Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e73e6b3587a98e1537b82283f8935f770648b2e3
https://github.com/galaxyproject/galaxy/commit/e73e6b3587a98e1537b82283f893…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Allow disabling separating tools commands into their own script.
Forcing them there broke Pulsar-on-Windows functionality - this fix is courtesy of @jj-umn.
Commit: 54bffd93ac2a78f248e0d937ae0ea8e1aaafb131
https://github.com/galaxyproject/galaxy/commit/54bffd93ac2a78f248e0d937ae0e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Spelling fix thanks to @nsoranzo.
Commit: 4bf9955d0333af12d5b6dbdfe4336fda64f5a55e
https://github.com/galaxyproject/galaxy/commit/4bf9955d0333af12d5b6dbdfe433…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Backport fac2efc4bd6b2214fa6d17e27b43d26fe4de7d37 to 16.04 to enable functional stats on main.
Commit: e1cafd6ab45d385cfa46b16a2c4ab120fc3fde6f
https://github.com/galaxyproject/galaxy/commit/e1cafd6ab45d385cfa46b16a2c4a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org.
Commit: 2aab4ee72198651a5017d37676853e74edec3b46
https://github.com/galaxyproject/galaxy/commit/2aab4ee72198651a5017d3767685…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/web/framework/middleware/statsd.py
Log Message:
-----------
More backporting of stats to make it functional on main.
Commit: 8ef8522d68ea4d6b6c9a736ec4439306877fff13
https://github.com/galaxyproject/galaxy/commit/8ef8522d68ea4d6b6c9a736ec443…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #2497 from dannon/backport_onion_rearrangement
[16.04] Backport of stats fixes/prefix work.
Commit: 7d962ee0cb6bcc83033363111d30be375a48a920
https://github.com/galaxyproject/galaxy/commit/7d962ee0cb6bcc83033363111d30…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-15 (Wed, 15 Jun 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Merge pull request #2492 from jmchilton/windows_no_shell
[16.04] Allow disabling separating tools commands into their own script.
Commit: 1b110299afbf01cfc275108b8de6193f17fbcbd8
https://github.com/galaxyproject/galaxy/commit/1b110299afbf01cfc275108b8de6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-15 (Wed, 15 Jun 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/f078365acc66...1b110299afbf
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: e73e6b3587a98e1537b82283f8935f770648b2e3
https://github.com/galaxyproject/galaxy/commit/e73e6b3587a98e1537b82283f893…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Allow disabling separating tools commands into their own script.
Forcing them there broke Pulsar-on-Windows functionality - this fix is courtesy of @jj-umn.
Commit: 54bffd93ac2a78f248e0d937ae0ea8e1aaafb131
https://github.com/galaxyproject/galaxy/commit/54bffd93ac2a78f248e0d937ae0e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Spelling fix thanks to @nsoranzo.
Commit: 7d962ee0cb6bcc83033363111d30be375a48a920
https://github.com/galaxyproject/galaxy/commit/7d962ee0cb6bcc83033363111d30…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-15 (Wed, 15 Jun 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Merge pull request #2492 from jmchilton/windows_no_shell
[16.04] Allow disabling separating tools commands into their own script.
Compare: https://github.com/galaxyproject/galaxy/compare/8ef8522d68ea...7d962ee0cb6b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 419594845d15fc040d6c58f80096663e76fb3b80
https://github.com/galaxyproject/galaxy/commit/419594845d15fc040d6c58f80096…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fixes the ability for users to toggle their filters. There's no reason to require a user_id here since it's locked to trans and require_login is set.
Commit: 0c4fd995c5562863cbeb6945e95d13283506ea15
https://github.com/galaxyproject/galaxy/commit/0c4fd995c5562863cbeb6945e95d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fix module resolution for migrated toolbox filters path -- reuses (in a hacky way) the filtering function that was duplicated to galaxy.tools.toolbox.filters. Pushing more of this functionality (the docs, etc) into the FilterFactory might be nice down the road.
Commit: f078365acc66748b272a00b81f9dcec7febf81fa
https://github.com/galaxyproject/galaxy/commit/f078365acc66748b272a00b81f9d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Merge pull request #2499 from dannon/user_tool_filter_fixes
Toolbox filter fixes
Compare: https://github.com/galaxyproject/galaxy/compare/bb851d6645bb...f078365acc66
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 4bf9955d0333af12d5b6dbdfe4336fda64f5a55e
https://github.com/galaxyproject/galaxy/commit/4bf9955d0333af12d5b6dbdfe433…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Backport fac2efc4bd6b2214fa6d17e27b43d26fe4de7d37 to 16.04 to enable functional stats on main.
Commit: e1cafd6ab45d385cfa46b16a2c4ab120fc3fde6f
https://github.com/galaxyproject/galaxy/commit/e1cafd6ab45d385cfa46b16a2c4a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org.
Commit: 2aab4ee72198651a5017d37676853e74edec3b46
https://github.com/galaxyproject/galaxy/commit/2aab4ee72198651a5017d3767685…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/web/framework/middleware/statsd.py
Log Message:
-----------
More backporting of stats to make it functional on main.
Commit: 8ef8522d68ea4d6b6c9a736ec4439306877fff13
https://github.com/galaxyproject/galaxy/commit/8ef8522d68ea4d6b6c9a736ec443…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #2497 from dannon/backport_onion_rearrangement
[16.04] Backport of stats fixes/prefix work.
Compare: https://github.com/galaxyproject/galaxy/compare/6ccfd13ab4e5...8ef8522d68ea
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a80eaae7fa380b0f6d484307bcfde179809dac54
https://github.com/galaxyproject/galaxy/commit/a80eaae7fa380b0f6d484307bcfd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/wrapped.py
Log Message:
-----------
Reduce duplication in galaxy.tools.parameters.wrapped.
Commit: 6ddb2c2a6a44c2947e7e9b6edbaa4e11ad289595
https://github.com/galaxyproject/galaxy/commit/6ddb2c2a6a44c2947e7e9b6edbaa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
A lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/special_tools.py
A lib/galaxy/tools/unzip_collection.xml
A lib/galaxy/tools/zip_collection.xml
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/twilltestcase.py
Log Message:
-----------
Implement framework for model tools.
This special class of tools leverages the infrastructure for tool inputs, tool state tracking, tool module for workflows, tool API, etc... without actually producing command-line jobs. Instead these tools are provided the input model objects and are expected to produce output model objects directly. This provides an oppertunity to copy HDAs without copying the underlying datasets.
The first driving use case for these tools are also included - namely tools that allow zipping and unzipping paired collections. These tools can be mapped over lists (e.g. list:paired to (list, list) or the inverse) using much of the existing infrastructure for tools. Test cases included that validate these work with mapping operations and in workflows.
The most obvious advantage of these versus traditional tools that do the same thing is that the data isn't copied on disk - new HDAs are created directly from the source datasets.
Testing:
This PR includes various API test cases for functionality, these can be run with the following command:
```
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_unzip_collection
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_zip_inputs
./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_zip_list_inputs
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_zip_collections
```
Commit: ddeff4ec0cdb0c6a803ae09843d0c70e2a70556b
https://github.com/galaxyproject/galaxy/commit/ddeff4ec0cdb0c6a803ae09843d0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/special_tools.py
M test/api/helpers.py
M test/api/test_tools.py
A test/functional/tools/exit_code_from_file.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
New model tool that filters failed datasets out of a collection.
This differs from a traditional tool in that its inputs don't need to be in an 'ok' state and instead of creating new datasets and duplicating data on disk, new HDAs are created from the existing datasets.
Commit: 68a72069433a029e690535f14c1b4c91d1603499
https://github.com/galaxyproject/galaxy/commit/68a72069433a029e690535f14c1b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/special_tools.py
Log Message:
-----------
New model tool that flattens any collection into a list.
Testing:
```
./run_tests.sh -framework -id __FLATTEN__
```
Commit: 8a0056530fec23d487f45e45dfa99ef6e61cc757
https://github.com/galaxyproject/galaxy/commit/8a0056530fec23d487f45e45dfa9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/tools/toolbox/base.py
M static/maps/mvc/tool/tools.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/mvc/tool/tools.js
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Improve configuration and display of collection operation tools.
Commit: a2578eb31a9a676355aab9c44b173b5d6f3a854c
https://github.com/galaxyproject/galaxy/commit/a2578eb31a9a676355aab9c44b17…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M test/api/test_tools.py
Log Message:
-----------
Update unzip collection action to allow it to be mapped over.
Commit: d9a108ab10277bc0f2c967285f0ffd42f1141192
https://github.com/galaxyproject/galaxy/commit/d9a108ab10277bc0f2c967285f0f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/unzip_collection.xml
Log Message:
-----------
fix few typos
Commit: 80ac816af94d43d7214671582db127483baea2d3
https://github.com/galaxyproject/galaxy/commit/80ac816af94d43d7214671582db1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/dataset_matcher.py
Log Message:
-----------
More general handling of what tool inputs are required in what state.
Commit: d8ca09bcbe04ed665f4ebecbbd258b6c6e8494be
https://github.com/galaxyproject/galaxy/commit/d8ca09bcbe04ed665f4ebecbbd25…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M test/api/test_tools.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_parameter_parsing.py
Log Message:
-----------
Test and linting fixes for fewer_collection_opts branch.
Commit: af5f3bbdb5dbb7e065bd9b0413da39ddaa37c7cd
https://github.com/galaxyproject/galaxy/commit/af5f3bbdb5dbb7e065bd9b0413da…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
Update "description" of filter_failed_collection to mention only lists.
Should address some confusion caused by the tool and reference in this review (https://github.com/galaxyproject/galaxy/pull/2434#issuecomment-225682424).
Commit: 0ed456ec47b10a4c9d3948e647c41d555e3b44e0
https://github.com/galaxyproject/galaxy/commit/0ed456ec47b10a4c9d3948e647c4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M config/tool_conf.xml.sample
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
A lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/filter_failed_collection.xml
A lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/tools/unzip_collection.xml
A lib/galaxy/tools/zip_collection.xml
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tools.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/mvc/tool/tools.js
M test/api/helpers.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/twilltestcase.py
A test/functional/tools/exit_code_from_file.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_parameter_parsing.py
Log Message:
-----------
Merge pull request #2434 from jmchilton/fewer_collection_opts
Collection Operations (Limited)
Compare: https://github.com/galaxyproject/galaxy/compare/20f035dce887...0ed456ec47b1
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 16dfca86e69597796e60e604ae410dcf6667291c
https://github.com/galaxyproject/galaxy/commit/16dfca86e69597796e60e604ae41…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-04-30 (Sat, 30 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: 78c866fd34181ecda09488b6d19d2e37f6c69d02
https://github.com/galaxyproject/galaxy/commit/78c866fd34181ecda09488b6d19d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-04 (Sat, 04 Jun 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Relax validation condition
Commit: a44f30140990c93aa92b8cb5f0f87b819942b116
https://github.com/galaxyproject/galaxy/commit/a44f30140990c93aa92b8cb5f0f8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
M test/unit/tools/test_select_parameters.py
Log Message:
-----------
Revise contradicting test case, workflow injection through api attempts full validation without available datasets
Commit: d9d51d362e8ef3197e01c0440289e60a50ad85e8
https://github.com/galaxyproject/galaxy/commit/d9d51d362e8ef3197e01c0440289…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-06 (Mon, 06 Jun 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add break to interrupt loop
Commit: 2cf95d8a134bb84cec0408b016e751fc840327c1
https://github.com/galaxyproject/galaxy/commit/2cf95d8a134bb84cec0408b016e7…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M config/galaxy.ini.sample
M doc/source/releases/16.01.rst
A doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
A doc/source/releases/16.07_announce.rst
M doc/source/releases/index.rst
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/histories.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/checkers.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/run.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/repository_types/metadata.py
M static/maps/mvc/form/form-input.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M templates/show_params.mako
M templates/webapps/galaxy/data_manager/view_job.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/galaxy/workflow/sharing.mako
A test-data/biom1_metadata_test.txt
A test-data/input_taxonomy.biom1
A test/functional/tools/metadata_biom1.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/managers/test_HistoryManager.py
M tools/filters/axt_to_lav.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: 7610f82a421edb422b8ba8f7731a1ae23fb9ac41
https://github.com/galaxyproject/galaxy/commit/7610f82a421edb422b8ba8f7731a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-09 (Thu, 09 Jun 2016)
Changed paths:
M templates/webapps/galaxy/workflow/sharing.mako
Log Message:
-----------
fix markup for button links on sharing template
(ff would fail to generate images)
turn of autocomplete
Commit: 574740d0b299d9cd84d9065f4746204f6399d891
https://github.com/galaxyproject/galaxy/commit/574740d0b299d9cd84d9065f4746…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
Log Message:
-----------
Reset exception retries after successful job status check
Commit: 08fb160b38fbcd9bcdfd776bb75ae5c92ca002d1
https://github.com/galaxyproject/galaxy/commit/08fb160b38fbcd9bcdfd776bb75a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M templates/webapps/galaxy/workflow/sharing.mako
Log Message:
-----------
Merge pull request #2481 from martenson/fix-html-sharing
[16.04] fix markup for button links on sharing template
Commit: 4cf8d691e525142125af56b0627f804eb1bddd7c
https://github.com/galaxyproject/galaxy/commit/4cf8d691e525142125af56b0627f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
fix image generation for workflows with missing tools
currently this ends up with a server error
Commit: fdf9520783ae55795a01e4092b1d6718c5fca5b4
https://github.com/galaxyproject/galaxy/commit/fdf9520783ae55795a01e4092b1d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
drop unnecessary raise and fix capitalization
incorporate comments of Bjoern and Nicola
Commit: 43694be8647e3d1686b6c4fa80d0300bb9c96d42
https://github.com/galaxyproject/galaxy/commit/43694be8647e3d1686b6c4fa80d0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M test/unit/tools/test_select_parameters.py
Log Message:
-----------
Merge pull request #2456 from guerler/fix_building_mode
[16.04] Relax validation condition for dynamic parameters
Commit: 5245e8a693fc3633762f29a468b84e3487083133
https://github.com/galaxyproject/galaxy/commit/5245e8a693fc3633762f29a468b8…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #2488 from martenson/wrap-svg-for-missing-tools
[16.04] fix image generation for workflows with missing tools
Commit: b3a32ac2e19afda605f26f989bf3e16eaa1d27af
https://github.com/galaxyproject/galaxy/commit/b3a32ac2e19afda605f26f989bf3…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M templates/webapps/galaxy/workflow/sharing.mako
M test/unit/tools/test_select_parameters.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: 0017b3e9405e5e77904364025889c88cf0991744
https://github.com/galaxyproject/galaxy/commit/0017b3e9405e5e77904364025889…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
add IUC channel to the list
Commit: ec0d97327b0bf234021f5a3f5ab261b491baa091
https://github.com/galaxyproject/galaxy/commit/ec0d97327b0bf234021f5a3f5ab2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2490 from bgruening/iuc_conda_channel
[16.04] Add IUC conda channel
Commit: 6ccfd13ab4e500774a40a54deba949d29f719f2c
https://github.com/galaxyproject/galaxy/commit/6ccfd13ab4e500774a40a54deba9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
Log Message:
-----------
Merge pull request #2487 from nsoranzo/release_16.04_reset_exception_retries
[16.04] Reset exception retries after successful job status check
Commit: 20f035dce887e5fcd04a5d7bdec92f80ba1fc9e2
https://github.com/galaxyproject/galaxy/commit/20f035dce887e5fcd04a5d7bdec9…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M templates/webapps/galaxy/workflow/sharing.mako
M test/unit/tools/test_select_parameters.py
Log Message:
-----------
Merge branch 'release_16.04' into dev
Conflicts:
test/unit/tools/test_select_parameters.py
Compare: https://github.com/galaxyproject/galaxy/compare/c797d2bc9e99...20f035dce887
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 16dfca86e69597796e60e604ae410dcf6667291c
https://github.com/galaxyproject/galaxy/commit/16dfca86e69597796e60e604ae41…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-04-30 (Sat, 30 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: 2cf95d8a134bb84cec0408b016e751fc840327c1
https://github.com/galaxyproject/galaxy/commit/2cf95d8a134bb84cec0408b016e7…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M config/galaxy.ini.sample
M doc/source/releases/16.01.rst
A doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
A doc/source/releases/16.07_announce.rst
M doc/source/releases/index.rst
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/histories.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/checkers.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/run.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/repository_types/metadata.py
M static/maps/mvc/form/form-input.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M templates/show_params.mako
M templates/webapps/galaxy/data_manager/view_job.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/galaxy/workflow/sharing.mako
A test-data/biom1_metadata_test.txt
A test-data/input_taxonomy.biom1
A test/functional/tools/metadata_biom1.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/managers/test_HistoryManager.py
M tools/filters/axt_to_lav.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: b3a32ac2e19afda605f26f989bf3e16eaa1d27af
https://github.com/galaxyproject/galaxy/commit/b3a32ac2e19afda605f26f989bf3…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M templates/webapps/galaxy/workflow/sharing.mako
M test/unit/tools/test_select_parameters.py
Log Message:
-----------
Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04
Commit: 0017b3e9405e5e77904364025889c88cf0991744
https://github.com/galaxyproject/galaxy/commit/0017b3e9405e5e77904364025889…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
add IUC channel to the list
Commit: ec0d97327b0bf234021f5a3f5ab261b491baa091
https://github.com/galaxyproject/galaxy/commit/ec0d97327b0bf234021f5a3f5ab2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2490 from bgruening/iuc_conda_channel
[16.04] Add IUC conda channel
Compare: https://github.com/galaxyproject/galaxy/compare/5245e8a693fc...ec0d97327b0b