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Author SHA1 Message Date
Bjoern Gruening 23c6b1c6ff add a conda clean function to remove downloaded tarballs after installation 2016-11-27 23:22:16 +01:00
mvdbeek 3ebbb37c4d Add dependency_resolvers/clean endpoint 2016-11-27 23:16:56 +01:00
mvdbeek 8ff7ffa063 Add force_rebuild param to build_dependency_cache 
This will remove a pre-existing cached dependency directory.
 2016-11-27 22:55:58 +01:00
mvdbeek 3e48f3792b Install the correct converter dependency 2016-11-27 18:15:22 +01:00
mvdbeek e905b8baeb Add integration test-case for install tool dependency API endpoint 2016-11-27 17:52:38 +01:00
mvdbeek 40a95a3003 Add API to install resolver tool dependencies 
and to build a tool dependency cache (if activated in galaxy.ini).

An example to install dependencies for the twobit converter:
```
import bioblend.galaxy
url = 'http://localhost:8080/'
api_key = 'admin_api_key'
tool_id = 'CONVERTER_fasta_to_2bit'
endpoint = "api/tools/%s/install_dependencies" % tool_id
gi = bioblend.galaxy.GalaxyInstance(url, api_key)
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
If `use_cached_dependency_manager` is activated in the galaxy.ini,
a cached environment can be built like this:
```
endpoint = "api/tools/%s/build_dependency_cache" % tool_id
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
 2016-11-27 17:00:52 +01:00
Martin Cech 1ad8951154 Merge pull request #3216 from jmchilton/when_datatype_isinstance 
Fix conditional when datatype in XML schema.
 2016-11-23 18:46:53 -05:00
John Chilton ad0e6a437e Merge pull request #3215 from nsoranzo/flake8-import-order 
Fix I201 errors from flake8-import-order
 2016-11-23 16:02:25 -05:00
John Chilton 7d945f762e Fix https://github.com/galaxyproject/galaxy/issues/3213 discovered by @nsoranzo. 2016-11-23 15:55:19 -05:00
Nicola Soranzo 3d57c22b63 Fix I201 errors from flake8-import-order 
Also fix Python3 compatibility.
Remove unused method
galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() .
 2016-11-23 18:31:04 +00:00
Aysam Guerler fef5523ed4 Merge pull request #3214 from dannon/tour_routing 
Tour routing tweaks, allows us to drop the model out of menu
 2016-11-23 12:01:57 -05:00
Dannon Baker 6aab802e5a Tour routing tweaks, allows us to drop the model out of menu 2016-11-23 11:02:42 -05:00
John Chilton db93fd3285 Merge pull request #3106 from mvdbeek/cached_dep_manager 
Add cached dependency manager
 2016-11-23 09:33:44 -05:00
mvdbeek 21b859e555 Fix NameError 2016-11-23 11:03:14 +01:00
mvdbeek df93db40b1 Only attempt to build cache once per install 
and override __eq__ for ToolRequirement, to simplify
checking if ToolRequirements are already installed/cached.
 2016-11-23 09:26:10 +01:00
mvdbeek 66af4295cb Build dependency cache at install time 
and only activate cached environments if they exist.
 2016-11-23 09:26:10 +01:00
mvdbeek 5606d84f22 Rework cached dependencies to be more robust 
to updates or changes in depedencies, folder structure and resolver
configuration. Instead of hashing name, type and version of a
dependency, hash the json representation of the dependencies returned by
the dependency resolver, which include the path to the environment and
the depedency type. This is only applied to resolvers whose cacheable
attribute is set to True (conda-only, currently).
 2016-11-23 09:26:10 +01:00
mvdbeek 185856f6af Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) 2016-11-23 09:23:51 +01:00
mvdbeek bbc403b2e1 Add cached dependency manager 
Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement
a mechanism that allows tool dependencies to be cached.

If the `use_cached_dependency_manager` option is set to True in
galaxy.ini, we build a hash of the combination of a tools' requirements,
and store the resulting environment in a directory specified by the
`tool_dependency_cache_dir` option in galaxy.ini.
 2016-11-23 09:23:50 +01:00
Martin Cech 097300ea62 Merge pull request #3206 from jmchilton/tour_fixes 
Fixes for core.galaxy_ui.yaml.
 2016-11-21 17:18:53 -05:00
John Chilton c122e74240 Fixes for core.galaxy_ui.yaml. 
Neither of these prevent the tour from working but I think they are bugs. The extra click isn't an elemment that is clickable at that point in the tour and the referenced id isn't available so nothing in particular is tagged in the UI at that point.
 2016-11-21 16:49:41 -05:00
Martin Cech d2c95b43fa Merge pull request #3204 from galaxyproject/release_16.10 
Merge release_16.10 into dev
 2016-11-21 14:40:05 -05:00
Martin Cech aadc14d967 Merge pull request #3203 from blankenberg/fix_history_delete_16.10 
[16.10] Fixes for deleting histories
 2016-11-21 14:09:01 -05:00
Björn Grüning 78b533d1b5 Merge pull request #3201 from mvdbeek/do_not_load_tools_from_hidden_paths 
Don't load tools from paths that start with `.` or `_`
 2016-11-21 19:58:57 +01:00
Daniel Blankenberg 5ba8201163 Pack scripts 2016-11-21 11:02:20 -05:00
Daniel Blankenberg 548d3e6f05 Fixes for deleting histories broken in 1cc57b1eb2 2016-11-21 10:53:37 -05:00
mvdbeek c0a7fabc35 Don't load tools from paths that start with . or _ 2016-11-21 15:20:21 +01:00
Martin Cech 52c8e495dc Merge pull request #3200 from erasche/user-info-page 
Fix table
 2016-11-19 14:48:12 -05:00
Eric Rasche 3ea730f734 Fix table 2016-11-18 21:20:26 +00:00
Dannon Baker 3f27777e76 Merge pull request #3198 from martenson/fix-search-config 
[16.10] remove unused (and unintended) config override
 2016-11-18 11:19:33 -05:00
Martin Cech 5c4ac18b44 remove unused override 
this caused Help/Search to point at /root/tool_search
 2016-11-18 11:05:28 -05:00
Martin Cech 33894ca744 Merge pull request #3190 from jmchilton/test_cleanup 
Various Test Cleanups and Refactorings
 2016-11-17 10:08:23 -05:00
John Chilton b83cfe434a Refactor generic FunctionalTestCase from TwillTestCase. 
ApiTestCase uses this newer, smaller base class since these tests do not depend on Twill.
 2016-11-17 08:41:52 -05:00
John Chilton 2bf1cf50a3 Reduce requirements for using get_filename in TwillTestCase. 
Do not use a self.tool_shed_test_file and make self.shed_tools_dict optional.
 2016-11-17 08:41:52 -05:00
John Chilton a209523639 Large cleanup of unused methods from twilltestcase. 
In addition to deleting unused methods, this also moves ones only used by test_library_templates into that file.
 2016-11-17 08:41:52 -05:00
Dannon Baker 50f5c15f63 Merge pull request #3192 from dannon/version-17.01.dev 
Version 17.01.dev
 2016-11-17 06:10:27 -05:00
Dannon Baker 6fd58afa6d Merge pull request #3191 from dannon/version-16.10 
Update version to 16.10.rc1
 2016-11-17 06:10:18 -05:00
Dannon Baker 3dd28291c3 Merge branch 'version-16.10' into version-17.01.dev 2016-11-17 06:03:37 -05:00
Dannon Baker e5b56f102a Update version to 17.01.dev 2016-11-17 06:03:37 -05:00
Dannon Baker 9d45f1e48a Update version to 16.10.rc1 2016-11-17 06:03:36 -05:00
Dannon Baker d8c75e2dff Merge pull request #3187 from mvdbeek/samtools_1_3_fix 
Make sam to bam converter tool compatible with samtools >= 1.3
 2016-11-17 05:51:11 -05:00
mvdbeek 8ace021c0a Single quote variables in sam-to-bam conversion 2016-11-17 10:06:07 +01:00
Martin Cech 164a0ad20c Merge pull request #3188 from dannon/startup_output_tweaks 
Slight clarification of run.sh messaging when using conda.
 2016-11-16 16:19:35 -05:00
Dannon Baker 0b395a7fb3 Slight clarification of run.sh messaging when using conda. 2016-11-16 16:16:33 -05:00
mvdbeek 592f15c7b5 Add sam-to-bam conversion test tool 2016-11-16 22:01:47 +01:00
Martin Cech 92105d99fa Merge pull request #2818 from erasche/rstudio-1610 
Return of RStudio
 2016-11-16 16:01:12 -05:00
Nicola Soranzo 31b73fd586 Merge pull request #3180 from dannon/venv_over_conda 
Prefer existing .venv over conda, when both are available.
 2016-11-16 20:53:49 +00:00
Dannon Baker 0b8fc7c8cc Merge remote-tracking branch 'guerler/validate_workflow' into dev 2016-11-16 15:43:32 -05:00
mvdbeek efde00d80a Handle samtools 0.x 2016-11-16 21:37:43 +01:00
John Chilton e5b69a711d Merge pull request #2966 from dannon/workflow_intermediates_ux 
Change wording to be more clear about how workflow output cleanup wor…
 2016-11-16 15:20:41 -05:00