January 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/c9fdb6e3efd2...1c0c378debde

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[galaxyproject/galaxy]
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] ce0780: Custom dbkey builds: additional variable escaping
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce0780abef5fd1e832175975b6243525a6e4cbad https://github.com/galaxyproject/galaxy/commit/ce0780abef5fd1e832175975b624… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Custom dbkey builds: additional variable escaping Commit: 1b589f252ed12eefc48c37f018e04faf142e5898 https://github.com/galaxyproject/galaxy/commit/1b589f252ed12eefc48c37f018e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/schema_template.md M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/dependencies.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/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.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/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/unit/tools/test_tool_deps.py M tools/plotting/bar_chart.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into escape_vis Conflicts: static/scripts/bundled/libs.bundled.js.map Commit: d19f22e3fabfd7f22b6970fe857ed636462ca8e5 https://github.com/galaxyproject/galaxy/commit/d19f22e3fabfd7f22b6970fe857e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/controllers/user.py 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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #3448 from yhoogstrate/escape_vis Custom dbkey builds: additional variable escaping Compare: https://github.com/galaxyproject/galaxy/compare/8daa58adcc6c...d19f22e3fabf

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[galaxyproject/galaxy] 56ed9d: Fix linting of <conditional>s
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56ed9db21d16e5c42e0d05c7102b681089ba2354 https://github.com/galaxyproject/galaxy/commit/56ed9db21d16e5c42e0d05c7102b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Fix linting of <conditional>s If the first param is boolean with truevalue="True" or falsavalue="False", or a select with an option having value "True" or "False", the linter was wrongly complaining with both: No <when /> block found for select option 'True' and: No <option /> block found for when block 'true' Commit: 8daa58adcc6c28004a2697407bce8f28d8bb5411 https://github.com/galaxyproject/galaxy/commit/8daa58adcc6c28004a2697407bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Merge pull request #3464 from nsoranzo/conditional_linting Fix linting of <conditional>s Compare: https://github.com/galaxyproject/galaxy/compare/98ee91f46703...8daa58adcc6c

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[galaxyproject/galaxy] cd2cf4: Allow finer grain specification of requirements.
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd2cf494fe1ede4ae5b43417f0da21b2ca6473a0 https://github.com/galaxyproject/galaxy/commit/cd2cf494fe1ede4ae5b43417f0da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: 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/conda.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/requirement_specification_1.xml A test/functional/tools/requirement_specification_2.xml Log Message: ----------- Allow finer grain specification of requirements. This adapts CWL-style ``SoftwareRequirement`` ``specs`` to solve #1927. Here I'm trying to implement the CWL specification in a way that helps enable the feasibility of Conda packaging in Galaxy. It is a delicate balancing act aimed to upset as many interested parties as I can. To understand the problem - consider the ``blast+`` requirement found in the Galaxy wrappers. It looks something like this: ``` <requirement type="package" version="2.2.31" name="blast+"> ``` Great, that works for Galaxy and Tool Shed packages. It doesn't work for bioconda at all. I think this problem is fairly uncommon - most packages have simple names shared across Debian, Brew, Conda, etc... - but it does happen in some cases that there are inconsistencies. Some people have taken to duplicating the requirement - this is bad and should not be done since they are mutually exclusive and Galaxy will attempt to resolve both. This introduces the following syntax for tools with profile >= 16.10: ``` <requirement type="package" version="2.2.31" name="blast+"> <specification uri="https://anaconda.org/bioconda/blast" /> <specification uri="https://packages.debian.org/sid/ncbi-blast+" version="2.2.31-3" /> </requirement> ``` This allows finer grain resolution of the requirement without sacrificing the abstract name at the top. It allows the name and the version to be adapted by resolvers as needed (hopefully rarely so). This syntax is the future facing one, but obviously this tool would not work on older Galaxy versions. To remedy this - an alternative syntax can be used for tools targetting Galaxy verions pre-16.10: ``` <requirement type="package" version="2.2" specification_uris="https://anaconda.org/bioconda/blast@2.2.31,https://packages.debian.org/jess…">blast+</requirement> ``` This syntax sucks - but it does give newer Galaxies the ability to resolve the specifications without breaking the more simple functionality for older Galaxies. For more information on the CWL side of this - checkout the discussion on https://github.com/common-workflow-language/cwltool/pull/214. The CWL specification information is defined at http://www.commonwl.org/v1.0/CommandLineTool.html#SoftwarePackage. Conflicts: lib/galaxy/tools/deps/__init__.py test/functional/tools/samples_tool_conf.xml Commit: 330d71d37ce7eaa60b5c8c20ae83aeb36fec4a6c https://github.com/galaxyproject/galaxy/commit/330d71d37ce7eaa60b5c8c20ae83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/xsd/galaxy.xsd R test/functional/tools/requirement_specification_1.xml R test/functional/tools/requirement_specification_2.xml Log Message: ----------- Remove tool XML modifications for requirement specifications. Per discussion on #3117 - some people were in favor of the idea but some were opposed. I think it is still important to implement this for CWL tools and useful from a library perspective. This just removes changes to Galaxy tool XML. Commit: baf9b82847fc526af56ed8efa7aba4d31d62f400 https://github.com/galaxyproject/galaxy/commit/baf9b82847fc526af56ed8efa7ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- More modular config option handling for dependency resolvers. The handling of global configuration options for Conda specific options was hacky and a poor design. This is much more modular and allows the elegant cascading option sources for all resolvers. Commit: 49a11073a49242fbd86e3ec05fb5029194ec23fd https://github.com/galaxyproject/galaxy/commit/49a11073a49242fbd86e3ec05fb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Give resolver's with a resolve_all method an interface. This follows the existing pattern within the module. Commit: 8e20e71556cfc90da548243d390deb52d4e9110d https://github.com/galaxyproject/galaxy/commit/8e20e71556cfc90da548243d390d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: 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 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 test/unit/tools/test_tool_deps.py Log Message: ----------- Change interface of depependency resolver's resolve for consistency. If resolve_all takes in requirements, then so should resolve. Commit: 35b2b735ff7495576de88b7469c7118f65cb2838 https://github.com/galaxyproject/galaxy/commit/35b2b735ff7495576de88b7469c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Modify specification interface with better name. Commit: 2fad74ddcf63c03fc2d7fd77fa3838de637a1bf4 https://github.com/galaxyproject/galaxy/commit/2fad74ddcf63c03fc2d7fd77fa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Implement dependency mapping for environment modules, galaxy packages, and Conda. Commit: 3d9cdeb70c0170b7795c35e458c878ebe19caf1a https://github.com/galaxyproject/galaxy/commit/3d9cdeb70c0170b7795c35e458c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M run.sh A scripts/manage_tool_dependencies.py Log Message: ----------- Outline infrastructure for managing Conda installations outside of Galaxy. - Construct a DependencyManager according to Galaxy's configuration before Galaxy starts to allow auto installation of Conda. - Add script for managing tool dependencies outside of a Galaxy environment. - Refactor to allow this to be done without duplicating logic related to defaults, configuration handling, etc.... Implements #3426. Commit: 312f941e46fdbbe6198b6b0e6a3f00867946a6bd https://github.com/galaxyproject/galaxy/commit/312f941e46fdbbe6198b6b0e6a3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Swap default for Conda "auto_init" to True. Everyone gets a Conda when Galaxy starts up. Commit: 0b7c6761c8dbb2baf7391dc4a08c4dbed2ccc7f2 https://github.com/galaxyproject/galaxy/commit/0b7c6761c8dbb2baf7391dc4a08c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M scripts/manage_tool_dependencies.py Log Message: ----------- Rework #3433 for changes in #3444. Commit: 9baf6d6d8d8d089a8d2c2687ef498a396006b920 https://github.com/galaxyproject/galaxy/commit/9baf6d6d8d8d089a8d2c2687ef49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: A config/local_conda_mapping.yml.sample M lib/galaxy/config.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py Log Message: ----------- Samples and defaults for Conda mapping. - Map R to r-base and blast+ to blast for conda dependencies. - Add sample environment modules file showing off the new mapping feature. - Add integration test case to verify the default conda mapping (R -> r-base in particular). Commit: 3e3d41fb94c00a9c6b068626b6f541e714b2500e https://github.com/galaxyproject/galaxy/commit/3e3d41fb94c00a9c6b068626b6f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix unit test test_tool_deps to not auto-install Conda. This became the default behavior with conda_auto_init defaulting to True. Commit: 98ee91f467039f27f4e10d730f78057d1421e833 https://github.com/galaxyproject/galaxy/commit/98ee91f467039f27f4e10d730f78… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.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/util/properties.py M run.sh A scripts/manage_tool_dependencies.py A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3444 from jmchilton/deps_framework_overhaul Implement Dependency Resolver Mapping Compare: https://github.com/galaxyproject/galaxy/compare/5bd8a0fa0232...98ee91f46703

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[galaxyproject/galaxy] 20632b: Adding fuzzy search to tool search
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20632b2757f789bc751faa280fa34eebe78e41db https://github.com/galaxyproject/galaxy/commit/20632b2757f789bc751faa280fa3… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/search/__init__.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding fuzzy search to tool search Commit: 659679005d0e0db7a9689cc738114742bf3140fc https://github.com/galaxyproject/galaxy/commit/659679005d0e0db7a9689cc73811… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/tours/core.history.yaml M lib/galaxy/config.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/asserts/text.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M run_tests.sh M scripts/functional_tests.py R scripts/run_selenium_tests.sh M static/maps/layout/menu.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-view.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/layout/menu.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js M templates/ind_share_base.mako M templates/show_params.mako R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py A test/api/test_visualizations.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R 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test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/manual/workflows_scaling.py 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_stock_tours.py M 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_support.py M test/unit/workflows/workflow_support.py R tools/filters/gff/sort_gtf.py M tox.ini Log Message: ----------- Merging with dev Commit: ea0d50648c2c64abb7093fba47acec020919163f https://github.com/galaxyproject/galaxy/commit/ea0d50648c2c64abb7093fba47ac… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako 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 M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/binary.py 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 lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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 A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test/api/test_workflows.py M test/docker/README.md 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/implicit_conversion.xml A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merging with dev Commit: a4dec71b7ac0fedcd5f14179b7ace172d1466308 https://github.com/galaxyproject/galaxy/commit/a4dec71b7ac0fedcd5f14179b7ac… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Adding Whoosh NgramFilter and making it configurable through config Commit: 28133bead15e955e70fcbec8e09d1de06598b345 https://github.com/galaxyproject/galaxy/commit/28133bead15e955e70fcbec8e09d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding and removing blank lines Commit: 54b527b1fc35d6ea66215df04144491f42e558e4 https://github.com/galaxyproject/galaxy/commit/54b527b1fc35d6ea66215df04144… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.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/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merging with dev Commit: 2573699c0ac1a12f808acb4006bc9e5f05f822a9 https://github.com/galaxyproject/galaxy/commit/2573699c0ac1a12f808acb4006bc… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding line breaks for import section Commit: 5bd8a0fa0232f5fa56cc4ace557d3b8f0d5cbdf0 https://github.com/galaxyproject/galaxy/commit/5bd8a0fa0232f5fa56cc4ace557d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #3356 from bgruening/fuzzysearch Fuzzy search for tools search Compare: https://github.com/galaxyproject/galaxy/compare/4eade311dbeb...5bd8a0fa0232

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[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Compare: https://github.com/galaxyproject/galaxy/compare/5b3debc51088...915b653b91af

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[galaxyproject/galaxy] 596d12: Implement ToolRequirements class
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 596d12da44908e158905d7c1bce30d9e3557b258 https://github.com/galaxyproject/galaxy/commit/596d12da44908e158905d7c1bce3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py A lib/galaxy/util/oset.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Implement ToolRequirements class This class holds indiviual ToolRequirement objects as an ordered set. This makes it easier to compare, intersect, and get unions of multiple ToolRequirements and to filter for resolvable or package type dependencies. This will be useful when installing tool dependencies in batch. Commit: 5ee7e2e3e26bdbdecec0b74ed4154734d9b56ae4 https://github.com/galaxyproject/galaxy/commit/5ee7e2e3e26bdbdecec0b74ed415… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Log failed dep resolution just once Commit: 9c9b405b6f969421c2073a53dad117ffefed17c6 https://github.com/galaxyproject/galaxy/commit/9c9b405b6f969421c2073a53dad1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Add test for set on list of ToolRequirements Commit: 4eade311dbebdf90168821fafe3e4d09f4423565 https://github.com/galaxyproject/galaxy/commit/4eade311dbebdf90168821fafe3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py A lib/galaxy/util/oset.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3461 from mvdbeek/ToolRequirements Implement ToolRequirements class Compare: https://github.com/galaxyproject/galaxy/compare/00d1e15f74be...4eade311dbeb

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[galaxyproject/galaxy] e5de94: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5de94ceb9b6a8876a646d4cfc281d5c12f1125a https://github.com/galaxyproject/galaxy/commit/e5de94ceb9b6a8876a646d4cfc28… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 00d1e15f74bec373934bceeb0d7ca73d8a93da78 https://github.com/galaxyproject/galaxy/commit/00d1e15f74bec373934bceeb0d7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3462 from bgruening/fix_condor_containers fix condor containers Compare: https://github.com/galaxyproject/galaxy/compare/7700c3cf7f07...00d1e15f74be

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[galaxyproject/galaxy] 45bf7a: Make requirement tags in bar_chart.xml functional ...
by GitHub 22 Jan '17

22 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45bf7ad8c4437edc95847de47e2f46a393fc1726 https://github.com/galaxyproject/galaxy/commit/45bf7ad8c4437edc95847de47e2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M tools/plotting/bar_chart.xml Log Message: ----------- Make requirement tags in bar_chart.xml functional with default dependency resolver. I'm not sure if we need to update the version since previously these tags were purely for documentation and had no functional purpose. xref this comment https://github.com/galaxyproject/galaxy/pull/3444#issuecomment-273909855 from @bgruening Commit: 7700c3cf7f0789a4a921f32ff9b1e8037634d63e https://github.com/galaxyproject/galaxy/commit/7700c3cf7f0789a4a921f32ff9b1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M tools/plotting/bar_chart.xml Log Message: ----------- Merge pull request #3454 from jmchilton/gnuplot_deps Make requirement tags in bar_chart.xml functional with default dependency resolvers. Compare: https://github.com/galaxyproject/galaxy/compare/d9f9a31c32b9...7700c3cf7f07

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