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
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
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
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 test/api/workflows_format_2/converter.py
R test/api/workflows_format_2/interface.py
R 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/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
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