: allow filtering by update/create times, inclusion in type_id list; models: add type_id as sql property on HDCAs and HDAs; managers: allow count; testing Commit: 1561759919073caa77d25eec9930b0f2235a82a1 https://github.com/galaxyproject/galaxy/commit/1561759919073caa77d25eec9930… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/onload.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/manage_repository.mako M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml M tools/phenotype_association/linkToDavid.xml M tox.ini Log Message: ----------- (merge conflicts with dev) Commit: 1e46198becdba27f98f7ce93bb27f21ae59392a1 https://github.com/galaxyproject/galaxy/commit/1e46198becdba27f98f7ce93bb27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #1602 from carlfeberhard/history.contents API, history contents: allow filters, limit/offset, and ordering Compare: https://github.com/galaxyproject/galaxy/compare/6a5d2653a706...1e46198becdb

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[galaxyproject/galaxy] 167eb5: Modify show_param input walking to account for mul...
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 167eb50dd39cd362126ca6fecf2d1d20b111464b https://github.com/galaxyproject/galaxy/commit/167eb50dd39cd362126ca6fecf2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Modify show_param input walking to account for multiple data parmaeters. xref https://github.com/galaxyproject/galaxy/pull/1561 fixes https://github.com/galaxyproject/galaxy/issues/1660 Commit: 6a5d2653a706fd82979d83f245ec4fbb89de71ff https://github.com/galaxyproject/galaxy/commit/6a5d2653a706fd82979d83f245ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1670 from jmchilton/input_param_walking_fix Modify show_param input walking to account for multiple data parameters. Compare: https://github.com/galaxyproject/galaxy/compare/74c3ff0f5618...6a5d2653a706

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[galaxyproject/galaxy] bf4e73: Update david identifier types
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080 https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server. Commit: 776180ab80b352a60713fbf6576adbfc4934ed85 https://github.com/galaxyproject/galaxy/commit/776180ab80b352a60713fbf6576a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- show all available information for current library and the opened folder Commit: 65d9ec9cab2b6e46fa7a067948bba69e3255c1ff https://github.com/galaxyproject/galaxy/commit/65d9ec9cab2b6e46fa7a067948bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1705 from martenson/fix-location-info [16.01] libraries - fix location info Commit: db9c0b89ab56d5ba0b272bb7ddaa220ed3b48c14 https://github.com/galaxyproject/galaxy/commit/db9c0b89ab56d5ba0b272bb7ddaa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge release_16.01 into dev Commit: 22e84e4814b09a3fff4fcd8c44b7f83394ebc640 https://github.com/galaxyproject/galaxy/commit/22e84e4814b09a3fff4fcd8c44b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- repack client after merge conflicts Commit: 74c3ff0f56184fa32f53fdde8928ce65bd079f1a https://github.com/galaxyproject/galaxy/commit/74c3ff0f56184fa32f53fdde8928… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1708 from martenson/dev merge 16.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/5e7dd07db653...74c3ff0f5618

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