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Merge remote-tracking branch 'upstream/release_18.09' into release_19.01

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This commit is contained in:
Nate Coraor
2019-02-22 13:23:16 -05:00
parent 8651e1eea3 9b72f5a880
commit 808aa5bef7
9 changed files with 108 additions and 129 deletions
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config/galaxy.yml.sample
+18 -12
View File
@@ -66,6 +66,14 @@ uwsgi:
# Reports, etc.) that you are loading.
module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Mount the web application (e.g. Galaxy, Reports, etc.) at the given
# URL prefix. Cannot be used together with 'module:' above.
#mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-
# points. Set this to true if a URL prefix is used.
manage-script-name: false
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: false
@@ -90,16 +98,11 @@ uwsgi:
galaxy:
# 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.
#filter-with: proxy-prefix
# If proxy-prefix is enabled and you're running more than one Galaxy
# instance behind one hostname, you will want to set this to the 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.
# When running multiple Galaxy instances under separate URL prefixes
# on a single hostname, you will want to set this to the same path as
# the prefix set in the uWSGI "mount" configuration option above. This
# value becomes the "path" attribute set in the cookie so the cookies
# from one instance will not clobber those from another.
#cookie_path: ''
# By default, Galaxy uses a SQLite database at
@@ -167,10 +170,13 @@ galaxy:
# not recommended for production use.
#database_auto_migrate: false
# Dataset files are stored in this directory.
# Where dataset files are stored. It must accessible at the same path
# on any cluster nodes that will run Galaxy jobs, unless using Pulsar.
#file_path: database/files
# Temporary files are stored in this directory.
# Where temporary files are stored. It must accessible at the same
# path on any cluster nodes that will run Galaxy jobs, unless using
# Pulsar.
#new_file_path: database/tmp
# Tool config files, defines what tools are available in Galaxy. Tools
config/reports.yml.sample
+16 -15
View File
@@ -48,6 +48,14 @@ uwsgi:
# Reports, etc.) that you are loading.
module: galaxy.webapps.reports.buildapp:uwsgi_app()
# Mount the web application (e.g. Galaxy, Reports, etc.) at the given
# URL prefix. Cannot be used together with 'module:' above.
#mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-
# points. Set this to true if a URL prefix is used.
manage-script-name: false
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: false
@@ -72,34 +80,27 @@ uwsgi:
reports:
# 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.
#filter-with: proxy-prefix
# If proxy-prefix is enabled and you're running more than one Galaxy
# instance behind one hostname, you will want to set this to the 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.
# When running multiple Galaxy Reports instances under separate URL
# prefixes on a single hostname, you will want to set this to the same
# path as the prefix set in the uWSGI "mount" configuration option
# above. This value becomes the "path" attribute set in the cookie so
# the cookies from one instance will not clobber those from another.
#cookie_path: null
# Verbosity of console log messages. Acceptable values can be found
# here: https://docs.python.org/2/library/logging.html#logging-levels
#log_level: DEBUG
# Database connection Galaxy reports are intended for production
# Database connection. Galaxy Reports are intended for production
# Galaxy instances, so sqlite (and the default value below) is not
# supported. An SQLAlchemy connection string should be used specify an
# external database.
#database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
# Where dataset files are saved Temporary storage for additional
# datasets, this should be shared through the cluster
# Where dataset files are stored.
#file_path: database/files
# Where dataset files are saved Temporary storage for additional
# datasets, this should be shared through the cluster
# Where temporary files are stored.
#new_file_path: database/tmp
# Mako templates are compiled as needed and cached for reuse, this
config/tool_shed.yml.sample
+17 -10
View File
@@ -48,6 +48,14 @@ uwsgi:
# Reports, etc.) that you are loading.
module: galaxy.webapps.tool_shed.buildapp:uwsgi_app()
# Mount the web application (e.g. Galaxy, Reports, etc.) at the given
# URL prefix. Cannot be used together with 'module:' above.
#mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
# Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-
# points. Set this to true if a URL prefix is used.
manage-script-name: false
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: false
@@ -87,11 +95,10 @@ tool_shed:
# installation directory.
#hgweb_config_dir: null
# Where tool shed repositories are stored.
# Where Tool Shed repositories are stored.
#file_path: database/community_files
# Temporary storage for additional datasets, this should be shared
# through the cluster
# Where temporary files are stored.
#new_file_path: database/tmp
# File containing old-style genome builds
@@ -225,10 +232,10 @@ tool_shed:
# Allow administrators to delete accounts.
#allow_user_deletion: false
# For use by email messages sent from the tool shed
# For use by email messages sent from the Tool Shed.
#smtp_server: smtp.your_tool_shed_server
# For use by email messages sent from the tool shed
# For use by email messages sent from the Tool Shed.
#email_from: your_tool_shed_email@server
# If your SMTP server requires a username and password, you can
@@ -344,11 +351,11 @@ tool_shed:
# store this information.
#citation_cache_lock_dir: database/citations/lock
# If proxy-prefix is enabled and you're running more than one Galaxy
# instance behind one hostname, you will want to set this to the 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.
# When running multiple Tool Shed instances under separate URL
# prefixes on a single hostname, you will want to set this to the same
# path as the prefix set in the uWSGI "mount" configuration option
# above. This value becomes the "path" attribute set in the cookie so
# the cookies from one instance will not clobber those from another.
#cookie_path: null
# Enable authentication via OpenID. Allows users to log in to their
doc/source/admin/galaxy_options.rst
+11 -19
View File
@@ -1,25 +1,13 @@
~~~~~~~~~~~~~~~
``filter-with``
~~~~~~~~~~~~~~~
:Description:
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``
:Type: str
~~~~~~~~~~~~~~~
``cookie_path``
~~~~~~~~~~~~~~~
:Description:
If proxy-prefix is enabled and you're running more than one Galaxy
instance behind one hostname, you will want to set this to the
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.
When running multiple Galaxy instances under separate URL prefixes
on a single hostname, you will want to set this to the same path
as the prefix set in the uWSGI "mount" configuration option above.
This value becomes the "path" attribute set in the cookie so the
cookies from one instance will not clobber those from another.
:Default: ````
:Type: str
@@ -173,7 +161,9 @@
~~~~~~~~~~~~~
:Description:
Dataset files are stored in this directory.
Where dataset files are stored. It must accessible at the same
path on any cluster nodes that will run Galaxy jobs, unless using
Pulsar.
:Default: ``database/files``
:Type: str
@@ -183,7 +173,9 @@
~~~~~~~~~~~~~~~~~
:Description:
Temporary files are stored in this directory.
Where temporary files are stored. It must accessible at the same
path on any cluster nodes that will run Galaxy jobs, unless using
Pulsar.
:Default: ``database/tmp``
:Type: str
doc/source/admin/reports_options.rst
+9 -22
View File
@@ -1,25 +1,14 @@
~~~~~~~~~~~~~~~
``filter-with``
~~~~~~~~~~~~~~~
:Description:
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``
:Type: str
~~~~~~~~~~~~~~~
``cookie_path``
~~~~~~~~~~~~~~~
:Description:
If proxy-prefix is enabled and you're running more than one Galaxy
instance behind one hostname, you will want to set this to the
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.
When running multiple Galaxy Reports instances under separate URL
prefixes on a single hostname, you will want to set this to the
same path as the prefix set in the uWSGI "mount" configuration
option above. This value becomes the "path" attribute set in the
cookie so the cookies from one instance will not clobber those
from another.
:Default: ``None``
:Type: str
@@ -41,7 +30,7 @@
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Database connection Galaxy reports are intended for production
Database connection. Galaxy Reports are intended for production
Galaxy instances, so sqlite (and the default value below) is not
supported. An SQLAlchemy connection string should be used specify
an external database.
@@ -54,8 +43,7 @@
~~~~~~~~~~~~~
:Description:
Where dataset files are saved Temporary storage for additional
datasets, this should be shared through the cluster
Where dataset files are stored.
:Default: ``database/files``
:Type: str
@@ -65,8 +53,7 @@
~~~~~~~~~~~~~~~~~
:Description:
Where dataset files are saved Temporary storage for additional
datasets, this should be shared through the cluster
Where temporary files are stored.
:Default: ``database/tmp``
:Type: str
lib/galaxy/webapps/config_manage.py
+10
View File
@@ -111,6 +111,16 @@ UWSGI_OPTIONS = OrderedDict([
'default': '$uwsgi_module',
'type': 'str',
}),
('#mount', {
'desc': """Mount the web application (e.g. Galaxy, Reports, etc.) at the given URL prefix. Cannot be used together with 'module:' above.""",
'default': '/galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()',
'type': 'str',
}),
('manage-script-name', {
'desc': """Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-points. Set this to true if a URL prefix is used.""",
'default': False,
'type': 'bool',
}),
('thunder-lock', {
'desc': """It is usually a good idea to set this to ``true`` if processes is greater than 1.""",
'default': False,
lib/galaxy/webapps/galaxy/config_schema.yml
+9 -24
View File
@@ -25,33 +25,16 @@ mapping:
required: true
mapping:
filter-with:
type: str
default: gzip
required: false
desc: |
If not running behind a proxy server, you may want to enable gzip compression
to decrease the size of data transferred over the network. If using a proxy
server, please enable gzip compression there instead.
filter-with:
type: str
default: proxy-prefix
required: false
desc: |
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.
cookie_path:
type: str
default: ''
required: false
desc: |
If proxy-prefix is enabled and you're running more than one Galaxy instance
behind one hostname, you will want to set this to the 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.
When running multiple Galaxy instances under separate URL prefixes on a
single hostname, you will want to set this to the same path as the prefix set
in the uWSGI "mount" configuration option above. This value becomes the "path"
attribute set in the cookie so the cookies from one instance will not clobber
those from another.
database_connection:
type: str
@@ -161,14 +144,16 @@ mapping:
default: database/files
required: false
desc: |
Dataset files are stored in this directory.
Where dataset files are stored. It must accessible at the same path on any cluster
nodes that will run Galaxy jobs, unless using Pulsar.
new_file_path:
type: str
default: database/tmp
required: false
desc: |
Temporary files are stored in this directory.
Where temporary files are stored. It must accessible at the same path on any cluster
nodes that will run Galaxy jobs, unless using Pulsar.
tool_config_file:
type: str
lib/galaxy/webapps/reports/config_schema.yml
+9 -18
View File
@@ -7,21 +7,14 @@ mapping:
desc: |
Galaxy Reports configuration options.
mapping:
filter-with:
type: str
default: proxy-prefix
desc: |
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.
cookie_path:
type: str
desc: |
If proxy-prefix is enabled and you're running more than one Galaxy instance
behind one hostname, you will want to set this to the 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.
When running multiple Galaxy Reports instances under separate URL prefixes on a
single hostname, you will want to set this to the same path as the prefix set
in the uWSGI "mount" configuration option above. This value becomes the "path"
attribute set in the cookie so the cookies from one instance will not clobber
those from another.
log_level:
type: str
@@ -34,8 +27,8 @@ mapping:
type: str
default: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
desc: |
Database connection
Galaxy reports are intended for production Galaxy instances, so sqlite (and the default value
Database connection.
Galaxy Reports are intended for production Galaxy instances, so sqlite (and the default value
below) is not supported. An SQLAlchemy connection string should be used specify an external
database.
@@ -43,15 +36,13 @@ mapping:
type: str
default: database/files
desc: |
Where dataset files are saved
Temporary storage for additional datasets, this should be shared through the cluster
Where dataset files are stored.
new_file_path:
type: str
default: database/tmp
desc: |
Where dataset files are saved
Temporary storage for additional datasets, this should be shared through the cluster
Where temporary files are stored.
template_cache_path:
type: str
lib/galaxy/webapps/tool_shed/config_schema.yml
+9 -9
View File
@@ -37,15 +37,14 @@ mapping:
default: database/community_files
required: false
desc: |
Where tool shed repositories are stored.
Where Tool Shed repositories are stored.
new_file_path:
type: str
default: database/tmp
required: false
desc: |
Temporary storage for additional datasets,
this should be shared through the cluster
Where temporary files are stored.
builds_file_path:
type: str
@@ -293,14 +292,14 @@ mapping:
default: smtp.your_tool_shed_server
required: false
desc: |
For use by email messages sent from the tool shed
For use by email messages sent from the Tool Shed.
email_from:
type: str
default: your_tool_shed_email@server
required: false
desc: |
For use by email messages sent from the tool shed
For use by email messages sent from the Tool Shed.
smtp_username:
type: str
@@ -522,10 +521,11 @@ mapping:
default: null
required: false
desc: |
If proxy-prefix is enabled and you're running more than one Galaxy instance
behind one hostname, you will want to set this to the 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.
When running multiple Tool Shed instances under separate URL prefixes on a
single hostname, you will want to set this to the same path as the prefix set
in the uWSGI "mount" configuration option above. This value becomes the "path"
attribute set in the cookie so the cookies from one instance will not clobber
those from another.
enable_openid:
type: bool