Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 132e284d371992995c14eefbc299110533ec48b4 https://github.com/galaxyproject/galaxy/commit/132e284d371992995c14eefbc2991... Author: anuprulez anup.rulez@gmail.com Date: 2016-12-21 (Wed, 21 Dec 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: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages

Commit: ef82eec6109721c4a5c2f4ab2e760f73bf46c7ce https://github.com/galaxyproject/galaxy/commit/ef82eec6109721c4a5c2f4ab2e760... Author: anuprulez anup.rulez@gmail.com Date: 2016-12-21 (Wed, 21 Dec 2016)

Changed paths: M .ci/jenkins/integration/run_tests.sh M Makefile M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/dataset.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/webpack.config.js A display_applications/igv/genome_fasta.xml M doc/source/admin/dependency_resolvers.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst M doc/source/project/organization.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/galaxy_install/install_manager.py M run_tests.sh M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.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/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.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 M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_mapper.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml

Log Message: ----------- Merging with dev

Commit: bb80c842777efd0ffd980060410cb72b253f9f45 https://github.com/galaxyproject/galaxy/commit/bb80c842777efd0ffd980060410cb... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-12-28 (Wed, 28 Dec 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 #3349 from bgruening/mastheadwebhookextend

Masthead Webhook bug fix

Compare: https://github.com/galaxyproject/galaxy/compare/4c22cefadd87...bb80c842777e