galaxy-commits January 2017

galaxy-commits@lists.galaxyproject.org

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134 discussions

[galaxyproject/usegalaxy-playbook] 4e1e2d: Run kraken on multi on main
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4e1e2d7f8ed03ab5b779992216b4f1a1df50fcfa https://github.com/galaxyproject/usegalaxy-playbook/commit/4e1e2d7f8ed03ab5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Run kraken on multi on main

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[galaxyproject/usegalaxy-playbook] 11d622: Mutable config changes
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 11d6228991affe1b8d4bd2e18fea3b86c4bc49fc https://github.com/galaxyproject/usegalaxy-playbook/commit/11d6228991affe1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable config changes Commit: 708381c3800b6115e5e4d447b5a36699721f7389 https://github.com/galaxyproject/usegalaxy-playbook/commit/708381c3800b6115… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M production/group_vars/galaxywebservers.yml Log Message: ----------- Add docker_connect_port workaround Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/62539b46cf01...…

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[galaxyproject/galaxy] f3af2a: jsonify initial value when returned through to_dic...
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3af2a06c3af09a8c96283e133910b32659916bd https://github.com/galaxyproject/galaxy/commit/f3af2a06c3af09a8c96283e13391… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- jsonify initial value when returned through to_dict caller Commit: 98cd33d4ae70606d10ce2d4602663f6d5ef632fe https://github.com/galaxyproject/galaxy/commit/98cd33d4ae70606d10ce2d460266… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use security Commit: 68ab629723fe5ab900d115d1e6bf1b619de5a2c7 https://github.com/galaxyproject/galaxy/commit/68ab629723fe5ab900d115d1e6bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3513 from guerler/jsonify_initial_value_in_dict jsonify initial value when returned through to_dict caller Compare: https://github.com/galaxyproject/galaxy/compare/04a7ce6f1016...68ab629723fe

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[galaxyproject/galaxy] 496fa5: Improve dataset state information in selection fie...
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 496fa5144dc373952c0d815b844b17fef394f632 https://github.com/galaxyproject/galaxy/commit/496fa5144dc373952c0d815b844b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Improve dataset state information in selection fields Commit: ccacbb7c3b7dc453b687fb7ec332f4d6793d689d https://github.com/galaxyproject/galaxy/commit/ccacbb7c3b7dc453b687fb7ec332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use dataset matcher for unhidden datasets only Commit: 78a37b2a191403a87ea05fc88f890504fad400c4 https://github.com/galaxyproject/galaxy/commit/78a37b2a191403a87ea05fc88f89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix test case Commit: 54036e9f7d41606f40d87859c45dbc35f794b2b3 https://github.com/galaxyproject/galaxy/commit/54036e9f7d41606f40d87859c45d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix test case for deleted mock hdas Commit: 02dd2e4708e7167248c48b2452621cf31a6bdba6 https://github.com/galaxyproject/galaxy/commit/02dd2e4708e7167248c48b245262… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge pull request #3495 from guerler/fix_dataset_label [17.01] Properly label hidden datasets in dataset selectors Compare: https://github.com/galaxyproject/galaxy/compare/f51355a18385...02dd2e4708e7

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[galaxyproject/galaxy] 809c08: - add Webhooks tests
by GitHub 29 Jan '17

29 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 809c087a8a50e30c7606b7b09e8c989d2b3ed6c8 https://github.com/galaxyproject/galaxy/commit/809c087a8a50e30c7606b7b09e8c… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/webhooks/__init__.py A test/api/test_webhooks.py Log Message: ----------- - add Webhooks tests - small code improvements Commit: 867e8dc4ca9aa3055a0149de594bae8fab4f8d13 https://github.com/galaxyproject/galaxy/commit/867e8dc4ca9aa3055a0149de594b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css Log Message: ----------- Treat demo/test webhooks like demo/test tools. - Populate test server with demo webhooks by default. - Eliminate special logic needed to treat the demo directory differently. - Document how to enable the demo webhooks in galaxy.ini.sample. - Populate the demo webhooks when starting Galaxy with GALAXY_RUN_WITH_TEST_TOOLS=1 set. Commit: 8b30d874b539aa9665387bc298e1fbb528c242d0 https://github.com/galaxyproject/galaxy/commit/8b30d874b539aa9665387bc298e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M test/api/test_webhooks.py Log Message: ----------- Update webhooks API test to set expectations independent of implementation. It may seem like this is testing less since fewer API calls are being made - but when you use the backend to generate the data you trust in the test case - the correlation lands up meaning relatively less is tested. For instance, if there is some problem arises in the to_dict method of a webhook - it is going to arise in both the implementation and in the test case and so the test case will just be asserting that the response is broken ... and it will be. Testing more concrete things is also good for ensuring backward compatibility. Commit: a9ba71c07be195f0e0b1774a802ed919d3a4f2b1 https://github.com/galaxyproject/galaxy/commit/a9ba71c07be195f0e0b1774a802e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh M test/api/test_webhooks.py M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css Log Message: ----------- Merge pull request #3 from jmchilton/webhooks_reorg Improve abstraction in webhook API tests. Commit: 41d4eac28ff14b334bf413e75e81401a458334e0 https://github.com/galaxyproject/galaxy/commit/41d4eac28ff14b334bf413e75e81… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A display_applications/igv/genome_fasta.xml M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst M lib/galaxy/auth/providers/__init__.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py A lib/galaxy/datatypes/converters/fasta_to_fai.xml A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A 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test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/README.md M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/paired_collection_map_over_structured_like.xml A test/functional/tools/param_text_option.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/phdcomics/static/script.js R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/tests/workflow_editor_tests.js A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py R tools/filters/gff/sort_gtf.py M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into feature/webhooks_tests Commit: 4cb7617bb815b455edb5307759318822944f5a3c https://github.com/galaxyproject/galaxy/commit/4cb7617bb815b455edb530775931… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M config/galaxy.ini.sample R config/plugins/webhooks/demo/history_test1/config/history_test1.yml R config/plugins/webhooks/demo/history_test2/config/history_test2.yml R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml R config/plugins/webhooks/demo/phdcomics/helper/__init__.py R config/plugins/webhooks/demo/phdcomics/static/script.js R config/plugins/webhooks/demo/phdcomics/static/styles.css R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml R config/plugins/webhooks/demo/trans_object/helper/__init__.py R config/plugins/webhooks/demo/xkcd/config/xkcd.yml R config/plugins/webhooks/demo/xkcd/static/script.js R config/plugins/webhooks/demo/xkcd/static/styles.css M lib/galaxy/webhooks/__init__.py M run.sh A test/api/test_webhooks.py M test/base/driver_util.py A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css Log Message: ----------- Merge pull request #3469 from anatskiy/feature/webhooks_tests Webhooks: add tests Compare: https://github.com/galaxyproject/galaxy/compare/30b462190ac7...4cb7617bb815

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[galaxyproject/galaxy] a6b169: Do not select first value as default if select val...
by GitHub 28 Jan '17

28 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6b16954796a3e32ee405779647ea337d1cc86d9 https://github.com/galaxyproject/galaxy/commit/a6b16954796a3e32ee405779647e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Do not select first value as default if select value is optional in repeats Commit: 46fb84aa34fe2a3d49ffa13446bee75c21519d54 https://github.com/galaxyproject/galaxy/commit/46fb84aa34fe2a3d49ffa13446be… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove space Commit: e1f87f17fc118d84646007ec3a55960fd18657d1 https://github.com/galaxyproject/galaxy/commit/e1f87f17fc118d84646007ec3a55… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove secondary initial value handling from basic parameters Commit: 74bddbfee7be79b5f330722f216b9507c288961b https://github.com/galaxyproject/galaxy/commit/74bddbfee7be79b5f330722f216b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Determine initial values in tool.pys to_json/build_module caller Commit: 251842e452adebe111418e85b308d5f1b510a5c9 https://github.com/galaxyproject/galaxy/commit/251842e452adebe111418e85b308… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix inherited to_dict caller Commit: 3aa6a3b94f7c14fb40f8fb4ca668f0c38cd943c2 https://github.com/galaxyproject/galaxy/commit/3aa6a3b94f7c14fb40f8fb4ca668… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix tests, remove redundant initial value callers Commit: 6838593f2287f6a17aaaf3fc0b8ec9fc608db968 https://github.com/galaxyproject/galaxy/commit/6838593f2287f6a17aaaf3fc0b8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M README.rst M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.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/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/util/workflow_util.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-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/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_workflows.py A test/functional/tools/legacy_r.xml A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'dev' into fix_repeat_defaults Commit: 30b462190ac7b6795935a0de7fa41118ff23af3d https://github.com/galaxyproject/galaxy/commit/30b462190ac7b6795935a0de7fa4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-28 (Sat, 28 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3472 from guerler/fix_repeat_defaults Do not select first value as default if select value is optional Compare: https://github.com/galaxyproject/galaxy/compare/1b179e2b57b2...30b462190ac7

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[galaxyproject/usegalaxy-playbook] 62539b: Dropped PAG slide from rotation.
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 62539b46cf0145f10efd3be24732df4dc3897208 https://github.com/galaxyproject/usegalaxy-playbook/commit/62539b46cf0145f1… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped PAG slide from rotation.

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[galaxyproject/usegalaxy-playbook] 4cb0cb: Additional playbook updates
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4cb0cb7c5418f1fdcd6547be789db1f212f98c46 https://github.com/galaxyproject/usegalaxy-playbook/commit/4cb0cb7c5418f1fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M galaxy.yml M stage/galaxy_version.yml M stage/group_vars/all.yml M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Additional playbook updates

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[galaxyproject/galaxy] 3dcdad: Add sam_to_bam to list of tools requiring Galaxy's...
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 3dcdad9eba31bf1b689f9bfb2e95908f8c4c2c55 https://github.com/galaxyproject/galaxy/commit/3dcdad9eba31bf1b689f9bfb2e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: f51355a183852565a857f825776bd38321cf2ff8 https://github.com/galaxyproject/galaxy/commit/f51355a183852565a857f825776b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3506 from martenson/release_17.01 [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Compare: https://github.com/galaxyproject/galaxy/compare/a396b280dc6a...f51355a18385

1 0

[galaxyproject/galaxy] 3dcdad: Add sam_to_bam to list of tools requiring Galaxy's...
by GitHub 27 Jan '17

27 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dcdad9eba31bf1b689f9bfb2e95908f8c4c2c55 https://github.com/galaxyproject/galaxy/commit/3dcdad9eba31bf1b689f9bfb2e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: 1b179e2b57b257ed6d60433e04d9d5766468e3ec https://github.com/galaxyproject/galaxy/commit/1b179e2b57b257ed6d60433e04d9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Log Message: ----------- Merge pull request #3505 from martenson/release_17.01 [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Compare: https://github.com/galaxyproject/galaxy/compare/457083a7b767...1b179e2b57b2

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