mirror of
https://github.com/galaxyproject/galaxy.git
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Merge pull request #5745 from nsoranzo/release_18.01_fix_config
[18.01] Configuration fixes
This commit is contained in:
Dannon Baker
@@ -752,12 +752,7 @@ galaxy:
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# Redirect. This should be set to the path defined in the nginx
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# config as an internal redirect with access to Galaxy's data files
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# (see documentation linked above).
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#nginx_x_accel_redirect_base: false
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# nginx can make use of mod_zip to create zip files containing
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# multiple library files. If using X-Accel-Redirect, this can be the
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# same value as that option.
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#nginx_x_archive_files_base: false
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#nginx_x_accel_redirect_base: null
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# If using compression in the upstream proxy server, use this option
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# to disable gzipping of library .tar.gz and .zip archives, since the
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@@ -779,24 +774,24 @@ galaxy:
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# in detail in the documentation linked above. The upload store is a
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# temporary directory in which files uploaded by the upload module
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# will be placed.
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#nginx_upload_store: false
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#nginx_upload_store: null
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# This value overrides the action set on the file upload form, e.g.
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# the web path where the nginx_upload_module has been configured to
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# intercept upload requests.
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#nginx_upload_path: false
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#nginx_upload_path: null
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# Galaxy can also use nginx_upload_module to receive files staged out
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# upon job completion by remote job runners (i.e. Pulsar) that
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# initiate staging operations on the remote end. See the Galaxy nginx
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# documentation for the corresponding nginx configuration.
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#nginx_upload_job_files_store: false
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#nginx_upload_job_files_store: null
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# Galaxy can also use nginx_upload_module to receive files staged out
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# upon job completion by remote job runners (i.e. Pulsar) that
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# initiate staging operations on the remote end. See the Galaxy nginx
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# documentation for the corresponding nginx configuration.
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#nginx_upload_job_files_path: false
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#nginx_upload_job_files_path: null
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# Have Galaxy manage dynamic proxy component for routing requests to
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# other services based on Galaxy's session cookie. It will attempt to
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+50
-11
@@ -2,20 +2,59 @@ uwsgi:
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# The address and port on which to listen. By default, only listen to
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# localhost (reports will not be accessible over the network). Use
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# '0.0.0.0' to listen on all available network interfaces.
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# ':9001' to listen on all available network interfaces.
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http: 127.0.0.1:9001
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threads: 8
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# Number of web server (worker) processes to fork after the
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# application has loaded.
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processes: 1
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http-raw-body: True
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# Number of threads for each web server process.
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threads: 4
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offload-threads: 8
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# Number of threads for serving static content and handling internal
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# routing requests.
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offload-threads: 2
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# Mapping to serve style content.
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static-map: /static/style=static/style/blue
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# Mapping to serve the remainder of the static content.
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static-map: /static=static
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# Enable the master process manager. Disabled by default for maximum
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# compatibility with CTRL+C, but should be enabled for use with
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# --daemon and/or production deployments.
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master: false
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# Path to the application's Python virtual environment.
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virtualenv: .venv
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# Path to the application's Python library.
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pythonpath: lib
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# The entry point which returns the web application (e.g. Galaxy,
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# Reports, etc.) that you are loading.
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module: galaxy.webapps.reports.buildapp:uwsgi_app()
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# Cause uWSGI to respect the traditional behavior of dying on SIGTERM
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# (its default is to brutally reload workers)
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die-on-term: true
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# Cause uWSGI to gracefully reload workers and mules upon receipt of
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# SIGINT (its default is to brutally kill workers)
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hook-master-start: unix_signal:2 gracefully_kill_them_all
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# Cause uWSGI to gracefully reload workers and mules upon receipt of
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# SIGTERM (its default is to brutally kill workers)
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hook-master-start: unix_signal:15 gracefully_kill_them_all
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# Feature necessary for proper mule signal handling
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py-call-osafterfork: true
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# Ensure application threads will run if `threads` is unset.
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enable-threads: true
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reports:
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# If running behind a proxy server and Galaxy is served from a
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@@ -28,7 +67,7 @@ reports:
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# path as the prefix in the filter above. This value becomes the
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# "path" attribute set in the cookie so the cookies from each instance
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# will not clobber each other.
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#cookie_path: None
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#cookie_path: null
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# Verbosity of console log messages. Acceptable values can be found
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# here: https://docs.python.org/2/library/logging.html#logging-levels
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@@ -38,7 +77,7 @@ reports:
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# Galaxy instances, so sqlite (and the default value below) is not
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# supported. An SQLAlchemy connection string should be used specify an
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# external database.
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#database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
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#database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
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# Where dataset files are saved Temporary storage for additional
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# datasets, this should be shared through the cluster
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@@ -53,20 +92,20 @@ reports:
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#template_cache_path: database/compiled_templates/reports
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# Configuration for debugging middleware
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#debug: False
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#debug: false
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# Check for WSGI compliance.
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#use_lint: False
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#use_lint: false
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# NEVER enable this on a public site (even test or QA)
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#use_interactive: True
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#use_interactive: true
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# Write thread status periodically to 'heartbeat.log' (careful, uses
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# disk space rapidly!)
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#use_heartbeat: True
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#use_heartbeat: true
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# Profiling middleware (cProfile based)
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#use_profile: True
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#use_profile: true
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# Mail
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#smtp_server: yourserver@yourfacility.edu
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+66
-24
@@ -2,20 +2,59 @@ uwsgi:
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# The address and port on which to listen. By default, only listen to
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# localhost (tool_shed will not be accessible over the network). Use
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# '0.0.0.0' to listen on all available network interfaces.
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# ':9009' to listen on all available network interfaces.
|
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http: 127.0.0.1:9009
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threads: 8
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# Number of web server (worker) processes to fork after the
|
||||
# application has loaded.
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processes: 1
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http-raw-body: True
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# Number of threads for each web server process.
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||||
threads: 4
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offload-threads: 8
|
||||
# Number of threads for serving static content and handling internal
|
||||
# routing requests.
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||||
offload-threads: 2
|
||||
|
||||
# Mapping to serve style content.
|
||||
static-map: /static/style=static/style/blue
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||||
|
||||
# Mapping to serve the remainder of the static content.
|
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static-map: /static=static
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||||
|
||||
# Enable the master process manager. Disabled by default for maximum
|
||||
# compatibility with CTRL+C, but should be enabled for use with
|
||||
# --daemon and/or production deployments.
|
||||
master: false
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||||
|
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# Path to the application's Python virtual environment.
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virtualenv: .venv
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||||
|
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# Path to the application's Python library.
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pythonpath: lib
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# The entry point which returns the web application (e.g. Galaxy,
|
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# Reports, etc.) that you are loading.
|
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module: galaxy.webapps.tool_shed.buildapp:uwsgi_app()
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# Cause uWSGI to respect the traditional behavior of dying on SIGTERM
|
||||
# (its default is to brutally reload workers)
|
||||
die-on-term: true
|
||||
|
||||
# Cause uWSGI to gracefully reload workers and mules upon receipt of
|
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# SIGINT (its default is to brutally kill workers)
|
||||
hook-master-start: unix_signal:2 gracefully_kill_them_all
|
||||
|
||||
# Cause uWSGI to gracefully reload workers and mules upon receipt of
|
||||
# SIGTERM (its default is to brutally kill workers)
|
||||
hook-master-start: unix_signal:15 gracefully_kill_them_all
|
||||
|
||||
# Feature necessary for proper mule signal handling
|
||||
py-call-osafterfork: true
|
||||
|
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# Ensure application threads will run if `threads` is unset.
|
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enable-threads: true
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tool_shed:
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# Verbosity of console log messages. Acceptable values can be found
|
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@@ -27,11 +66,11 @@ tool_shed:
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# string to specify an external database instead. This string takes
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# many options which are explained in detail in the config file
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# documentation.
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#database_connection: sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
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#database_connection: 'sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE'
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# Where the hgweb.config file is stored. The default is the Galaxy
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# installation directory.
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#hgweb_config_dir: None
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#hgweb_config_dir: null
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# Where tool shed repositories are stored.
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#file_path: database/community_files
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@@ -57,7 +96,7 @@ tool_shed:
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# allow full text API searching over the repositories and tools within
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# the Tool Shed given that you specify the following two config
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# options.
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#toolshed_search_on: True
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#toolshed_search_on: true
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# -- Repository and Tool search Using the script located at
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# scripts/build_ts_whoosh_index.py you can generate search index and
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@@ -98,7 +137,7 @@ tool_shed:
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# You can enter tracking code here to track visitor's behavior through
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# your Google Analytics account. Example: UA-XXXXXXXX-Y
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#ga_code: None
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#ga_code: null
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# The Tool Shed encodes various internal values when these values will
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# be output in some format (for example, in a URL or cookie). You
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@@ -115,7 +154,7 @@ tool_shed:
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# header in the request. Enabling remote user disables regular logins.
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# For more information, see:
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# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
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#use_remote_user: False
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#use_remote_user: false
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# If use_remote_user is enabled, anyone who can log in to the Galaxy
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# host may impersonate any other user by simply sending the
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@@ -126,22 +165,25 @@ tool_shed:
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#remote_user_secret: changethisinproductiontoo
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# Configuration for debugging middleware
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#debug: False
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#debug: false
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# Check for WSGI compliance.
|
||||
#use_lint: False
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#use_lint: false
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# Intercept print statements and show them on the returned page.
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#use_printdebug: true
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# NEVER enable this on a public site (even test or QA)
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#use_interactive: True
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#use_interactive: true
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# Administrative users - set this to a comma-separated list of valid
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# Tool Shed users (email addresses). These users will have access to
|
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# the Admin section of the server, and will have access to create
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# users, groups, roles, libraries, and more.
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#admin_users: None
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#admin_users: null
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# Force everyone to log in (disable anonymous access)
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#require_login: False
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#require_login: false
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# For use by email messages sent from the tool shed
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#smtp_server: smtp.your_tool_shed_server
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@@ -152,44 +194,44 @@ tool_shed:
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# If your SMTP server requires a username and password, you can
|
||||
# provide them here (password in cleartext here, but if your server
|
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# supports STARTTLS it will be sent over the network encrypted).
|
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#smtp_username: None
|
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#smtp_username: null
|
||||
|
||||
# If your SMTP server requires a username and password, you can
|
||||
# provide them here (password in cleartext here, but if your server
|
||||
# supports STARTTLS it will be sent over the network encrypted).
|
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#smtp_password: None
|
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#smtp_password: null
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|
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# If your SMTP server requires SSL from the beginning of the
|
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# connection
|
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#smtp_ssl: False
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#smtp_ssl: false
|
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|
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# The URL linked by the "Support" link in the "Help" menu.
|
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#support_url: https://wiki.galaxyproject.org/Support
|
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#support_url: 'https://wiki.galaxyproject.org/Support'
|
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|
||||
# Address to join mailing list
|
||||
#mailing_join_addr: galaxy-announce-join@bx.psu.edu
|
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|
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# Write thread status periodically to 'heartbeat.log' (careful, uses
|
||||
# disk space rapidly!)
|
||||
#use_heartbeat: True
|
||||
#use_heartbeat: true
|
||||
|
||||
# Profiling middleware (cProfile based)
|
||||
#use_profile: True
|
||||
#use_profile: true
|
||||
|
||||
# Enable creation of Galaxy flavor Docker Image
|
||||
#enable_galaxy_flavor_docker_image: False
|
||||
#enable_galaxy_flavor_docker_image: false
|
||||
|
||||
# Show a message box under the masthead.
|
||||
#message_box_visible: False
|
||||
#message_box_visible: false
|
||||
|
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# Show a message box under the masthead.
|
||||
#message_box_content: None
|
||||
#message_box_content: null
|
||||
|
||||
# Show a message box under the masthead.
|
||||
#message_box_class: info
|
||||
|
||||
# Serving static files (needed if running standalone)
|
||||
#static_enabled: True
|
||||
#static_enabled: true
|
||||
|
||||
# Serving static files (needed if running standalone)
|
||||
#static_cache_time: 360
|
||||
|
||||
@@ -71,7 +71,7 @@
|
||||
gone away", you will want to set this to some positive value (7200
|
||||
should work).
|
||||
:Default: ``-1``
|
||||
:Type: str
|
||||
:Type: int
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
@@ -429,7 +429,7 @@
|
||||
scheme that may work in wider range of scenarios than the watchdog
|
||||
default.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
@@ -594,7 +594,7 @@
|
||||
which will use a less efficient monitoring scheme that may work in
|
||||
wider range of scenarios than the watchdog default.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~
|
||||
@@ -1517,20 +1517,8 @@
|
||||
Redirect. This should be set to the path defined in the nginx
|
||||
config as an internal redirect with access to Galaxy's data files
|
||||
(see documentation linked above).
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
``nginx_x_archive_files_base``
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
:Description:
|
||||
nginx can make use of mod_zip to create zip files containing
|
||||
multiple library files. If using X-Accel-Redirect, this can be
|
||||
the same value as that option.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Default: ``None``
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~
|
||||
@@ -1572,8 +1560,8 @@
|
||||
explained in detail in the documentation linked above. The upload
|
||||
store is a temporary directory in which files uploaded by the
|
||||
upload module will be placed.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Default: ``None``
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~
|
||||
@@ -1584,8 +1572,8 @@
|
||||
This value overrides the action set on the file upload form, e.g.
|
||||
the web path where the nginx_upload_module has been configured to
|
||||
intercept upload requests.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Default: ``None``
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
@@ -1597,8 +1585,8 @@
|
||||
out upon job completion by remote job runners (i.e. Pulsar) that
|
||||
initiate staging operations on the remote end. See the Galaxy
|
||||
nginx documentation for the corresponding nginx configuration.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Default: ``None``
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
@@ -1610,8 +1598,8 @@
|
||||
out upon job completion by remote job runners (i.e. Pulsar) that
|
||||
initiate staging operations on the remote end. See the Galaxy
|
||||
nginx documentation for the corresponding nginx configuration.
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
:Default: ``None``
|
||||
:Type: str
|
||||
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
@@ -6,7 +6,7 @@
|
||||
If running behind a proxy server and Galaxy is served from a
|
||||
subdirectory, enable the proxy-prefix filter and set the prefix in
|
||||
the [filter:proxy-prefix] section above.
|
||||
:Default: proxy-prefix
|
||||
:Default: ``proxy-prefix``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -20,7 +20,7 @@
|
||||
same path as the prefix in the filter above. This value becomes
|
||||
the "path" attribute set in the cookie so the cookies from each
|
||||
instance will not clobber each other.
|
||||
:Default: None
|
||||
:Default: ``None``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -32,7 +32,7 @@
|
||||
Verbosity of console log messages. Acceptable values can be found
|
||||
here: https://docs.python.org/2/library/logging.html#logging-
|
||||
levels
|
||||
:Default: DEBUG
|
||||
:Default: ``DEBUG``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -45,7 +45,7 @@
|
||||
Galaxy instances, so sqlite (and the default value below) is not
|
||||
supported. An SQLAlchemy connection string should be used specify
|
||||
an external database.
|
||||
:Default: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
|
||||
:Default: ``sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -56,7 +56,7 @@
|
||||
:Description:
|
||||
Where dataset files are saved Temporary storage for additional
|
||||
datasets, this should be shared through the cluster
|
||||
:Default: database/files
|
||||
:Default: ``database/files``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -67,7 +67,7 @@
|
||||
:Description:
|
||||
Where dataset files are saved Temporary storage for additional
|
||||
datasets, this should be shared through the cluster
|
||||
:Default: database/tmp
|
||||
:Default: ``database/tmp``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -78,7 +78,7 @@
|
||||
:Description:
|
||||
Mako templates are compiled as needed and cached for reuse, this
|
||||
directory is used for the cache
|
||||
:Default: database/compiled_templates/reports
|
||||
:Default: ``database/compiled_templates/reports``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -88,7 +88,7 @@
|
||||
|
||||
:Description:
|
||||
Configuration for debugging middleware
|
||||
:Default: False
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
|
||||
|
||||
@@ -98,7 +98,7 @@
|
||||
|
||||
:Description:
|
||||
Check for WSGI compliance.
|
||||
:Default: False
|
||||
:Default: ``false``
|
||||
:Type: bool
|
||||
|
||||
|
||||
@@ -108,7 +108,7 @@
|
||||
|
||||
:Description:
|
||||
NEVER enable this on a public site (even test or QA)
|
||||
:Default: True
|
||||
:Default: ``true``
|
||||
:Type: bool
|
||||
|
||||
|
||||
@@ -119,7 +119,7 @@
|
||||
:Description:
|
||||
Write thread status periodically to 'heartbeat.log' (careful, uses
|
||||
disk space rapidly!)
|
||||
:Default: True
|
||||
:Default: ``true``
|
||||
:Type: bool
|
||||
|
||||
|
||||
@@ -129,7 +129,7 @@
|
||||
|
||||
:Description:
|
||||
Profiling middleware (cProfile based)
|
||||
:Default: True
|
||||
:Default: ``true``
|
||||
:Type: bool
|
||||
|
||||
|
||||
@@ -139,7 +139,7 @@
|
||||
|
||||
:Description:
|
||||
Mail
|
||||
:Default: yourserver@yourfacility.edu
|
||||
:Default: ``yourserver@yourfacility.edu``
|
||||
:Type: str
|
||||
|
||||
|
||||
@@ -149,7 +149,7 @@
|
||||
|
||||
:Description:
|
||||
Mail
|
||||
:Default: your_bugs@bx.psu.edu
|
||||
:Default: ``your_bugs@bx.psu.edu``
|
||||
:Type: str
|
||||
|
||||
|
||||
|
||||
@@ -498,7 +498,6 @@ class Configuration(object):
|
||||
self.upstream_gzip = string_as_bool(kwargs.get('upstream_gzip', False))
|
||||
self.apache_xsendfile = string_as_bool(kwargs.get('apache_xsendfile', False))
|
||||
self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False)
|
||||
self.nginx_x_archive_files_base = kwargs.get('nginx_x_archive_files_base', False)
|
||||
self.nginx_upload_store = kwargs.get('nginx_upload_store', False)
|
||||
self.nginx_upload_path = kwargs.get('nginx_upload_path', False)
|
||||
self.nginx_upload_job_files_store = kwargs.get('nginx_upload_job_files_store', False)
|
||||
|
||||
@@ -751,10 +751,11 @@ def _parse_option_value(option_value):
|
||||
if isinstance(option_value, OptionValue):
|
||||
option = option_value.option
|
||||
value = option_value.value
|
||||
option = option_value.option
|
||||
# Hack to get nicer YAML values during conversion
|
||||
if option.get("type", "str") == "bool":
|
||||
value = str(value).lower() == "true"
|
||||
elif option.get("type", "str") == "int":
|
||||
value = int(value)
|
||||
else:
|
||||
value = option_value
|
||||
option = OPTION_DEFAULTS
|
||||
|
||||
@@ -82,7 +82,7 @@ mapping:
|
||||
processes.
|
||||
|
||||
database_engine_option_pool_recycle:
|
||||
type: str
|
||||
type: int
|
||||
default: -1
|
||||
required: false
|
||||
desc: |
|
||||
@@ -331,7 +331,7 @@ mapping:
|
||||
install from in the admin interface (.sample used if default does not exist).
|
||||
|
||||
watch_tools:
|
||||
type: bool
|
||||
type: str
|
||||
default: false
|
||||
required: false
|
||||
desc: |
|
||||
@@ -454,7 +454,7 @@ mapping:
|
||||
when installed from a ToolShed. Defaults to tool_data_path.
|
||||
|
||||
watch_tool_data_dir:
|
||||
type: bool
|
||||
type: str
|
||||
default: false
|
||||
required: false
|
||||
desc: |
|
||||
@@ -1139,22 +1139,14 @@ mapping:
|
||||
this to True to inform Galaxy that mod_xsendfile is enabled upstream.
|
||||
|
||||
nginx_x_accel_redirect_base:
|
||||
type: bool
|
||||
default: false
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
The same download handling can be done by nginx using X-Accel-Redirect. This
|
||||
should be set to the path defined in the nginx config as an internal redirect
|
||||
with access to Galaxy's data files (see documentation linked above).
|
||||
|
||||
nginx_x_archive_files_base:
|
||||
type: bool
|
||||
default: false
|
||||
required: false
|
||||
desc: |
|
||||
nginx can make use of mod_zip to create zip files containing multiple library
|
||||
files. If using X-Accel-Redirect, this can be the same value as that option.
|
||||
|
||||
upstream_gzip:
|
||||
type: bool
|
||||
default: false
|
||||
@@ -1179,8 +1171,8 @@ mapping:
|
||||
`X-Frame-Options` header.
|
||||
|
||||
nginx_upload_store:
|
||||
type: bool
|
||||
default: false
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
|
||||
@@ -1189,8 +1181,8 @@ mapping:
|
||||
which files uploaded by the upload module will be placed.
|
||||
|
||||
nginx_upload_path:
|
||||
type: bool
|
||||
default: false
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
This value overrides the action set on the file upload form, e.g. the web
|
||||
@@ -1198,8 +1190,8 @@ mapping:
|
||||
requests.
|
||||
|
||||
nginx_upload_job_files_store:
|
||||
type: bool
|
||||
default: false
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
Galaxy can also use nginx_upload_module to receive files staged out upon job
|
||||
@@ -1208,8 +1200,8 @@ mapping:
|
||||
corresponding nginx configuration.
|
||||
|
||||
nginx_upload_job_files_path:
|
||||
type: bool
|
||||
default: false
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
Galaxy can also use nginx_upload_module to receive files staged out upon job
|
||||
|
||||
Reference in New Issue
Block a user