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Merge pull request #10537 from ic4f/dev_config_doc_path

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Generate path resolution note for sample file, docs
This commit is contained in:
John Chilton
2020-10-27 14:55:28 -04:00
committed by GitHub
parent 7befbd8279 066a9bc78a
commit ddcaddd40e
4 changed files with 197 additions and 4 deletions
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doc/source/admin/galaxy_options.rst
+90 -1
View File
@@ -240,6 +240,8 @@
Where dataset files are stored. It must be accessible at the same
path on any cluster nodes that will run Galaxy jobs, unless using
Pulsar.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``objects``
:Type: str
@@ -252,6 +254,8 @@
Where temporary files are stored. It must be accessible at the
same path on any cluster nodes that will run Galaxy jobs, unless
using Pulsar.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``tmp``
:Type: str
@@ -267,6 +271,8 @@
config/tool_conf.xml does not exist). Can be a single file, a list
of files, or (for backwards compatibility) a comma-separated list
of files.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_conf.xml``
:Type: any
@@ -285,6 +291,8 @@
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.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``shed_tool_conf.xml``
:Type: str
@@ -314,6 +322,8 @@
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.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``migrated_tools_conf.xml``
:Type: str
@@ -377,6 +387,8 @@
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.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``dependency_resolvers_conf.xml``
:Type: str
@@ -482,6 +494,8 @@
Path to a file that provides a mapping from abstract packages to
concrete conda packages. See
`config/local_conda_mapping.yml.sample` for examples.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``local_conda_mapping.yml``
:Type: str
@@ -494,6 +508,8 @@
Path to a file that provides a mapping from abstract packages to
locally installed modules. See
`config/environment_modules_mapping.yml.sample` for examples.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``environment_modules_mapping.yml``
:Type: str
@@ -550,6 +566,8 @@
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).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_sheds_conf.xml``
:Type: str
@@ -637,6 +655,8 @@
:Description:
Configured FileSource plugins.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``file_sources_conf.yml``
:Type: str
@@ -745,6 +765,8 @@
XML config file that contains data table entries for the
ToolDataTableManager. This file is manually # maintained by the
Galaxy administrator (.sample used if default does not exist).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_data_table_conf.xml``
:Type: str
@@ -761,6 +783,8 @@
installation, these entries are automatically added to the
following file, which is parsed and applied to the
ToolDataTableManager at server start up.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``shed_tool_data_table_conf.xml``
:Type: str
@@ -826,6 +850,8 @@
:Description:
File that defines the builds (dbkeys) available at sites used by
display applications and the URL to those sites.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``build_sites.yml``
:Type: str
@@ -865,6 +891,8 @@
If a datatype appears in multiple files, the last definition is
used (though the first sniffer is used so limit sniffer
definitions to one file).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``datatypes_conf.xml``
:Type: str
@@ -972,6 +1000,8 @@
:Description:
If using a cluster, Galaxy will write job scripts and
stdout/stderr to this directory.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``pbs``
:Type: str
@@ -983,6 +1013,8 @@
:Description:
Mako templates are compiled as needed and cached for reuse, this
directory is used for the cache
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``compiled_templates``
:Type: str
@@ -1045,6 +1077,8 @@
stored at this path. Per tool_conf cache locations can be
configured in (shed_)tool_conf.xml files using the
tool_cache_data_dir attribute.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``tool_cache``
:Type: str
@@ -1054,7 +1088,8 @@
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Directory in which the toolbox search index is stored.
Directory in which the toolbox search index is stored. The value
of this option will be resolved with respect to <data_dir>.
:Default: ``tool_search_index``
:Type: str
@@ -1093,6 +1128,8 @@
fetched from external sources such as https://doi.org/ by Galaxy -
the following parameters can be used to control the caching used
to store this information.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``citations/data``
:Type: str
@@ -1106,6 +1143,8 @@
fetched from external sources such as https://doi.org/ by Galaxy -
the following parameters can be used to control the caching used
to store this information.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``citations/locks``
:Type: str
@@ -1129,6 +1168,8 @@
:Description:
Data directory used by beaker for caching mulled resolution
requests.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``mulled/data``
:Type: str
@@ -1140,6 +1181,8 @@
:Description:
Lock directory used by beaker for caching mulled resolution
requests.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``mulled/locks``
:Type: str
@@ -1151,6 +1194,8 @@
:Description:
Configuration file for the object store If this is set and exists,
it overrides any other objectstore settings.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``object_store_conf.xml``
:Type: str
@@ -1483,6 +1528,8 @@
:Description:
Map for interactivetool proxy.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``interactivetools_map.sqlite``
:Type: str
@@ -1575,6 +1622,8 @@
'doc' may be be specified as well for each entry.
If this is null (the default), a simple configuration containing
just Dockstore will be used.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``trs_servers_conf.yml``
:Type: str
@@ -1586,6 +1635,8 @@
:Description:
Location of the configuration file containing extra user
preferences.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``user_preferences_extra_conf.yml``
:Type: str
@@ -2025,6 +2076,8 @@
:Description:
The NodeJS dynamic proxy can use an SQLite database or a JSON file
for IPC, set that here.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``session_map.sqlite``
:Type: str
@@ -3226,6 +3279,8 @@
:Description:
Sets the path to OIDC configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``oidc_config.xml``
:Type: str
@@ -3236,6 +3291,8 @@
:Description:
Sets the path to OIDC backends configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``oidc_backends_config.xml``
:Type: str
@@ -3248,6 +3305,8 @@
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).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``auth_conf.xml``
:Type: str
@@ -3292,6 +3351,8 @@
:Description:
If OpenID is enabled, consumer cache directory to use.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``openid_consumer_cache``
:Type: str
@@ -3469,6 +3530,8 @@
:Description:
XML config file that contains the job metric collection
configuration.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_metrics_conf.xml``
:Type: str
@@ -3511,6 +3574,8 @@
:Description:
File where Data Managers are configured (.sample used if default
does not exist).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``data_manager_conf.xml``
:Type: str
@@ -3522,6 +3587,8 @@
:Description:
File where Tool Shed based Data Managers are configured. This file
will be created automatically upon data manager installation.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``shed_data_manager_conf.xml``
:Type: str
@@ -3552,6 +3619,8 @@
Jobs are run locally on the system on which Galaxy is started.
Advanced job running capabilities can be configured through the
job configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_conf.xml``
:Type: str
@@ -3879,6 +3948,8 @@
CSS file to apply to all Markdown exports to PDF - currently used
by WeasyPrint during rendering an HTML export of the document to
PDF.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``markdown_export.css``
:Type: str
@@ -3891,6 +3962,8 @@
CSS file to apply to "Galaxy Page" exports to PDF. Generally
prefer markdown_export_css, but this is here for deployments that
would like to tailor different kinds of exports.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``markdown_export_pages.css``
:Type: str
@@ -3903,6 +3976,8 @@
CSS file to apply to invocation report exports to PDF. Generally
prefer markdown_export_css, but this is here for deployments that
would like to tailor different kinds of exports.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``markdown_export_invocation_reports.css``
:Type: str
@@ -3982,6 +4057,8 @@
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.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_resource_params_conf.xml``
:Type: str
@@ -3996,6 +4073,8 @@
requires both a description of the fields available (which
defaults to the definitions in job_resource_params_file if not
set).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``workflow_resource_params_conf.xml``
:Type: str
@@ -4027,6 +4106,8 @@
:Description:
Optional configuration file similar to `job_config_file` to
specify which Galaxy processes should schedule workflows.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``workflow_schedulers_conf.xml``
:Type: str
@@ -4240,6 +4321,8 @@
removed from the recommendations and another is for adding
additional tools to be recommended along side those from the deep
learning model.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_recommendations_overwrite.yml``
:Type: str
@@ -4265,6 +4348,8 @@
:Description:
Path to error reports configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``error_report.yml``
:Type: str
@@ -4277,6 +4362,8 @@
Path to container interface configuration file. The containers
interface is only used if `enable_beta_containers_interface`
config option is set.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``containers_conf.yml``
:Type: str
@@ -4287,6 +4374,8 @@
:Description:
Path to dynamic tool destinations configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_destinations.yml``
:Type: str
lib/galaxy/config/config_manage.py
+11 -2
View File
@@ -411,7 +411,7 @@ def _write_option_rst(args, rst, key, heading_level, option_value):
heading = heading_level * len(title)
rst.write(f"{heading}\n{title}\n{heading}\n\n")
option, value = _parse_option_value(option_value)
desc = option["desc"]
desc = _get_option_desc(option)
rst.write(":Description:\n")
# Wrap and indent desc, replacing whitespaces with a space, except
# for double newlines which are replaced with a single newline.
@@ -737,7 +737,7 @@ def _write_header(f, section_header):
def _write_option(args, f, key, option_value, as_comment=False, uwsgi_hack=False):
option, value = _parse_option_value(option_value)
desc = option["desc"]
desc = _get_option_desc(option)
comment = ""
if desc and args.add_comments:
# Wrap and comment desc, replacing whitespaces with a space, except
@@ -806,6 +806,15 @@ def _warn(message):
print("WARNING: %s" % message)
def _get_option_desc(option):
desc = option["desc"]
parent_dir = option.get("path_resolves_to")
if parent_dir:
path_resolves = f"The value of this option will be resolved with respect to <{parent_dir}>."
return f"{desc}\n{path_resolves}" if desc else path_resolves
return desc
ACTIONS = {
"convert": _run_conversion,
"build_sample_yaml": _build_sample_yaml,
lib/galaxy/config/sample/galaxy.yml.sample
+90 -1
View File
@@ -215,11 +215,15 @@ galaxy:
# Where dataset files are stored. It must be accessible at the same
# path on any cluster nodes that will run Galaxy jobs, unless using
# Pulsar.
# The value of this option will be resolved with respect to
# <data_dir>.
#file_path: objects
# Where temporary files are stored. It must be accessible at the same
# path on any cluster nodes that will run Galaxy jobs, unless using
# Pulsar.
# The value of this option will be resolved with respect to
# <data_dir>.
#new_file_path: tmp
# Tool config files, defines what tools are available in Galaxy. Tools
@@ -228,6 +232,8 @@ galaxy:
# config/tool_conf.xml does not exist). Can be a single file, a list
# of files, or (for backwards compatibility) a comma-separated list of
# files.
# The value of this option will be resolved with respect to
# <config_dir>.
#tool_config_file: tool_conf.xml
# Tool config file for tools installed from the Galaxy Tool Shed. Must
@@ -239,6 +245,8 @@ 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.
# The value of this option will be resolved with respect to
# <managed_config_dir>.
#shed_tool_config_file: shed_tool_conf.xml
# Enable / disable checking if any tools defined in the above non-shed
@@ -253,6 +261,8 @@ 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.
# The value of this option will be resolved with respect to
# <managed_config_dir>.
#migrated_tools_config: migrated_tools_conf.xml
# File that contains the XML section and tool tags from all tool panel
@@ -288,6 +298,8 @@ galaxy:
# Conda if available. See
# https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst
# for more information on these options.
# 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
@@ -329,11 +341,15 @@ galaxy:
# Path to a file that provides a mapping from abstract packages to
# concrete conda packages. See `config/local_conda_mapping.yml.sample`
# for examples.
# The value of this option will be resolved with respect to
# <config_dir>.
#local_conda_mapping_file: local_conda_mapping.yml
# Path to a file that provides a mapping from abstract packages to
# locally installed modules. See
# `config/environment_modules_mapping.yml.sample` for examples.
# The value of this option will be resolved with respect to
# <config_dir>.
#modules_mapping_files: environment_modules_mapping.yml
# Certain dependency resolvers (namely Conda) take a considerable
@@ -362,6 +378,8 @@ 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).
# 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
@@ -407,6 +425,8 @@ galaxy:
#legacy_eager_objectstore_initialization: false
# Configured FileSource plugins.
# The value of this option will be resolved with respect to
# <config_dir>.
#file_sources_config_file: file_sources_conf.yml
# Enable Galaxy to fetch containers registered with quay.io generated
@@ -459,6 +479,8 @@ galaxy:
# XML config file that contains data table entries for the
# ToolDataTableManager. This file is manually # maintained by the
# Galaxy administrator (.sample used if default does not exist).
# The value of this option will be resolved with respect to
# <config_dir>.
#tool_data_table_config_path: tool_data_table_conf.xml
# XML config file that contains additional data table entries for the
@@ -468,6 +490,8 @@ galaxy:
# these entries are automatically added to the following file, which
# is parsed and applied to the ToolDataTableManager at server start
# up.
# The value of this option will be resolved with respect to
# <managed_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
@@ -498,6 +522,8 @@ galaxy:
# File that defines the builds (dbkeys) available at sites used by
# display applications and the URL to those sites.
# The value of this option will be resolved with respect to
# <config_dir>.
#build_sites_config_file: build_sites.yml
# File containing old-style genome builds.
@@ -516,6 +542,8 @@ galaxy:
# a datatype appears in multiple files, the last definition is used
# (though the first sniffer is used so limit sniffer definitions to
# one file).
# The value of this option will be resolved with respect to
# <config_dir>.
#datatypes_config_file: datatypes_conf.xml
# Enable sniffing of compressed datatypes. This can be
@@ -567,10 +595,14 @@ galaxy:
# If using a cluster, Galaxy will write job scripts and stdout/stderr
# to this directory.
# The value of this option will be resolved with respect to
# <data_dir>.
#cluster_files_directory: pbs
# Mako templates are compiled as needed and cached for reuse, this
# directory is used for the cache
# The value of this option will be resolved with respect to
# <data_dir>.
#template_cache_path: compiled_templates
# Set to false to disable various checks Galaxy will do to ensure it
@@ -598,9 +630,12 @@ galaxy:
# stored at this path. Per tool_conf cache locations can be configured
# in (shed_)tool_conf.xml files using the tool_cache_data_dir
# attribute.
# The value of this option will be resolved with respect to
# <data_dir>.
#tool_cache_data_dir: tool_cache
# Directory in which the toolbox search index is stored.
# Directory in which the toolbox search index is stored. The value of
# this option will be resolved with respect to <data_dir>.
#tool_search_index_dir: tool_search_index
# Set this to true to delay parsing of tool inputs and outputs until
@@ -618,12 +653,16 @@ galaxy:
# from external sources such as https://doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
# The value of this option will be resolved with respect to
# <data_dir>.
#citation_cache_data_dir: citations/data
# Citation related caching. Tool citations information maybe fetched
# from external sources such as https://doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
# The value of this option will be resolved with respect to
# <data_dir>.
#citation_cache_lock_dir: citations/locks
# Mulled resolution caching. Mulled resolution uses external APIs of
@@ -633,14 +672,20 @@ galaxy:
# Data directory used by beaker for caching mulled resolution
# requests.
# The value of this option will be resolved with respect to
# <data_dir>.
#mulled_resolution_cache_data_dir: mulled/data
# Lock directory used by beaker for caching mulled resolution
# requests.
# The value of this option will be resolved with respect to
# <data_dir>.
#mulled_resolution_cache_lock_dir: mulled/locks
# Configuration file for the object store If this is set and exists,
# it overrides any other objectstore settings.
# 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
@@ -799,6 +844,8 @@ galaxy:
#interactivetools_proxy_host: null
# Map for interactivetool proxy.
# The value of this option will be resolved with respect to
# <data_dir>.
#interactivetools_map: interactivetools_map.sqlite
# Show visualization tab and list in masthead.
@@ -834,10 +881,14 @@ galaxy:
# 'doc' may be be specified as well for each entry.
# If this is null (the default), a simple configuration containing
# just Dockstore will be used.
# The value of this option will be resolved with respect to
# <config_dir>.
#trs_servers_config_file: trs_servers_conf.yml
# Location of the configuration file containing extra user
# preferences.
# 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
@@ -1030,6 +1081,8 @@ galaxy:
# The NodeJS dynamic proxy can use an SQLite database or a JSON file
# for IPC, set that here.
# The value of this option will be resolved with respect to
# <data_dir>.
#dynamic_proxy_session_map: session_map.sqlite
# Set the port and IP for the dynamic proxy to bind to, this must
@@ -1588,14 +1641,20 @@ galaxy:
#enable_oidc: false
# Sets the path to OIDC configuration file.
# 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.
# 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).
# 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
@@ -1612,6 +1671,8 @@ galaxy:
#enable_openid: false
# If OpenID is enabled, consumer cache directory to use.
# The value of this option will be resolved with respect to
# <data_dir>.
#openid_consumer_cache_path: openid_consumer_cache
# Enable tool tags (associating tools with tags). This has its own
@@ -1691,6 +1752,8 @@ galaxy:
# XML config file that contains the job metric collection
# configuration.
# The value of this option will be resolved with respect to
# <config_dir>.
#job_metrics_config_file: job_metrics_conf.xml
# This option allows users to see the job metrics (except for
@@ -1705,10 +1768,14 @@ galaxy:
# File where Data Managers are configured (.sample used if default
# does not exist).
# The value of this option will be resolved with respect to
# <config_dir>.
#data_manager_config_file: data_manager_conf.xml
# File where Tool Shed based Data Managers are configured. This file
# will be created automatically upon data manager installation.
# The value of this option will be resolved with respect to
# <managed_config_dir>.
#shed_data_manager_config_file: shed_data_manager_conf.xml
# Directory to store Data Manager based tool-data. Defaults to the
@@ -1725,6 +1792,8 @@ galaxy:
# are run locally on the system on which Galaxy is started. Advanced
# job running capabilities can be configured through the job
# configuration file.
# The value of this option will be resolved with respect to
# <config_dir>.
#job_config_file: job_conf.xml
# Description of job running configuration, can be embedded into
@@ -1896,16 +1965,22 @@ galaxy:
# CSS file to apply to all Markdown exports to PDF - currently used by
# WeasyPrint during rendering an HTML export of the document to PDF.
# The value of this option will be resolved with respect to
# <config_dir>.
#markdown_export_css: markdown_export.css
# CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer
# markdown_export_css, but this is here for deployments that would
# like to tailor different kinds of exports.
# The value of this option will be resolved with respect to
# <config_dir>.
#markdown_export_css_pages: markdown_export_pages.css
# CSS file to apply to invocation report exports to PDF. Generally
# prefer markdown_export_css, but this is here for deployments that
# would like to tailor different kinds of exports.
# The value of this option will be resolved with respect to
# <config_dir>.
#markdown_export_css_invocation_reports: markdown_export_invocation_reports.css
# Prologue Markdown/HTML to apply to markdown exports to PDF. Allowing
@@ -1936,12 +2011,16 @@ 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.
# 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).
# 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
@@ -1959,6 +2038,8 @@ galaxy:
# Optional configuration file similar to `job_config_file` to specify
# which Galaxy processes should schedule workflows.
# 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),
@@ -2057,6 +2138,8 @@ galaxy:
# removed from the recommendations and another is for adding
# additional tools to be recommended along side those from the deep
# learning model.
# The value of this option will be resolved with respect to
# <config_dir>.
#admin_tool_recommendations_path: tool_recommendations_overwrite.yml
# Overwrite or append to the tool recommendations by the deep learning
@@ -2068,13 +2151,19 @@ galaxy:
#overwrite_model_recommendations: false
# Path to error reports configuration file.
# The value of this option will be resolved with respect to
# <config_dir>.
#error_report_file: error_report.yml
# Path to container interface configuration file. The containers
# interface is only used if `enable_beta_containers_interface` config
# option is set.
# The value of this option will be resolved with respect to
# <config_dir>.
#containers_config_file: containers_conf.yml
# Path to dynamic tool destinations configuration file.
# The value of this option will be resolved with respect to
# <config_dir>.
#tool_destinations_config_file: tool_destinations.yml
lib/galaxy/config/sample/tool_shed.yml.sample
+6
View File
@@ -408,6 +408,8 @@ tool_shed:
# 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).
# The value of this option will be resolved with respect to
# <config_dir>.
#auth_config_file: auth_conf.xml
# XML config file that contains additional data table entries for the
@@ -417,6 +419,8 @@ tool_shed:
# these entries are automatically added to the following file, which
# is parsed and applied to the ToolDataTableManager at server start
# up.
# The value of this option will be resolved with respect to
# <managed_config_dir>.
#shed_tool_data_table_config: shed_tool_data_table_conf.xml
# Datatypes config file(s), defines what data (file) types are
@@ -424,5 +428,7 @@ tool_shed:
# a datatype appears in multiple files, the last definition is used
# (though the first sniffer is used so limit sniffer definitions to
# one file).
# The value of this option will be resolved with respect to
# <config_dir>.
#datatypes_config_file: datatypes_conf.xml