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v16.07
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12590 Commits
Author SHA1 Message Date
John Chilton e0aad7af47 Update version to 16.07 2016-08-25 13:41:10 -04:00
Bjoern Gruening e9d81500ca shorten Conda environment names 2016-08-24 15:12:54 -04:00
Marius van den Beek a2f234d566 Create default tool_dependency dir if it doesn't exist 2016-08-24 15:12:44 -04:00
Marius van den Beek 8b67ddfa37 Acquire lock before attempting to install conda 2016-08-24 15:12:38 -04:00
Marius van den Beek 873f34f079 Inject HOME, so that conda doens't attempt to write to ~/.conda 2016-08-20 19:05:11 +02:00
Nicola Soranzo f4806e9dd4 Merge branch 'release_16.04' into release_16.07 2016-08-18 15:49:30 +01:00
Dave Bouvier a134587c89 Correctly check set_environment declarations when updating repository. 2016-08-18 14:08:40 +01:00
Martin Cech 6c2468832b Merge pull request #2809 from carlfeberhard/fix.hdca-dnd 
[16.07] API, history contents: allow 'source' in payload
 2016-08-17 16:08:14 -04:00
Nate Coraor c3d7ca8eef Revert str.split() syntax for Python 2 compatibility 2016-08-17 14:02:15 -04:00
carlfeberhard bf9a15389e API, history contents: allow 'source' in payload 
In create, checks both kwd and payload for 'source' parameter when
creating a new hdca. This allows source to be passed in the body and
not query string.

This fixes the copy call in history-contents when copying an hdca
by drag and drop in the multi history view.
 2016-08-17 13:08:27 -04:00
Marius van den Beek d1c58f7ab0 Merge pull request #2800 from jmchilton/dbkey_output_without_cond 
[16.04] Fix dbkey problem discovered by @hrhotz
 2016-08-17 09:12:17 +02:00
Dannon Baker 8d512c98e2 Merge branch 'release_16.04' into release_16.07 2016-08-16 16:45:11 -04:00
John Chilton e06cf9a978 Add None check to fill_template... 
... as requested by @nsoranzo.
 2016-08-16 14:12:17 -04:00
John Chilton 88d02dba6e Don't fill in a cheetah default if unavailable. 
... in metadata hack from #961.
 2016-08-16 12:55:56 -04:00
Nate Coraor c431d8c06c Fix import linting error 2016-08-15 17:12:16 -04:00
Nate Coraor 59e88fa6f7 Do not instantiate the raven (sentry) client until uWSGI postfork 2016-08-15 16:18:44 -04:00
Nate Coraor c3c97cef1e Do not start tool conf watchdog threads until postfork 2016-08-15 16:17:45 -04:00
Marius van den Beek 30a14e3c39 Raise a more specific exception 2016-08-15 19:38:32 +02:00
Marius van den Beek 0cc10d184d Move can_install_conda and is_conda_installed into CondaContext 2016-08-15 19:36:04 +02:00
Marius van den Beek 85aaa23785 Make conda install and resolver status more robust 
We disable the conda resolver if conda_exec is not found and we are
unable to install conda. Skip installing conda if it won't be used
(because conda exec is outside of conda_prefix).
Install conda if conda_prefix is an empty directory.
 2016-08-15 18:34:06 +02:00
Dannon Baker 43320aa8d1 Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. 2016-08-15 12:25:17 -04:00
Dannon Baker d87fbdd5b8 Merge pull request #2774 from natefoo/uwsgi-fork 
[16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork
 2016-08-15 12:15:18 -04:00
Dannon Baker be7c5bce1d Words. 2016-08-15 12:08:25 -04:00
Dannon Baker 699e955d7f Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available. 2016-08-15 12:00:05 -04:00
Dannon Baker efbd8f2d9f Separates the decorator from the injected uwsgi package to fix 
'process_is_uwsgi' logic.
 2016-08-15 11:29:39 -04:00
Dannon Baker 66e725b6e3 Merge branch 'release_16.04' into release_16.07 2016-08-12 13:34:41 -04:00
guerler d24ce8b0a4 Add implicit conversions target extension to hda name when listed as selection option 2016-08-12 18:01:45 +01:00
Dannon Baker 7c5cadbe7d Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future. 2016-08-12 08:12:19 -04:00
Dannon Baker 7ebf7e5706 Force update repository manager to launch postfork. 2016-08-12 07:55:57 -04:00
Nate Coraor af533a7a6f Create a uWSGI postfork function registry. Also, start the tool conf 
watcher thread post-fork.
 2016-08-11 12:28:09 -04:00
Björn Grüning a7be24e111 Merge pull request #2759 from martenson/conda_config 
[16.07] install Conda at startup; enable conda_auto_init in sample conf
 2016-08-11 10:11:13 +02:00
Nicola Soranzo 9c03d4c16f Merge branch 'release_16.04' into release_16.07 
flake8 pinned also for py27-lint-imports-include-list testenv
 2016-08-10 16:31:51 +01:00
Nicola Soranzo f2f62f340e Merge branch 'release_16.01' into release_16.04 
Conflicts:
	.ci/flake8_blacklist.txt
	tox.ini
 2016-08-10 16:19:19 +01:00
Nicola Soranzo 33c4025fab Fix misplaced parenthesis 
Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304
 2016-08-10 14:34:08 +01:00
Martin Cech 730233f48a Merge pull request #15 from mvdbeek/fix_string_substitution 
Fix string substitution
 2016-08-09 19:12:45 -04:00
Marius van den Beek fd3c875370 Fix string substitution 2016-08-09 23:16:58 +02:00
Martin Cech 9d467ddd52 enable conda_auto_init in sample, adjust wording 2016-08-09 13:34:18 -04:00
Martin Cech a297a04671 Merge pull request #2750 from mvdbeek/list_resolver_toolshed_packages 
List resolver toolshed packages
 2016-08-09 12:52:55 -04:00
Nicola Soranzo a72f9d8865 Pass installed_tool_dependencies as a parameter 2016-08-09 16:12:05 +01:00
Marius van den Beek 7e3d7ced81 Avoid changes in requested_requirements 2016-08-09 12:52:14 +02:00
Marius van den Beek f8fef32697 Change DependencyType class variable to dependency_type 2016-08-09 12:42:47 +02:00
Marius van den Beek 0bfa56f010 Fix list of public objects 2016-08-08 18:01:42 +02:00
Marius van den Beek 45d357e7c3 Introduce ToolShedDependency as subclass of GalaxyPackageDependency 2016-08-08 17:53:10 +02:00
Dannon Baker a334b189ba Merge branch 'release_16.04' into release_16.07 2016-08-08 11:25:34 -04:00
Martin Cech a7664f00f9 Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default 
[16.04] Fix to mount job directory in Docker for #1688.
 2016-08-08 10:40:38 -04:00
Martin Cech 7d5bbf7a44 Merge pull request #2749 from jmchilton/backport_2748 
[16.07] Backport #2748
 2016-08-08 10:38:21 -04:00
Marius van den Beek 7f0d323aca Include toolshed resolved packages in tool requirements API 2016-08-08 16:04:21 +02:00
Marius van den Beek 370346ad9e List toolshed deps in 'Dependency Resolver Details' 
This should make it easier to understand/predict for admins how tool
dependencies will be resolved during tool execution.
 2016-08-08 16:04:21 +02:00
Manabu ISHII 64a55728d6 Fix docker command_list 
command_list always generates ***docker docker***
Without fix , docker runs new image which doesn't exist ,
docker fetch it in ***docker run*** command and it generates progress information to stderr.
It will end galaxy job as fail.

But rerun same job, it will be success , because of the image is already exists , fetch process never happens.
 2016-08-08 09:33:14 -04:00
John Chilton b39f2143fa Fix to mount job directory in Docker for #1688. 
The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done.
 2016-08-05 14:19:22 -04:00