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Author SHA1 Message Date
Dannon Baker 0fd152c0cc Merge branch 'release_16.04' into dev 2016-06-15 10:15:36 -04:00
Dannon Baker 37242c8a7c Merge branch 'release_16.01' into release_16.04 2016-06-15 10:15:07 -04:00
Dannon Baker 75cdec9b4b Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 
[16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem
 2016-06-15 10:14:32 -04:00
John Chilton dca91dae16 Merge pull request #2498 from phnmnl/feature/fixFilesFromWorkDirIssue 
Kubernetes runner: fixes result files from work directory not being recovered issue
 2016-06-15 09:53:15 -04:00
Dannon Baker 1b110299af Merge branch 'release_16.04' into dev 2016-06-15 09:32:31 -04:00
Dannon Baker 7d962ee0cb Merge pull request #2492 from jmchilton/windows_no_shell 
[16.04] Allow disabling separating tools commands into their own script.
 2016-06-15 09:31:15 -04:00
Martin Cech f078365acc Merge pull request #2499 from dannon/user_tool_filter_fixes 
Toolbox filter fixes
 2016-06-14 15:42:03 -04:00
Dannon Baker 0c4fd995c5 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. 2016-06-14 14:30:31 -04:00
Dannon Baker 419594845d 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. 2016-06-14 14:01:32 -04:00
Martin Cech bb851d6645 Merge pull request #2494 from jmchilton/galaxy-lib-update-2 
Update against latest galaxy-lib.
 2016-06-14 12:01:14 -04:00
Pablo Moreno f3d73f37a2 Removes incorrect FALSE option for include_work_dir which makes certain jobs that discover files from working directories to fail recovering files when running through Kubernetes. 2016-06-14 17:14:57 +03:00
Pablo Moreno 2fce4553d8 Merge pull request #4 from galaxyproject/dev 
Stays up-to-date with dev of galaxy project
 2016-06-14 15:01:19 +01:00
Nate Coraor 8ef8522d68 Merge pull request #2497 from dannon/backport_onion_rearrangement 
[16.04] Backport of stats fixes/prefix work.
 2016-06-13 21:33:11 -04:00
Martin Cech 0ed456ec47 Merge pull request #2434 from jmchilton/fewer_collection_opts 
Collection Operations (Limited)
 2016-06-13 16:20:44 -04:00
Dannon Baker 2aab4ee721 More backporting of stats to make it functional on main. 2016-06-13 15:57:16 -04:00
Dannon Baker e1cafd6ab4 Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. 2016-06-13 15:55:53 -04:00
Dannon Baker 4bf9955d03 Backport fac2efc4bd to 16.04 to enable functional stats on main. 2016-06-13 15:52:41 -04:00
John Chilton af5f3bbdb5 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).
 2016-06-13 15:46:19 -04:00
John Chilton 1a47485197 Update against latest galaxy-lib. 
In return it needed to be updated for recent changes to cwltool and Galaxy.
 2016-06-13 15:03:11 -04:00
Nicola Soranzo 20f035dce8 Merge branch 'release_16.04' into dev 
Conflicts:
	test/unit/tools/test_select_parameters.py
 2016-06-13 17:02:09 +01:00
Martin Cech 6ccfd13ab4 Merge pull request #2487 from nsoranzo/release_16.04_reset_exception_retries 
[16.04] Reset exception retries after successful job status check
 2016-06-13 11:51:50 -04:00
John Chilton 54bffd93ac Spelling fix thanks to @nsoranzo. 2016-06-13 10:51:41 -04:00
Björn Grüning c797d2bc9e Merge pull request #2489 from shiltemann/dev 
mothur datatypes: don't generate error for pairwise distance matrices
 2016-06-13 15:44:53 +02:00
Dannon Baker ec0d97327b Merge pull request #2490 from bgruening/iuc_conda_channel 
[16.04] Add IUC conda channel
 2016-06-13 07:43:37 -04:00
Bjoern Gruening 0017b3e940 add IUC channel to the list 2016-06-11 18:17:39 +02:00
Bjoern Gruening b3a32ac2e1 Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 2016-06-11 18:15:52 +02:00
Nicola Soranzo 5245e8a693 Merge pull request #2488 from martenson/wrap-svg-for-missing-tools 
[16.04] fix image generation for workflows with missing tools
 2016-06-11 10:11:36 +01:00
Martin Cech 43694be864 Merge pull request #2456 from guerler/fix_building_mode 
[16.04] Relax validation condition for dynamic parameters
 2016-06-10 20:49:23 -04:00
Martin Cech fdf9520783 drop unnecessary raise and fix capitalization 
incorporate comments of Bjoern and Nicola
 2016-06-10 20:42:12 -04:00
Martin Cech 4cf8d691e5 fix image generation for workflows with missing tools 
currently this ends up with a server error
 2016-06-10 16:02:58 -04:00
Björn Grüning 08fb160b38 Merge pull request #2481 from martenson/fix-html-sharing 
[16.04] fix markup for button links on sharing template
 2016-06-10 21:47:07 +02:00
John Chilton d8ca09bcbe Test and linting fixes for fewer_collection_opts branch. 2016-06-10 14:50:44 -04:00
Nicola Soranzo 574740d0b2 Reset exception retries after successful job status check 2016-06-10 19:39:22 +01:00
Nicola Soranzo 77bd1d996d Merge branch 'release_16.04' into dev 2016-06-10 19:25:31 +01:00
John Chilton 80ac816af9 More general handling of what tool inputs are required in what state. 2016-06-10 13:34:19 -04:00
Martin Cech d9a108ab10 fix few typos 2016-06-10 13:34:19 -04:00
John Chilton a2578eb31a Update unzip collection action to allow it to be mapped over. 2016-06-10 13:34:19 -04:00
John Chilton 8a0056530f Improve configuration and display of collection operation tools. 2016-06-10 13:34:18 -04:00
John Chilton 68a7206943 New model tool that flattens any collection into a list. 
Testing:

```
./run_tests.sh -framework -id __FLATTEN__
```
 2016-06-10 13:34:18 -04:00
John Chilton ddeff4ec0c 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.
 2016-06-10 13:34:18 -04:00
John Chilton 6ddb2c2a6a 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
```
 2016-06-10 13:34:18 -04:00
John Chilton a80eaae7fa Reduce duplication in galaxy.tools.parameters.wrapped. 2016-06-10 13:34:18 -04:00
Nicola Soranzo 14844e48eb Merge branch 'release_16.01' into release_16.04 
Conflicts:
	lib/galaxy/jobs/runners/drmaa.py
 2016-06-10 17:31:10 +01:00
Martin Cech dbbf1edef3 Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 
[16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries
 2016-06-10 12:06:41 -04:00
Saskia Hiltemann fcc069042e don't generate error for pairwise distance matrices 2016-06-10 17:57:10 +02:00
Nicola Soranzo 933f42619e Log all failed job status checks 2016-06-10 12:34:48 +01:00
Nicola Soranzo 7c40c85034 Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries 2016-06-10 12:31:00 +01:00
John Chilton e73e6b3587 Allow disabling separating tools commands into their own script. 
Forcing them there broke Pulsar-on-Windows functionality - this fix is courtesy of @jj-umn.
 2016-06-10 00:18:11 -04:00
Björn Grüning 8f647b763f Merge pull request #2480 from jmchilton/tool_dependencies_default 
Set a default for tool_dependencies_dir.
 2016-06-09 21:39:05 +02:00
Martin Cech 7610f82a42 fix markup for button links on sharing template 
(ff would fail to generate images)
turn of autocomplete
 2016-06-09 15:38:57 -04:00