opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Drop use_interactive from config schema and rebuild.

Browse Source
This commit is contained in:
Dannon Baker
2019-10-24 14:54:12 -04:00
parent aba277c23b
commit 2d1864fb2f
4 changed files with 159 additions and 128 deletions
Download Patch File Download Diff File Expand all files Collapse all files
doc/source/admin/galaxy_options.rst
+75 -59
View File
@@ -29,10 +29,8 @@
:Description:
By default, Galaxy uses a SQLite database at
'database/universe.sqlite'. You may use a SQLAlchemy connection
string to specify an external database instead. This string takes
many options which are explained in detail in the config file
documentation.
'<data_dir>/universe.sqlite'. You may use a SQLAlchemy connection
string to specify an external database instead.
Sample default
'sqlite:///<data_dir>/universe.sqlite?isolation_level=IMMEDIATE'
:Default: ``None``
@@ -255,7 +253,9 @@
this option is preferable. This file will be created automatically
upon tool installation, whereas Galaxy will fail to start if any
files in tool_config_file cannot be read.
:Default: ``config/shed_tool_conf.xml``
The value of this option will be resolved with respect to
<mutable_config_dir>.
:Default: ``shed_tool_conf.xml``
:Type: str
@@ -284,8 +284,8 @@
migration scripts to install tools that have been migrated to the
tool shed upon a new release, they will be added to this tool
config file.
Default value will be resolved to 'config/migrated_tools_conf.xml'
where 'config' is the default value of the 'config_dir' option).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``migrated_tools_conf.xml``
:Type: str
@@ -329,8 +329,8 @@
handling. If this option is set to none or an invalid path,
installing tools with dependencies from the Tool Shed or in Conda
will fail.
Default value will be resolved to 'database/dependencies' where
'database' is the default value of the 'data_dir' option).
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``dependencies``
:Type: str
@@ -347,7 +347,9 @@
then use Conda if available. See
https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst
for more information on these options.
:Default: ``config/dependency_resolvers_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``dependency_resolvers_conf.xml``
:Type: str
@@ -496,7 +498,9 @@
File containing the Galaxy Tool Sheds that should be made
available to install from in the admin interface (.sample used if
default does not exist).
:Default: ``config/tool_sheds_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_sheds_conf.xml``
:Type: str
@@ -603,7 +607,8 @@
the Galaxy host. This is ignored if the relevant container
resolver isn't enabled, and will install on demand unless
involucro_auto_init is set to false.
Value will be resolved with respect to '<tool_dependency_dir>'.
The value of this option will be resolved with respect to
<tool_dependency_dir>.
:Default: ``involucro``
:Type: str
@@ -696,7 +701,9 @@
installation, these entries are automatically added to the
following file, which is parsed and applied to the
ToolDataTableManager at server start up.
:Default: ``config/shed_tool_data_table_conf.xml``
The value of this option will be resolved with respect to
<mutable_config_dir>.
:Default: ``shed_tool_data_table_conf.xml``
:Type: str
@@ -747,8 +754,9 @@
~~~~~~~~~~~~~~~~~~~~
:Description:
File containing old-style genome builds. Value will be resolved
with respect to <tool_data_path>.
File containing old-style genome builds.
The value of this option will be resolved with respect to
<tool_data_path>.
:Default: ``shared/ucsc/builds.txt``
:Type: str
@@ -759,7 +767,8 @@
:Description:
Directory where chrom len files are kept, currently mainly used by
trackster. Value will be resolved with respect to
trackster.
The value of this option will be resolved with respect to
<tool_data_path>.
:Default: ``shared/ucsc/chrom``
:Type: str
@@ -869,8 +878,8 @@
Each job is given a unique empty directory as its current working
directory. This option defines in what parent directory those
directories will be created.
Default value will be resolved to 'database/jobs_directory' where
'database' is the default value of the 'data_dir' option).
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``jobs_directory``
:Type: str
@@ -992,7 +1001,9 @@
:Description:
Configuration file for the object store If this is set and exists,
it overrides any other objectstore settings.
:Default: ``config/object_store_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``object_store_conf.xml``
:Type: str
@@ -1325,7 +1336,7 @@
Format string used when showing date and time information. The
string may contain: - the directives used by Python
time.strftime() function (see
https://docs.python.org/library/time.html#time.strftime ), -
https://docs.python.org/library/time.html#time.strftime), -
$locale (complete format string for the server locale), - $iso8601
(complete format string as specified by ISO 8601 international
standard).
@@ -1340,7 +1351,9 @@
:Description:
Location of the configuration file containing extra user
preferences.
:Default: ``config/user_preferences_extra_conf.yml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``user_preferences_extra_conf.yml``
:Type: str
@@ -2093,8 +2106,8 @@
:Description:
Debug enables access to various config options useful for
development and debugging: use_lint, use_profile, use_printdebug
and use_interactive. It also causes the files used by PBS/SGE
development and debugging: use_lint, use_profile, and
use_printdebug. It also causes the files used by PBS/SGE
(submission script, output, and error) to remain on disk after the
job is complete.
:Default: ``false``
@@ -2131,17 +2144,6 @@
:Type: bool
~~~~~~~~~~~~~~~~~~~
``use_interactive``
~~~~~~~~~~~~~~~~~~~
:Description:
Enable live debugging in your browser. This should NEVER be
enabled on a public site.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``monitor_thread_join_timeout``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -2970,7 +2972,9 @@
:Description:
Sets the path to OIDC configuration file.
:Default: ``config/oidc_config.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``oidc_config.xml``
:Type: str
@@ -2980,7 +2984,9 @@
:Description:
Sets the path to OIDC backends configuration file.
:Default: ``config/oidc_backends_config.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``oidc_backends_config.xml``
:Type: str
@@ -2992,7 +2998,9 @@
XML config file that allows the use of different authentication
providers (e.g. LDAP) instead or in addition to local
authentication (.sample is used if default does not exist).
:Default: ``config/auth_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``auth_conf.xml``
:Type: str
@@ -3213,7 +3221,9 @@
:Description:
File where Tool Shed based Data Managers are configured. This file
will be created automatically upon data manager installation.
:Default: ``config/shed_data_manager_conf.xml``
The value of this option will be resolved with respect to
<mutable_config_dir>.
:Default: ``shed_data_manager_conf.xml``
:Type: str
@@ -3459,9 +3469,9 @@
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html
#submitting-jobs-as-the-real-user) this script is used to run the
job script Galaxy generates for a tool execution.
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
jobs-as-the-real-user) this script is used to run the job script
Galaxy generates for a tool execution.
Example value 'sudo -E scripts/drmaa_external_runner.py
--assign_all_groups'
:Default: ``None``
@@ -3474,9 +3484,9 @@
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html
#submitting-jobs-as-the-real-user) this script is used to kill
such jobs by Galaxy (e.g. if the user cancels the job).
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
jobs-as-the-real-user) this script is used to kill such jobs by
Galaxy (e.g. if the user cancels the job).
Example value 'sudo -E scripts/drmaa_external_killer.py'
:Default: ``None``
:Type: str
@@ -3488,10 +3498,10 @@
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html
#submitting-jobs-as-the-real-user) this script is used transfer
permissions back and forth between the Galaxy user and the user
that is running the job.
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
jobs-as-the-real-user) this script is used transfer permissions
back and forth between the Galaxy user and the user that is
running the job.
Example value 'sudo -E scripts/external_chown_script.py'
:Default: ``None``
:Type: str
@@ -3503,14 +3513,14 @@
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html
#submitting-jobs-as-the-real-user) Galaxy can extract the user
name from the email address (actually the local-part before the @)
or the username which are both stored in the Galaxy data base. The
latter option is particularly useful for installations that get
the authentication from LDAP. Also, Galaxy can accept the name of
a common system user (eg. galaxy_worker) who can run every job
being submitted. This user should not be the same user running the
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
jobs-as-the-real-user) Galaxy can extract the user name from the
email address (actually the local-part before the @) or the
username which are both stored in the Galaxy data base. The latter
option is particularly useful for installations that get the
authentication from LDAP. Also, Galaxy can accept the name of a
common system user (eg. galaxy_worker) who can run every job being
submitted. This user should not be the same user running the
galaxy system. Possible values are user_email (default), username
or <common_system_user>
:Default: ``user_email``
@@ -3545,7 +3555,9 @@
definition. These fields will be presented to users in the tool
forms and allow them to overwrite default job resources such as
number of processors, memory and walltime.
:Default: ``config/job_resource_params_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_resource_params_conf.xml``
:Type: str
@@ -3559,7 +3571,9 @@
requires both a description of the fields available (which
defaults to the definitions in job_resource_params_file if not
set).
:Default: ``config/workflow_resource_params_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``workflow_resource_params_conf.xml``
:Type: str
@@ -3588,7 +3602,9 @@
:Description:
Optional configuration file similar to `job_config_file` to
specify which Galaxy processes should schedule workflows.
:Default: ``config/workflow_schedulers_conf.xml``
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``workflow_schedulers_conf.xml``
:Type: str
lib/galaxy/config/sample/galaxy.yml.sample
+79 -56
View File
@@ -110,10 +110,8 @@ galaxy:
#data_dir: null
# By default, Galaxy uses a SQLite database at
# 'database/universe.sqlite'. You may use a SQLAlchemy connection
# string to specify an external database instead. This string takes
# many options which are explained in detail in the config file
# documentation.
# '<data_dir>/universe.sqlite'. You may use a SQLAlchemy connection
# string to specify an external database instead.
# Sample default
# 'sqlite:///<data_dir>/universe.sqlite?isolation_level=IMMEDIATE'
#database_connection: null
@@ -215,7 +213,9 @@ galaxy:
# preferable. This file will be created automatically upon tool
# installation, whereas Galaxy will fail to start if any files in
# tool_config_file cannot be read.
#shed_tool_config_file: config/shed_tool_conf.xml
# The value of this option will be resolved with respect to
# <mutable_config_dir>.
#shed_tool_config_file: shed_tool_conf.xml
# Enable / disable checking if any tools defined in the above non-shed
# tool_config_files (i.e., tool_conf.xml) have been migrated from the
@@ -229,8 +229,8 @@ galaxy:
# migration scripts to install tools that have been migrated to the
# tool shed upon a new release, they will be added to this tool config
# file.
# Default value will be resolved to 'config/migrated_tools_conf.xml'
# where 'config' is the default value of the 'config_dir' option).
# The value of this option will be resolved with respect to
# <config_dir>.
#migrated_tools_config: migrated_tools_conf.xml
# File that contains the XML section and tool tags from all tool panel
@@ -253,8 +253,8 @@ galaxy:
# handling. If this option is set to none or an invalid path,
# installing tools with dependencies from the Tool Shed or in Conda
# will fail.
# Default value will be resolved to 'database/dependencies' where
# 'database' is the default value of the 'data_dir' option).
# The value of this option will be resolved with respect to
# <data_dir>.
#tool_dependency_dir: dependencies
# The dependency resolvers config file specifies an ordering and
@@ -264,7 +264,9 @@ galaxy:
# Conda if available. See
# https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst
# for more information on these options.
#dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#dependency_resolvers_config_file: dependency_resolvers_conf.xml
# conda_prefix is the location on the filesystem where Conda packages
# and environments are installed.
@@ -328,7 +330,9 @@ galaxy:
# File containing the Galaxy Tool Sheds that should be made available
# to install from in the admin interface (.sample used if default does
# not exist).
#tool_sheds_config_file: config/tool_sheds_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#tool_sheds_config_file: tool_sheds_conf.xml
# Monitor the tools and tool directories listed in any tool config
# file specified in tool_config_file option. If changes are found,
@@ -386,7 +390,8 @@ galaxy:
# the Galaxy host. This is ignored if the relevant container resolver
# isn't enabled, and will install on demand unless involucro_auto_init
# is set to false.
# Value will be resolved with respect to '<tool_dependency_dir>'.
# The value of this option will be resolved with respect to
# <tool_dependency_dir>.
#involucro_path: involucro
# Install involucro as needed to build Docker or Singularity
@@ -430,7 +435,9 @@ galaxy:
# these entries are automatically added to the following file, which
# is parsed and applied to the ToolDataTableManager at server start
# up.
#shed_tool_data_table_config: config/shed_tool_data_table_conf.xml
# The value of this option will be resolved with respect to
# <mutable_config_dir>.
#shed_tool_data_table_config: shed_tool_data_table_conf.xml
# Directory where data used by tools is located. See the samples in
# that directory and the Galaxy Community Hub for help:
@@ -453,12 +460,15 @@ galaxy:
# scenarios than the watchdog default.
#watch_tool_data_dir: 'false'
# File containing old-style genome builds. Value will be resolved with
# respect to <tool_data_path>.
# File containing old-style genome builds.
# The value of this option will be resolved with respect to
# <tool_data_path>.
#builds_file_path: shared/ucsc/builds.txt
# Directory where chrom len files are kept, currently mainly used by
# trackster. Value will be resolved with respect to <tool_data_path>.
# trackster.
# The value of this option will be resolved with respect to
# <tool_data_path>.
#len_file_path: shared/ucsc/chrom
# Datatypes config file(s), defines what data (file) types are
@@ -511,8 +521,8 @@ galaxy:
# Each job is given a unique empty directory as its current working
# directory. This option defines in what parent directory those
# directories will be created.
# Default value will be resolved to 'database/jobs_directory' where
# 'database' is the default value of the 'data_dir' option).
# The value of this option will be resolved with respect to
# <data_dir>.
#job_working_directory: jobs_directory
# If using a cluster, Galaxy will write job scripts and stdout/stderr
@@ -564,7 +574,9 @@ galaxy:
# Configuration file for the object store If this is set and exists,
# it overrides any other objectstore settings.
#object_store_config_file: config/object_store_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#object_store_config_file: object_store_conf.xml
# What Dataset attribute is used to reference files in an ObjectStore
# implementation, default is 'id' but can also be set to 'uuid' for
@@ -711,14 +723,16 @@ galaxy:
# Format string used when showing date and time information. The
# string may contain: - the directives used by Python time.strftime()
# function (see
# https://docs.python.org/library/time.html#time.strftime ), - $locale
# https://docs.python.org/library/time.html#time.strftime), - $locale
# (complete format string for the server locale), - $iso8601 (complete
# format string as specified by ISO 8601 international standard).
#pretty_datetime_format: $locale (UTC)
# Location of the configuration file containing extra user
# preferences.
#user_preferences_extra_conf_path: config/user_preferences_extra_conf.yml
# The value of this option will be resolved with respect to
# <config_dir>.
#user_preferences_extra_conf_path: user_preferences_extra_conf.yml
# Default localization for Galaxy UI. Allowed values are listed at the
# end of client/galaxy/scripts/nls/locale.js. With the default value
@@ -864,8 +878,8 @@ galaxy:
# prevent a class of attack called clickjacking
# (https://www.owasp.org/index.php/Clickjacking). If you configure a
# proxy in front of Galaxy - please ensure this header remains intact
# to protect your users. Uncomment and leave empty to not set the `X
# -Frame-Options` header.
# to protect your users. Uncomment and leave empty to not set the
# `X-Frame-Options` header.
#x_frame_options: SAMEORIGIN
# nginx can also handle file uploads (user-to-Galaxy) via
@@ -1041,8 +1055,8 @@ galaxy:
#trust_jupyter_notebook_conversion: false
# Debug enables access to various config options useful for
# development and debugging: use_lint, use_profile, use_printdebug and
# use_interactive. It also causes the files used by PBS/SGE
# development and debugging: use_lint, use_profile, and
# use_printdebug. It also causes the files used by PBS/SGE
# (submission script, output, and error) to remain on disk after the
# job is complete.
#debug: false
@@ -1056,10 +1070,6 @@ galaxy:
# Intercept print statements and show them on the returned page.
#use_printdebug: true
# Enable live debugging in your browser. This should NEVER be enabled
# on a public site.
#use_interactive: false
# When stopping Galaxy cleanly, how much time to give various
# monitoring/polling threads to finish before giving up on joining
# them. Set to 0 to disable this and terminate without waiting. Among
@@ -1458,15 +1468,21 @@ galaxy:
#enable_oidc: false
# Sets the path to OIDC configuration file.
#oidc_config_file: config/oidc_config.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#oidc_config_file: oidc_config.xml
# Sets the path to OIDC backends configuration file.
#oidc_backends_config_file: config/oidc_backends_config.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#oidc_backends_config_file: oidc_backends_config.xml
# XML config file that allows the use of different authentication
# providers (e.g. LDAP) instead or in addition to local authentication
# (.sample is used if default does not exist).
#auth_config_file: config/auth_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#auth_config_file: auth_conf.xml
# Optional list of email addresses of API users who can make calls on
# behalf of other users.
@@ -1554,7 +1570,9 @@ galaxy:
# File where Tool Shed based Data Managers are configured. This file
# will be created automatically upon data manager installation.
#shed_data_manager_config_file: config/shed_data_manager_conf.xml
# The value of this option will be resolved with respect to
# <mutable_config_dir>.
#shed_data_manager_config_file: shed_data_manager_conf.xml
# Directory to store Data Manager based tool-data; defaults to
# tool_data_path.
@@ -1680,39 +1698,38 @@ galaxy:
#cleanup_job: always
# When running DRMAA jobs as the Galaxy user
# (https://docs.galaxyproject.org/en/master/admin/cluster.html
# #submitting-jobs-as-the-real-user) this script is used to run the
# job script Galaxy generates for a tool execution.
# (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
# jobs-as-the-real-user) this script is used to run the job script
# Galaxy generates for a tool execution.
# Example value 'sudo -E scripts/drmaa_external_runner.py
# --assign_all_groups'
#drmaa_external_runjob_script: null
# When running DRMAA jobs as the Galaxy user
# (https://docs.galaxyproject.org/en/master/admin/cluster.html
# #submitting-jobs-as-the-real-user) this script is used to kill such
# jobs by Galaxy (e.g. if the user cancels the job).
# (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
# jobs-as-the-real-user) this script is used to kill such jobs by
# Galaxy (e.g. if the user cancels the job).
# Example value 'sudo -E scripts/drmaa_external_killer.py'
#drmaa_external_killjob_script: null
# When running DRMAA jobs as the Galaxy user
# (https://docs.galaxyproject.org/en/master/admin/cluster.html
# #submitting-jobs-as-the-real-user) this script is used transfer
# permissions back and forth between the Galaxy user and the user that
# is running the job.
# (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
# jobs-as-the-real-user) this script is used transfer permissions back
# and forth between the Galaxy user and the user that is running the
# job.
# Example value 'sudo -E scripts/external_chown_script.py'
#external_chown_script: null
# When running DRMAA jobs as the Galaxy user
# (https://docs.galaxyproject.org/en/master/admin/cluster.html
# #submitting-jobs-as-the-real-user) Galaxy can extract the user name
# from the email address (actually the local-part before the @) or the
# username which are both stored in the Galaxy data base. The latter
# option is particularly useful for installations that get the
# authentication from LDAP. Also, Galaxy can accept the name of a
# common system user (eg. galaxy_worker) who can run every job being
# submitted. This user should not be the same user running the galaxy
# system. Possible values are user_email (default), username or
# <common_system_user>
# (https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-
# jobs-as-the-real-user) Galaxy can extract the user name from the
# email address (actually the local-part before the @) or the username
# which are both stored in the Galaxy data base. The latter option is
# particularly useful for installations that get the authentication
# from LDAP. Also, Galaxy can accept the name of a common system user
# (eg. galaxy_worker) who can run every job being submitted. This user
# should not be the same user running the galaxy system. Possible
# values are user_email (default), username or <common_system_user>
#real_system_username: user_email
# File to source to set up the environment when running jobs. By
@@ -1731,13 +1748,17 @@ galaxy:
# These fields will be presented to users in the tool forms and allow
# them to overwrite default job resources such as number of
# processors, memory and walltime.
#job_resource_params_file: config/job_resource_params_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#job_resource_params_file: job_resource_params_conf.xml
# Similar to the above parameter, workflows can describe parameters
# used to influence scheduling of jobs within the workflow. This
# requires both a description of the fields available (which defaults
# to the definitions in job_resource_params_file if not set).
#workflow_resource_params_file: config/workflow_resource_params_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#workflow_resource_params_file: workflow_resource_params_conf.xml
# This parameter describes how to map users and workflows to a set of
# workflow resource parameter to present (typically input IDs from
@@ -1752,7 +1773,9 @@ galaxy:
# Optional configuration file similar to `job_config_file` to specify
# which Galaxy processes should schedule workflows.
#workflow_schedulers_config_file: config/workflow_schedulers_conf.xml
# The value of this option will be resolved with respect to
# <config_dir>.
#workflow_schedulers_config_file: workflow_schedulers_conf.xml
# If using job concurrency limits (configured in job_config_file),
# several extra database queries must be performed to determine the
lib/galaxy/config/sample/tool_shed.yml.sample
+2 -2
View File
@@ -177,8 +177,8 @@ tool_shed:
# User authentication can be delegated to an upstream proxy server
# (usually Apache). The upstream proxy should set a REMOTE_USER
# header in the request. Enabling remote user disables regular logins.
# For more information, see: https://galaxyproject.org/admin/config
# /apache-external-user-auth/
# For more information, see:
# https://galaxyproject.org/admin/config/apache-external-user-auth/
#use_remote_user: false
# If use_remote_user is enabled, anyone who can log in to the Galaxy
lib/galaxy/webapps/galaxy/config_schema.yml
+3 -11
View File
@@ -1558,9 +1558,9 @@ mapping:
default: false
required: false
desc: |
Debug enables access to various config options useful for development and
debugging: use_lint, use_profile, use_printdebug and use_interactive. It
also causes the files used by PBS/SGE (submission script, output, and error)
Debug enables access to various config options useful for development
and debugging: use_lint, use_profile, and use_printdebug. It also
causes the files used by PBS/SGE (submission script, output, and error)
to remain on disk after the job is complete.
use_lint:
@@ -1584,14 +1584,6 @@ mapping:
desc: |
Intercept print statements and show them on the returned page.
use_interactive:
type: bool
default: false
required: false
desc: |
Enable live debugging in your browser. This should NEVER be enabled on a
public site.
monitor_thread_join_timeout:
type: int
default: 30