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Author SHA1 Message Date
mvdbeek cf769dd09d 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})
```
 2016-11-29 17:42:08 +01:00
mvdbeek 64bc9241ed Fix NameError 2016-11-29 17:41:06 +01:00
mvdbeek 82f30e7645 Only attempt to build cache once per install 
and override __eq__ for ToolRequirement, to simplify
checking if ToolRequirements are already installed/cached.
 2016-11-29 17:41:06 +01:00
mvdbeek f919a98601 Build dependency cache at install time 
and only activate cached environments if they exist.
 2016-11-29 17:41:06 +01:00
mvdbeek 2b1765751b 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).
 2016-11-29 17:41:06 +01:00
mvdbeek 0a9b6d8755 Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) 2016-11-29 17:41:06 +01:00
mvdbeek 94edc94b73 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.
 2016-11-29 17:41:06 +01:00
John Chilton 0b2d0c1746 Merge pull request #3210 from guerler/fix_output_label_handler 
[16.10] Preserve custom event handler for form inputs
 2016-11-22 15:17:55 -05:00
guerler a9dab631fb Preserve custom event handler for form inputs 2016-11-22 14:24:54 -05:00
Martin Cech ec08ec60bb Merge pull request #3205 from blankenberg/history-current-options-name_16.10 
[16.10] Change 'History Actions' to 'Current History' in history options menu.
 2016-11-21 17:18:31 -05:00
Daniel Blankenberg 74d8faac9f Change 'History Actions' to 'Current History' in history options menu. 
as it was before 1cc57b1eb2.
 2016-11-21 14:37:54 -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
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
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
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 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
Ignacio 5bb86a3b68 correct indentation 2016-11-16 20:53:41 +01:00
Ignacio 953ee32599 change parameters to samtools sort command (new samtools vers) 2016-11-16 20:53:41 +01:00
Dannon Baker 5028e2a251 Merge remote-tracking branch 'upstream/dev' into workflow_intermediates_ux 2016-11-16 14:23:07 -05:00
Dannon Baker ac5b7efc5f Merge pull request #3130 from mvdbeek/fix_invalid_section_key 
Update ToolPanelElements instance locally
 2016-11-16 14:14:43 -05:00
Nicola Soranzo 2f08dd72c3 Merge pull request #3184 from afgane/dev 
Fix a typo in the intro tour
 2016-11-16 16:52:25 +00:00
Enis Afgan 45259b7f16 Fix typo 2016-11-16 11:47:38 -05:00
guerler 4e6e7d36f8 Validate cycles and step size before building model for workflow execution 2016-11-16 11:43:17 -05:00
Dannon Baker 985bd0dffd Because common_startup is executed and not sourced, this block needs to remain in run.sh 2016-11-16 11:41:13 -05:00
John Chilton 2f2d21aea2 Merge pull request #3177 from nsoranzo/flake8-import-order 
Fix import order and Python3 compatibility for test/unit/
 2016-11-16 11:40:26 -05:00
Dannon Baker 7f5d9d2fbd More startup logic tweaks, .venv > conda > new_venv 2016-11-16 11:04:42 -05:00
Dannon Baker 72d360e942 Change startup logic for .venv sourcing. If a .venv exists, use it. If not, if conda is there, use it. If no conda, create a .venv. 2016-11-16 10:44:48 -05:00
Dannon Baker d48817adb1 Remove redundant .venv activation -- this is handled in common_startup 2016-11-16 10:41:32 -05:00
Nicola Soranzo a8746c4f52 Fix import order and Python3 compatibility for test/unit/ 2016-11-16 10:29:09 +00:00
Nicola Soranzo dd556090c1 Fix import broken in b4c77b7617 2016-11-16 10:29:09 +00:00
Dannon Baker a86a457230 Merge pull request #3176 from martenson/add-tours-to-welcome 
add links to local tours to sample welcome
 2016-11-15 22:05:44 -05:00
Martin Cech 2c756ff170 drop leading slash to work with proxy prefix, thanks @dannon 2016-11-15 18:55:57 -05:00
Martin Cech 063bb61d07 add links to local tours to sample welcome 2016-11-15 16:15:44 -05:00
Nate Coraor 594e44b4fb Merge pull request #3170 from nsoranzo/dev 
Fixes for pycodestyle 2.2.0
 2016-11-15 10:43:31 -07:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Dannon Baker 3f4033c05d Merge remote-tracking branch 'tmcgowan/issue_2100' into dev 2016-11-15 09:54:06 -05:00
Nicola Soranzo 7e988bbe09 Merge pull request #3169 from jmchilton/galaxy-lib-update-3 
Bring in updates from galaxy-lib.
 2016-11-14 19:45:58 +00:00
John Chilton 00b147a664 Bring in updates from galaxy-lib. 2016-11-14 12:45:04 -05:00