galaxy-commits April 2017

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[galaxyproject/infrastructure-playbook] 97fe8f: Two more redirects for hub
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 97fe8f28d0e9f91fd422db185706d1e39214c9e4 https://github.com/galaxyproject/infrastructure-playbook/commit/97fe8f28d0e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Two more redirects for hub

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[galaxyproject/infrastructure-playbook] 32d21f: Admin/Interface redirect
by GitHub 28 Apr '17

28 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 32d21f9efdbd2ca03532d0fa38184fde4db21d89 https://github.com/galaxyproject/infrastructure-playbook/commit/32d21f9efdb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Admin/Interface redirect

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[galaxyproject/galaxy] 4b5311: Add missing imports for documentation builds
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b531179b0a19a45902f40f49e823cf5260bbd56 https://github.com/galaxyproject/galaxy/commit/4b531179b0a19a45902f40f49e82… Author: Athos Ribeiro <athoscr(a)fedoraproject.org> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add missing imports for documentation builds As mentioned in #3075, the build requirements for the project documentation were only listed in the Jenkins job. This commit adds those missing requirements to the project. Note that they should also be removed from the Jenkins build * fixes #3075 Commit: 647b4901c30d356f13f851a76c2a7c7ed8bfd808 https://github.com/galaxyproject/galaxy/commit/647b4901c30d356f13f851a76c2a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M Makefile M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- move reqs to dev-requirements and touch makefile Commit: d42fc9ae71b26caed30d6b904681a6b2065febbc https://github.com/galaxyproject/galaxy/commit/d42fc9ae71b26caed30d6b904681… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M .gitignore M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M 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M client/galaxy/style/source_material/circle.py M client/package.json M client/webpack.config.js A config/build_sites.yml.sample A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A 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test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.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 M tools/filters/gff/gtf_filter_by_attribute_values_list.py R tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.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.py M tools/filters/mergeCols.py M tools/filters/pasteWrapper.xml M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml 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/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.py M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.py M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.py M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.py M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.py M tools/maf/vcf_to_maf_customtrack.xml M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/fastq_gen_conv.xml M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into fix_documentation_build Commit: 7edfe39f20024f161a30be14406c0baa2a9807bf https://github.com/galaxyproject/galaxy/commit/7edfe39f20024f161a30be14406c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M Makefile Log Message: ----------- fix makefile help for docs thanks nsoranzo Commit: 7ba3662d29f0f8d9c6a24ea3fa66eee421f6059d https://github.com/galaxyproject/galaxy/commit/7ba3662d29f0f8d9c6a24ea3fa66… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M Makefile M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Merge pull request #3104 from athos-ribeiro/fix_documentation_build Add missing imports for documentation builds Compare: https://github.com/galaxyproject/galaxy/compare/26afd36a4d13...7ba3662d29f0

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[galaxyproject/galaxy] f369ab: Add login redirect for backbone router
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f369ab0668fcedf572346553d3e0b70564f81796 https://github.com/galaxyproject/galaxy/commit/f369ab0668fcedf572346553d3e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add login redirect for backbone router Commit: e431af074f4bb8a0d70f6a387af2654bfa21790b https://github.com/galaxyproject/galaxy/commit/e431af074f4bb8a0d70f6a387af2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Redirect through push Commit: 26afd36a4d1336825fa47e2e8f3921c4ee8e1486 https://github.com/galaxyproject/galaxy/commit/26afd36a4d1336825fa47e2e8f39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/login_routes' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3e14cd532074...26afd36a4d13

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[galaxyproject/galaxy] 60e000: Fix edge case for workflow mapping handling when t...
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 60e00088c8b27c04734c7f7adb3cdae6a9a9580f https://github.com/galaxyproject/galaxy/commit/60e00088c8b27c04734c7f7adb3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix edge case for workflow mapping handling when tools not available. Fixes #3960. Commit: 3fcd78564630fae9c4670cfbe198572f94f688c0 https://github.com/galaxyproject/galaxy/commit/3fcd78564630fae9c4670cfbe198… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #3962 from jmchilton/workflow_editor_mapping_test [17.01] Fix edge case for workflow mapping handling when tools not available. Compare: https://github.com/galaxyproject/galaxy/compare/f3c134abcb04...3fcd78564630

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[galaxyproject/galaxy] 78c263: Udpate Babel to a version compat. with sphinx.
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78c263ac7c6beb1b93269f252897b0dd6336b450 https://github.com/galaxyproject/galaxy/commit/78c263ac7c6beb1b93269f252897… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Udpate Babel to a version compat. with sphinx. Commit: 3e14cd532074d190def283ed2cce61ae22c0eee9 https://github.com/galaxyproject/galaxy/commit/3e14cd532074d190def283ed2cce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3986 from jmchilton/babel_update Udpate Babel to a version compat. with sphinx. Compare: https://github.com/galaxyproject/galaxy/compare/92d93c7ef964...3e14cd532074

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[galaxyproject/galaxy] 852fb4: Leasing container sometimes breaks things in docke...
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 852fb42945bc5176d15b22dbe624523b7b571035 https://github.com/galaxyproject/galaxy/commit/852fb42945bc5176d15b22dbe624… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Leasing container sometimes breaks things in docker galaxy Commit: 92d93c7ef96452ba343a43502fe519e0dea3f8bf https://github.com/galaxyproject/galaxy/commit/92d93c7ef96452ba343a43502fe5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #3263 from zfrenchee/patch-1 Azure - Leasing container sometimes breaks things in docker galaxy Compare: https://github.com/galaxyproject/galaxy/compare/291426a5dcd7...92d93c7ef964

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[galaxyproject/galaxy] c0fd3c: Display input parameters default value for runtime...
by GitHub 27 Apr '17

27 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0fd3c7c6ddef01b0546b485a1a4e88d215042e2 https://github.com/galaxyproject/galaxy/commit/c0fd3c7c6ddef01b0546b485a1a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Display input parameters default value for runtime values Commit: fba860f689d1af5e6727a946e20e1521f83620ed https://github.com/galaxyproject/galaxy/commit/fba860f689d1af5e6727a946e20e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) 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: ----------- Use local flag to handle runtime values Commit: 291426a5dcd7941e1d6711b5926418bf0dab0c4c https://github.com/galaxyproject/galaxy/commit/291426a5dcd7941e1d6711b59264… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3943 from guerler/show_default_value_for_runtime_values Show default value for runtime values Compare: https://github.com/galaxyproject/galaxy/compare/b7a8bea3cd67...291426a5dcd7

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[galaxyproject/galaxy] be7d12: Fix Travix builds which use flake8-docstrings
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be7d1294fd69618cbd415df4c562ce2c4ef88808 https://github.com/galaxyproject/galaxy/commit/be7d1294fd69618cbd415df4c562… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M tox.ini Log Message: ----------- Fix Travix builds which use flake8-docstrings flake8-docstrings is broken due to the release of pydocstyle 2.0.0 (see https://gitlab.com/pycqa/flake8-docstrings/issues/19 ), so temporarily add an extra dep in tox.ini to pin it. Commit: b7a8bea3cd67b8e889f44fd88b8529e47fe53cbc https://github.com/galaxyproject/galaxy/commit/b7a8bea3cd67b8e889f44fd88b85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3981 from nsoranzo/fix_py27-lint_build Fix Travix builds which use flake8-docstrings Compare: https://github.com/galaxyproject/galaxy/compare/d398c90dbd70...b7a8bea3cd67

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[galaxyproject/infrastructure-playbook] ebd39c: Redirects for both GetGalaxy and Get%20Galaxy
by GitHub 26 Apr '17

26 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ebd39cdbf1066fd30b8e4df370f7fb7d291f5213 https://github.com/galaxyproject/infrastructure-playbook/commit/ebd39cdbf10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Redirects for both GetGalaxy and Get%20Galaxy

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