Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy.

https://github.com/galaxyproject/galaxy/pull/2836

This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist.  Explicit usage still logs a failure.

This is a sensible enough default, and requiring the option to be set in
galaxy.ini is cumbersome and unnecessary since it's admin-only
functionality.

This way resolvers like the Module resolver work even if tool_dependency_dir is not set.

I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now.

 - Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes.
 - Refactoring and test improvements for existing tool monitoring code.
 - Implement toolbox shutdown process to ensure different watchers don't compete with each other.
 - Set the default tool conf to be monitored.

Introduce an app ToolCache to help ensure this operation remains speedy.

Also fix the log message.

Should work when mapping over collections or for big muli-run tool submissions.

Because of database tension with sqlalchemy it is not strictly a linear increase, but the end user walltime experience for a 24 dataset collection being submitted using 4 threads instead 1 drops execution time from 68 seconds to 35.

Rebased with fixes thanks to @nsoranzo - https://github.com/jmchilton/galaxy/commit/7f6514a21222ea787a0676764e4a4fe825891b27#commitcomment-14712999.

Webpack: allow extending options from template call, add /login as app entry point for login app (still allowing user/login), add root/welcome and /login to allowed paths when require_login, fix None type error for redirect when visiting user/login directly, fix rendering of masthead, add query string to object util, correct job_id loading from index

These "Text file busy" errors are occasionally encountered in the wild in production settings and more commonly when running Galaxy in Docker containers.

Simply sycning the file system has proven insufficient to prevent the problem and I do not want to add an arbitrary sleep. So this new strategy is used.

 - Inject special functionality into each job script that when executed with a certain environment variable set causes the script to exit with a specific return code.
 - Have Galaxy rerun this script in that configuration until it can succeed in executing the script.
 - In between each iteration sleep for a small amount of time and try to cause a file system sync.

This entire is ... insane ... so I have added a configuration option to disable it entirely check_job_script_integrity=False.

Normally the proxy binds to :8800 and runs containers under
:8800/ipython/... which is great... until you have an upstream proxy
like apache wrapping that at the url FQDN/ipython and suddenly your
cookies aren't available because they're specific to /galaxy.

Thus, when an upstream proxy is in use, we correct the proxy's path to:
with :8800/{cookie_path}/gie_proxy/ipython/... which behaves much more
nicely with upstraem proxies.

Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger.

Remove old cloudlaunch in favor of https://github.com/galaxyproject/cloudlaunch, at launch.usegalaxy.org

Swap track_jobs_in_database to be True by default.  This removes the current multiprocess detection logic in favor of simplifying the configuration, and fixes a bug where uwsgi + 1 handler will not work.

Swap track_jobs_in_database to be True by default.  This removes the current multiprocess detection logic in favor of simplifying the configuration, and fixes a bug where uwsgi + 1 handler will not work.

Interactive environments: move static base url from 'visualizations' to 'interactive_environments' for int env plugins

`{eggs,pkg_resources}.require`. Probably broke some stuff where we were
trying to be smart about whether a particular egg was available, but
Galaxy does at least start.

Factor out is_uwsgi_process, apply to use_interactive so I don't have to keep changing my config (and hopefully to benefit others ;) )

sample config file. Also disables checks at startup.