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Rebuild schema...
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jmchilton committed Oct 5, 2024
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59 changes: 59 additions & 0 deletions doc/source/admin/galaxy_options.rst
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Expand Up @@ -5115,6 +5115,26 @@
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_scheduling_separate_materialization_iteration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
Workflows launched with URI/URL inputs that are not marked as
'deferred' are "materialized" (or undeferred) by the workflow
scheduler. This might be a lengthy process. Setting this to 'True'
will place the invocation back in the queue after materialization
before scheduling the workflow so it is less likely to starve
other workflow scheduling. Ideally, Galaxy would allow more fine
grain control of handlers but until then, this provides a way to
tip the balance between "doing more work" and "being more fair".
The default here is pretty arbitrary - it has been to False to
optimize Galaxy for automated, single user applications where
"fairness" is mostly irrelevant.
:Default: ``false``
:Type: bool


~~~~~~~~~~~~~~~~~~~~~~~~
``cache_user_job_count``
~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -5602,3 +5622,42 @@
This requires the help_forum_api_url to be set.
:Default: ``false``
:Type: bool


~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_temp_dir``
~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
Directory to store temporary files for file sources. This defaults
to new_file_path if not set.
:Default: ``None``
:Type: str


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_webdav_use_temp_files``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
Default value for use_temp_files for webdav plugins that don't
explicitly declare this.
:Default: ``true``
:Type: bool


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_listings_expiry_time``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:
Number of seconds before file source content listings are
refreshed. Shorter times will result in more queries while
browsing a file sources. Longer times will result in fewer
requests to file sources but outdated contents might be displayed
to the user. Currently only affects s3fs file sources.
:Default: ``60``
:Type: int



29 changes: 29 additions & 0 deletions lib/galaxy/config/sample/galaxy.yml.sample
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Expand Up @@ -2748,6 +2748,19 @@ galaxy:
# <config_dir>.
#workflow_schedulers_config_file: workflow_schedulers_conf.xml

# Workflows launched with URI/URL inputs that are not marked as
# 'deferred' are "materialized" (or undeferred) by the workflow
# scheduler. This might be a lengthy process. Setting this to 'True'
# will place the invocation back in the queue after materialization
# before scheduling the workflow so it is less likely to starve other
# workflow scheduling. Ideally, Galaxy would allow more fine grain
# control of handlers but until then, this provides a way to tip the
# balance between "doing more work" and "being more fair". The default
# here is pretty arbitrary - it has been to False to optimize Galaxy
# for automated, single user applications where "fairness" is mostly
# irrelevant.
#workflow_scheduling_separate_materialization_iteration: false

# If using job concurrency limits (configured in job_config_file),
# several extra database queries must be performed to determine the
# number of jobs a user has dispatched to a given destination. By
Expand Down Expand Up @@ -2978,3 +2991,19 @@ galaxy:
# Enable the integration of the Galaxy Help Forum in the tool panel.
# This requires the help_forum_api_url to be set.
#enable_help_forum_tool_panel_integration: false

# Directory to store temporary files for file sources. This defaults
# to new_file_path if not set.
#file_source_temp_dir: null

# Default value for use_temp_files for webdav plugins that don't
# explicitly declare this.
#file_source_webdav_use_temp_files: true

# Number of seconds before file source content listings are refreshed.
# Shorter times will result in more queries while browsing a file
# sources. Longer times will result in fewer requests to file sources
# but outdated contents might be displayed to the user. Currently only
# affects s3fs file sources.
#file_source_listings_expiry_time: 60

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