From 06481211481d6098e33da3d68c9d6f43be46eefb Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 4 Jun 2024 21:47:44 +0200
Subject: [PATCH 1/6] update config for 24.1

---
 files/galaxy/config/datatypes_conf.xml   |  30 ++++--
 group_vars/gxconfig.yml                  | 124 ++++++++++++++++++-----
 templates/galaxy/config/tool_conf.xml.j2 |   3 +
 3 files changed, 128 insertions(+), 29 deletions(-)

diff --git a/files/galaxy/config/datatypes_conf.xml b/files/galaxy/config/datatypes_conf.xml
index df59b8dfb..14266f14e 100644
--- a/files/galaxy/config/datatypes_conf.xml
+++ b/files/galaxy/config/datatypes_conf.xml
@@ -33,7 +33,7 @@
     <datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
+    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="A pairwise alignment format." description_url="https://genome.ucsc.edu/goldenPath/help/axt.html"/>
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
       <converter file="bam_to_bai.xml" target_datatype="bai"/>
@@ -225,9 +225,9 @@
       <display file="igv/interval_as_bed.xml" inherit="true"/>
     </datatype>
     <datatype extension="jellyfish" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" description="Jellyfish database files are k-mer counts in binary format with a readable head. They are operated on and converted to human-readable text through jellyfish commands." />
-    <datatype extension="ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
-    <datatype extension="hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
-    <datatype extension="prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="npy" type="galaxy.datatypes.binary:Numpy" description="Standard format for saving numpy arrays" display_in_upload="true" description_url="https://numpy.org/devdocs/reference/generated/numpy.lib.format.html"/>
 
     <!-- ISA data types -->
@@ -395,6 +395,7 @@
     <datatype extension="star" type="galaxy.datatypes.images:Star" display_in_upload="true" />
     <datatype extension="peff" type="galaxy.datatypes.proteomics:PEFF" display_in_upload="true" />
     <datatype extension="toml" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
+    <datatype extension="colab.tar" auto_compressed_types="gz" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <!-- FlowCytometry -->
     <datatype extension="fcs" type="galaxy.datatypes.flow:FCS" mimetype="application/octet-stream" display_in_upload="true" description="A FCS binary sequence file with a '.fcs' file extension." />
@@ -435,6 +436,8 @@
       <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
     </datatype>
+    <datatype extension="4dn_pairs" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true" description="The pairs format is a standard text format for pairs of genomic loci given as 1bp point positions" description_url="https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md#pairs-file"/>
+    <datatype extension="4dn_pairsam" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true" description="A simple tabular format to store the information on ligation junctions detected in sequences from Hi-C experiments." description_url="https://pairsamtools.readthedocs.io/en/latest/pairsam.html"/>
     <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf" display_in_upload="true"/>
     <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true">
       <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
@@ -947,10 +950,16 @@
     <!-- media datatypes -->
     <datatype extension="wav" type="galaxy.datatypes.media:Wav" display_in_upload="true" mimetype="audio/wav"/>
     <datatype extension="mp3" type="galaxy.datatypes.media:Mp3" display_in_upload="true" mimetype="audio/mp3"/>
+    <datatype extension="ogg" type="galaxy.datatypes.media:Ogg" display_in_upload="true" mimetype="audio/ogg"/>
+    <datatype extension="wma" type="galaxy.datatypes.media:Wma" display_in_upload="true" mimetype="audio/x-ms-wma"/>
     <datatype extension="mkv" type="galaxy.datatypes.media:Mkv" display_in_upload="true" mimetype="video/mkv"/>
     <datatype extension="mp4" type="galaxy.datatypes.media:Mp4" display_in_upload="true" mimetype="video/mp4"/>
     <datatype extension="flv" type="galaxy.datatypes.media:Flv" display_in_upload="true" mimetype="video/flv"/>
+    <datatype extension="webm" type="galaxy.datatypes.media:Webm" display_in_upload="true" mimetype="video/webm"/>
     <datatype extension="mpg" type="galaxy.datatypes.media:Mpg" display_in_upload="true" mimetype="video/mpeg"/>
+    <datatype extension="mov" type="galaxy.datatypes.media:Mov" display_in_upload="true" mimetype="video/quicktime"/>
+    <datatype extension="avi" type="galaxy.datatypes.media:Avi" display_in_upload="true" mimetype="video/x-msvideo"/>
+    <datatype extension="wmv" type="galaxy.datatypes.media:Wmv" display_in_upload="true" mimetype="video/x-ms-wmv"/>
     <!-- speech datatypes -->
     <datatype extension="textgrid" type="galaxy.datatypes.speech:TextGrid" display_in_upload="true" mimetype="text/plain"/>
     <datatype extension="par" type="galaxy.datatypes.speech:BPF" display_in_upload="true" mimetype="text/plain-bas"/>
@@ -1004,7 +1013,8 @@
     <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true" description="geospatial vector data format for geographic information system"/>
     <!-- Flexible Image Transport System (FITS) used in Astronomy https://fits.gsfc.nasa.gov/ https://fits.gsfc.nasa.gov/rfc4047.txt -->
     <datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
-    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true"/>
+    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
+    <datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
   </registration>
   <sniffers>
     <!--
@@ -1100,7 +1110,7 @@
     <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
     <sniffer type="galaxy.datatypes.binary:Xlsx"/>
-    <sniffer type="galaxy.datatypes.binary:Numpy"/>    
+    <sniffer type="galaxy.datatypes.binary:Numpy"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
@@ -1109,6 +1119,7 @@
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.chain:Chain"/>
+    <sniffer type="galaxy.datatypes.chain:Net"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>
     <sniffer type="galaxy.datatypes.images:Gifti" />
@@ -1261,7 +1272,14 @@
     <sniffer type="galaxy.datatypes.media:Mp3"/>
     <sniffer type="galaxy.datatypes.media:Mp4"/>
     <sniffer type="galaxy.datatypes.media:Flv"/>
+    <sniffer type="galaxy.datatypes.media:Ogg"/>
     <sniffer type="galaxy.datatypes.media:Mpg"/>
+    <sniffer type="galaxy.datatypes.media:Mov"/>
+    <sniffer type="galaxy.datatypes.media:Avi"/>
+    <sniffer type="galaxy.datatypes.media:Wmv"/>
+    <sniffer type="galaxy.datatypes.media:Wma"/>
+    <sniffer type="galaxy.datatypes.media:Webm"/>
+    <sniffer type="galaxy.datatypes.media:Mkv"/>
     <sniffer type="galaxy.datatypes.speech:TextGrid" />
     <sniffer type="galaxy.datatypes.speech:BPF" />
     <sniffer type="galaxy.datatypes.larch:FEFFInput" />
diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml
index d06d4f6e9..d2794ef4e 100644
--- a/group_vars/gxconfig.yml
+++ b/group_vars/gxconfig.yml
@@ -360,6 +360,54 @@ base_app_main: &BASE_APP_MAIN
   # FileSource plugins described embedded into Galaxy's config.
   #file_sources: null
 
+  # Configured Object Store templates configuration file.
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #object_store_templates_config_file: object_store_templates.yml
+
+  # Configured Object Store templates embedded into Galaxy's config.
+  #object_store_templates: null
+
+  # Configured user file source templates configuration file.
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #file_source_templates_config_file: file_source_templates.yml
+
+  # Configured user file source templates embedded into Galaxy's config.
+  #file_source_templates: null
+
+  # Configure URIs for user object stores to use either the object ID
+  # ('id') or UUIDs ('uuid'). Either is fine really, Galaxy doesn't
+  # typically expose database objects by 'id' but there isn't any
+  # obvious disadvantage to doing it in this case and it keeps user
+  # exposed URIs much smaller. The default of UUID feels a little more
+  # like a typical way to do this within Galaxy though. Do not change
+  # this value once user object stores have been created.
+  #user_config_templates_index_by: uuid
+
+  # User defined object stores and file sources are saved in the
+  # database with their last valid configuration. It may be the case
+  # that the admin changes file source and object store templates over
+  # time such that the variables and secrets an instance is saved with
+  # no longer match the configuration's expected values. For this
+  # reason, admins should always add new versions of templates instead
+  # of just changing them - however people take shortcuts and
+  # divergences might happen. If a template is changed in such a way it
+  # breaks or if a template disappears from the library of templates
+  # this parameter controls how and if the database version will be
+  # used.
+  # By default, it will simply be used as a 'fallback' if a
+  # configuration cannot be resolved against the template version in the
+  # configuration file. Using 'preferred' instead will mean the stored
+  # database version is always used. This ensures a greater degree of
+  # reproducibility without effort on the part of the admin but also
+  # means that small issues are not easy to fix. Using 'never' instead
+  # will ensure the config templates are always only loaded from the
+  # template library files - this might make sense for admins who want
+  # to disable templates without worrying about the contents of the
+  # database.
+  #user_config_templates_use_saved_configuration: fallback
+
   # Enable Galaxy to fetch containers registered with quay.io generated
   # from tool requirements resolved through Conda. These containers
   # (when available) have been generated using mulled -
@@ -687,7 +735,7 @@ base_app_main: &BASE_APP_MAIN
   # This option has no effect if the file specified by
   # object_store_config_file exists. Otherwise, if this option is set,
   # it overrides any other objectstore settings.
-  # The syntax, available instrumenters, and documentation of their
+  # The syntax, available storage plugins, and documentation of their
   # options is explained in detail in the object store sample
   # configuration file, `object_store_conf.sample.yml`
   #object_store_config: null
@@ -724,6 +772,13 @@ base_app_main: &BASE_APP_MAIN
   # for that object store entry.
   #object_store_cache_size: -1
 
+  # Set this to true to indicate in the UI that a user's object store
+  # selection isn't simply a "preference" that job destinations often
+  # respect but in fact will always be respected. This should be set to
+  # true to simplify the UI as long as job destinations never override
+  # 'object_store_id's for a jobs.
+  #object_store_always_respect_user_selection: false
+
   # What Dataset attribute is used to reference files in an ObjectStore
   # implementation, this can be 'uuid' or 'id'. The default will depend
   # on how the object store is configured, starting with 20.05 Galaxy
@@ -931,7 +986,7 @@ base_app_main: &BASE_APP_MAIN
   # defaults to "GLOBAL" if not set or the
   # `geographical_server_location_code` value is invalid or unsupported.
   # To see a full list of supported locations, visit
-  # https://galaxyproject.org/admin/carbon_emissions
+  # https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html
   #geographical_server_location_code: GLOBAL
 
   # The estimated power usage effectiveness of the data centre housing
@@ -1045,7 +1100,7 @@ base_app_main: &BASE_APP_MAIN
   # Allow import of workflows from the TRS servers configured in the
   # specified YAML or JSON file. The file should be a list with 'id',
   # 'label', and 'api_url' for each entry. Optionally, 'link_url' and
-  # 'doc' may be be specified as well for each entry.
+  # 'doc' may 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
@@ -1130,7 +1185,7 @@ base_app_main: &BASE_APP_MAIN
   # via a proxy server.  These options should be self explanatory and so
   # are not documented individually.  You can use these paths (or ones
   # in the proxy server) to point to your own styles.
-  static_enabled: true
+  #static_enabled: true
 
   # Serve static content, which must be enabled if you're not serving it
   # via a proxy server.  These options should be self explanatory and so
@@ -1241,10 +1296,15 @@ base_app_main: &BASE_APP_MAIN
   nginx_upload_job_files_path: "/_job_files"
 
   # The upload store is a temporary directory in which files uploaded by
-  # the tus middleware or server will be placed. Defaults to
-  # new_file_path if not set.
+  # the tus middleware or server for user uploads will be placed.
+  # Defaults to new_file_path if not set.
   tus_upload_store: "/data/jwd04/tus_upload/main"
 
+  # The upload store is a temporary directory in which files uploaded by
+  # the tus middleware or server for remote job files (Pulsar) will be
+  # placed. Defaults to tus_upload_store if not set.
+  #tus_upload_store_job_files: null
+
   # Galaxy can upload user files in chunks without using nginx. Enable
   # the chunk uploader by specifying a chunk size larger than 0. The
   # chunk size is specified in bytes (default: 10MB).
@@ -1426,6 +1486,10 @@ base_app_main: &BASE_APP_MAIN
   # job is complete.
   #debug: false
 
+  # Log request start as well as request end. Disables uvicorn access
+  # log handler.
+  #use_access_logging_middleware: false
+
   # Check for WSGI compliance.
   #use_lint: false
 
@@ -1448,12 +1512,12 @@ base_app_main: &BASE_APP_MAIN
   # Write thread status periodically to 'heartbeat.log',  (careful, uses
   # disk space rapidly!).  Useful to determine why your processes may be
   # consuming a lot of CPU.
-  use_heartbeat: true
+  #use_heartbeat: false
 
   # Control the period (in seconds) between dumps. Use -1 to disable.
   # Regardless of this setting, if use_heartbeat is enabled, you can
   # send a Galaxy process SIGUSR1 (`kill -USR1`) to force a dump.
-  heartbeat_interval: -1
+  #heartbeat_interval: 20
 
   # Heartbeat log filename. Can accept the template variables
   # {server_name} and {pid}
@@ -1883,12 +1947,13 @@ base_app_main: &BASE_APP_MAIN
   # <config_dir>.
   oidc_backends_config_file: "{{ galaxy_config_dir }}/oidc_backends_config.xml"
 
-  # Sets the prefix for OIDC scopes specific to this Galaxy instance.
-  # If an API call is made against this Galaxy instance using an OIDC bearer token,
-  # any scopes must be prefixed with this value e.g. https://galaxyproject.org/api.
-  # More concretely, to request all permissions that the user has, the scope
-  # would have to be specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
-  # Currently, only * is recognised as a valid scope, and future iterations may
+  # Sets the prefix for OIDC scopes specific to this Galaxy instance. If
+  # an API call is made against this Galaxy instance using an OIDC
+  # bearer token, any scopes must be prefixed with this value e.g.
+  # https://galaxyproject.org/api. More concretely, to request all
+  # permissions that the user has, the scope would have to be specified
+  # as "<prefix>:*". e.g "https://galaxyproject.org/api:*". Currently,
+  # only * is recognised as a valid scope, and future iterations may
   # provide more fine-grained scopes.
   #oidc_scope_prefix: https://galaxyproject.org/api
 
@@ -2038,7 +2103,7 @@ base_app_main: &BASE_APP_MAIN
   # with Galaxy there you can enable this option.
   enable_tool_source_display: true
 
-  # XML config file that contains the job metric collection
+  # YAML or XML config file that contains the job metric collection
   # configuration.
   # The value of this option will be resolved with respect to
   # <config_dir>.
@@ -2444,19 +2509,33 @@ base_app_main: &BASE_APP_MAIN
   amqp_internal_connection: "pyamqp://galaxy:{{ rabbitmq_password_galaxy }}@mq.galaxyproject.eu:5671/galaxy?ssl=1"
   #amqp_internal_connection: "amqp://galaxy:{{ rabbitmq_password_galaxy }}@localhost:5672/galaxy"
 
+  # Offload long-running tasks to a Celery task queue. Activate this
+  # only if you have setup a Celery worker for Galaxy and you have
+  # configured the `celery_conf` option below. Specifically, you need to
+  # set the `result_backend` option in the `celery_conf` option to a
+  # valid Celery result backend URL. By default, Galaxy uses an SQLite
+  # database at '<data_dir>/results.sqlite' for storing task results.
+  # For details, see
+  # https://docs.galaxyproject.org/en/master/admin/production.html#use-celery-for-asynchronous-tasks
+  enable_celery_tasks: true
+
   # Configuration options passed to Celery.
   # To refer to a task by name, use the template `galaxy.foo` where
   # `foo` is the function name of the task defined in the
   # galaxy.celery.tasks module.
-  # The `broker_url` option, if unset, defaults to the value of
-  # `amqp_internal_connection`. The `result_backend` option must be set
-  # if the `enable_celery_tasks` option is set.
+  # The `broker_url` option, if unset or null, defaults to the value of
+  # `amqp_internal_connection`. The `result_backend` option, if unset or
+  # null, defaults to an SQLite database at '<data_dir>/results.sqlite'
+  # for storing task results. Please use a more robust backend (e.g.
+  # Redis) for production setups.
   # The galaxy.fetch_data task can be disabled by setting its route to
   # "disabled": `galaxy.fetch_data: disabled`. (Other tasks cannot be
   # disabled on a per-task basis at this time.)
   # For details, see Celery documentation at
   # https://docs.celeryq.dev/en/stable/userguide/configuration.html.
   #celery_conf:
+  #  broker_url: null
+  #  result_backend: null
   #  task_routes:
   #    galaxy.fetch_data: galaxy.external
   #    galaxy.set_job_metadata: galaxy.external
@@ -2468,11 +2547,6 @@ base_app_main: &BASE_APP_MAIN
       # galaxy.fetch_data: galaxy.external
       galaxy.set_job_metadata: galaxy.external
 
-  # Offload long-running tasks to a Celery task queue. Activate this
-  # only if you have setup a Celery worker for Galaxy. For details, see
-  # https://docs.galaxyproject.org/en/master/admin/production.html
-  enable_celery_tasks: true
-
   # If set to a non-0 value, upper limit on number of tasks that can be
   # executed per user per second.
   #celery_user_rate_limit: 0.0
@@ -2596,6 +2670,10 @@ base_app_main: &BASE_APP_MAIN
   # a Celery task.
   #expired_notifications_cleanup_interval: 86400
 
+  # The interval in seconds between attempts to dispatch notifications
+  # to users (every 10 minutes by default). Runs in a Celery task.
+  #dispatch_notifications_interval: 600
+
   # The URL pointing to the Galaxy Help Forum API base URL. The API must
   # be compatible with Discourse API (https://docs.discourse.org/).
   #help_forum_api_url: https://help.galaxyproject.org/
diff --git a/templates/galaxy/config/tool_conf.xml.j2 b/templates/galaxy/config/tool_conf.xml.j2
index d7716e47e..bd0689179 100644
--- a/templates/galaxy/config/tool_conf.xml.j2
+++ b/templates/galaxy/config/tool_conf.xml.j2
@@ -10,6 +10,7 @@
     <tool file="/opt/galaxy/custom-tools/test/lftp.xml" />
     <tool file="data_source/ebi_sra.xml" />
     <tool file="data_source/sra.xml" />
+    <tool file="data_source/ebi_sra.xml" />
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/biomart_test.xml" />
@@ -49,6 +50,8 @@
     <tool file="${model_tools_path}/filter_from_file.xml" />
     <tool file="${model_tools_path}/sort_collection_list.xml" />
     <tool file="${model_tools_path}/harmonize_two_collections_list.xml" />
+    <tool file="${model_tools_path}/cross_product_flat.xml" />
+    <tool file="${model_tools_path}/cross_product_nested.xml" />
     <tool file="${model_tools_path}/tag_collection_from_file.xml" />
     <tool file="${model_tools_path}/apply_rules.xml" />
     <tool file="${model_tools_path}/build_list.xml" />

From ba2adab1fd3c2189d9a3026f4616cde86d5b05cd Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Tue, 4 Jun 2024 22:07:06 +0200
Subject: [PATCH 2/6] add file_source_template config file

---
 files/galaxy/config/file_source_templates.yml | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 files/galaxy/config/file_source_templates.yml

diff --git a/files/galaxy/config/file_source_templates.yml b/files/galaxy/config/file_source_templates.yml
new file mode 100644
index 000000000..7d725e8ac
--- /dev/null
+++ b/files/galaxy/config/file_source_templates.yml
@@ -0,0 +1,5 @@
+- include: ./lib/galaxy/files/templates/examples/production_azure.yml
+- include: ./lib/galaxy/files/templates/examples/production_ftp.yml
+- include: ./lib/galaxy/files/templates/examples/production_s3fs.yml
+- include: ./lib/galaxy/files/templates/examples/production_aws_private_bucket.yml
+- include: ./lib/galaxy/files/templates/examples/production_aws_public_bucket.yml

From bb01c94ca30589914217ea6cfb6941bdce6273fc Mon Sep 17 00:00:00 2001
From: Sanjay Kumar Srikakulam <sanjaysrikakulam@gmail.com>
Date: Fri, 5 Jul 2024 07:04:59 +0000
Subject: [PATCH 3/6] Add templates for object store and file sources, update
 playbook, and galaxy conf accordingly

---
 bin/diff-before-update                        | 16 +++
 files/galaxy/config/file_source_templates.yml |  5 -
 .../production_aws_private_bucket.yml         | 31 ++++++
 .../production_aws_public_bucket.yml          | 16 +++
 .../production_azure.yml                      | 44 +++++++++
 .../file_source_templates/production_ftp.yml  | 39 ++++++++
 .../file_source_templates/production_s3fs.yml | 57 +++++++++++
 .../production_aws_s3.yml                     | 35 +++++++
 .../production_aws_s3_legacy.yml              | 36 +++++++
 .../production_azure_blob.yml                 | 31 ++++++
 .../production_gcp_s3.yml                     | 41 ++++++++
 .../production_generic_s3.yml                 | 61 ++++++++++++
 .../production_generic_s3_legacy.yml          | 97 +++++++++++++++++++
 group_vars/gxconfig.yml                       |  4 +-
 group_vars/sn06.yml                           | 30 ++++++
 .../config/file_source_templates.yml.j2       |  5 +
 .../config/object_store_templates.yml.j2      |  6 ++
 17 files changed, 547 insertions(+), 7 deletions(-)
 delete mode 100644 files/galaxy/config/file_source_templates.yml
 create mode 100644 files/galaxy/config/file_source_templates/production_aws_private_bucket.yml
 create mode 100644 files/galaxy/config/file_source_templates/production_aws_public_bucket.yml
 create mode 100644 files/galaxy/config/file_source_templates/production_azure.yml
 create mode 100644 files/galaxy/config/file_source_templates/production_ftp.yml
 create mode 100644 files/galaxy/config/file_source_templates/production_s3fs.yml
 create mode 100644 files/galaxy/config/object_store_templates/production_aws_s3.yml
 create mode 100644 files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml
 create mode 100644 files/galaxy/config/object_store_templates/production_azure_blob.yml
 create mode 100644 files/galaxy/config/object_store_templates/production_gcp_s3.yml
 create mode 100644 files/galaxy/config/object_store_templates/production_generic_s3.yml
 create mode 100644 files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml
 create mode 100644 templates/galaxy/config/file_source_templates.yml.j2
 create mode 100644 templates/galaxy/config/object_store_templates.yml.j2

diff --git a/bin/diff-before-update b/bin/diff-before-update
index f62904b5e..37ab31674 100755
--- a/bin/diff-before-update
+++ b/bin/diff-before-update
@@ -51,3 +51,19 @@ compare files/$folder/config/user_preferences_extra_conf.yml	$GALAXY/config/user
 #compare templates/$folder/config/build_sites.yml.j2	$GALAXY/config/build_sites.yml.sample.sample
 
 compare group_vars/gxconfig${ext}.yml	$GALAXY/config/galaxy.yml.sample
+
+# Compare file source templates
+compare files/$folder/config/file_source_templates/production_aws_private_bucket.yml	$GALAXY/files/templates/examples/production_aws_private_bucket.yml
+compare files/$folder/config/file_source_templates/production_aws_public_bucket.yml	$GALAXY/files/templates/examples/production_aws_public_bucket.yml
+compare files/$folder/config/file_source_templates/production_azure.yml	$GALAXY/files/templates/examples/production_azure.yml
+compare files/$folder/config/file_source_templates/production_ftp.yml	$GALAXY/files/templates/examples/production_ftp.yml
+compare files/$folder/config/file_source_templates/production_s3fs.yml	$GALAXY/files/templates/examples/production_s3fs.yml
+
+# Compare object store templates
+compare files/$folder/config/object_store_templates/production_aws_s3_legacy.yml	$GALAXY/objectstore/templates/examples/production_aws_s3_legacy.yml
+compare files/$folder/config/object_store_templates/production_aws_s3.yml	$GALAXY/objectstore/templates/examples/production_aws_s3.yml
+compare files/$folder/config/object_store_templates/production_azure_blob.yml	$GALAXY/objectstore/templates/examples/production_azure_blob.yml
+compare files/$folder/config/object_store_templates/production_gcp_s3.yml	$GALAXY/objectstore/templates/examples/production_gcp_s3.yml
+compare files/$folder/config/object_store_templates/production_generic_s3_legacy.yml	$GALAXY/objectstore/templates/examples/production_generic_s3_legacy.yml
+compare files/$folder/config/object_store_templates/production_generic_s3.yml	$GALAXY/objectstore/templates/examples/production_generic_s3.yml
+compare files/$folder/config/object_store_templates/minio_example.yml	$GALAXY/objectstore/templates/examples/minio_example.yml
diff --git a/files/galaxy/config/file_source_templates.yml b/files/galaxy/config/file_source_templates.yml
deleted file mode 100644
index 7d725e8ac..000000000
--- a/files/galaxy/config/file_source_templates.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-- include: ./lib/galaxy/files/templates/examples/production_azure.yml
-- include: ./lib/galaxy/files/templates/examples/production_ftp.yml
-- include: ./lib/galaxy/files/templates/examples/production_s3fs.yml
-- include: ./lib/galaxy/files/templates/examples/production_aws_private_bucket.yml
-- include: ./lib/galaxy/files/templates/examples/production_aws_public_bucket.yml
diff --git a/files/galaxy/config/file_source_templates/production_aws_private_bucket.yml b/files/galaxy/config/file_source_templates/production_aws_private_bucket.yml
new file mode 100644
index 000000000..2770bfa1f
--- /dev/null
+++ b/files/galaxy/config/file_source_templates/production_aws_private_bucket.yml
@@ -0,0 +1,31 @@
+- id: aws_private
+  version: 0
+  name: Amazon Web Services Private Bucket
+  description: Setup access to a private AWS bucket using a secret access key.
+  configuration:
+    type: s3fs
+    bucket: '{{ bucket }}'
+    writable: '{{ writable }}'
+    secret: '{{ secret_key }}'
+    key: '{{ access_key }}'
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        The "access key ID" as defined in the [Amazon Documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html).
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [Amazon Web Services Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        access. This should be a bucket the user described by the Access Key ID has access to.
+    writable:
+      label: Writable?
+      type: boolean
+      help: Is this a bucket you have permission to write to?
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        The "secret access key" as defined in the [Amazon Documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html).
diff --git a/files/galaxy/config/file_source_templates/production_aws_public_bucket.yml b/files/galaxy/config/file_source_templates/production_aws_public_bucket.yml
new file mode 100644
index 000000000..fc55847ba
--- /dev/null
+++ b/files/galaxy/config/file_source_templates/production_aws_public_bucket.yml
@@ -0,0 +1,16 @@
+- id: aws_public
+  version: 0
+  name: Amazon Web Services Public Bucket
+  description: Setup anonymous access to a public AWS bucket.
+  configuration:
+    type: s3fs
+    bucket: '{{ variables.bucket }}'
+    writable: false
+    anon: true
+  variables:
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [Amazon Web Services Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        anonymously access.
diff --git a/files/galaxy/config/file_source_templates/production_azure.yml b/files/galaxy/config/file_source_templates/production_azure.yml
new file mode 100644
index 000000000..81437b91b
--- /dev/null
+++ b/files/galaxy/config/file_source_templates/production_azure.yml
@@ -0,0 +1,44 @@
+- id: azure
+  version: 0
+  name: Azure Blob Storage
+  description: |
+    This template allows connecting to [Azure Blob Storage](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction).
+  configuration:
+    type: azure
+    container_name: '{{ variables.container_name }}'
+    account_name: '{{ variables.account_name }}'
+    account_key: '{{ secrets.account_key }}'
+    namespace_type: "{{ 'hierarchical' if variables.hierarchical else 'flat' }}"
+    writable: '{{ variables.writable }}'
+  variables:
+    container_name:
+      label: Container Name
+      type: string
+      help: |
+        The name of your Azure Blob Storage container. More information on containers can be found
+        in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction#containers).
+    account_name:
+      label: Storage Account Name
+      type: string
+      help: |
+        The name of your Azure Blob Storage account. More information on containers can be found in the
+        [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-overview).
+    hierarchical:
+      label: Hierarchical?
+      type: boolean
+      default: true
+      help: |
+        Is this storage hierarchical (e.g. does it use a Azure Data Lake Storage Gen2 hierarchical namespace)?
+        More information on Data Lake Storage namespaces can be found in the
+        [Azure Blob Storage documentation](https://learn.microsoft.com/en-us/azure/storage/blobs/data-lake-storage-namespace).
+    writable:
+      label: Writable?
+      type: boolean
+      default: true
+      help: Allow Galaxy to write data to this Azure Blob Storage container.
+  secrets:
+    account_key:
+      label: Account Key
+      help: |
+        The Azure Blob Storage account key to use to access your Azure Blob Storage data. More information
+        on account keys can be found in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-keys-manage).
diff --git a/files/galaxy/config/file_source_templates/production_ftp.yml b/files/galaxy/config/file_source_templates/production_ftp.yml
new file mode 100644
index 000000000..04e334718
--- /dev/null
+++ b/files/galaxy/config/file_source_templates/production_ftp.yml
@@ -0,0 +1,39 @@
+- id: ftp
+  version: 0
+  name: An FTP Server
+  description: |
+    This template allows connecting to FTP servers. This file source plugin should
+    support FTP and FTPS servers.
+  configuration:
+    type: ftp
+    host: '{{ variables.host }}'
+    user: '{{ variables.user }}'
+    port: '{{ variables.port }}'
+    passwd: '{{ secrets.password }}'
+    writable: '{{ variables.writable }}'
+  variables:
+    host:
+      label: FTP Host
+      type: string
+      help: Host of FTP Server to connect to.
+    user:
+      label: FTP User
+      type: string
+      help: |
+        Username to connect with. Leave this blank to connect to the server
+        anonymously (if allowed by target server).
+    writable:
+      label: Writable?
+      type: boolean
+      help: Is this an FTP server you have permission to write to?
+    port:
+      label: FTP Port
+      type: integer
+      help: Port used to connect to the FTP server.
+      default: 21
+  secrets:
+    password:
+      label: FTP Password
+      help: |
+        Password to connect to FTP server with. Leave this blank to connect
+        to the server anonymously (if allowed by target server).
diff --git a/files/galaxy/config/file_source_templates/production_s3fs.yml b/files/galaxy/config/file_source_templates/production_s3fs.yml
new file mode 100644
index 000000000..dbe1c2323
--- /dev/null
+++ b/files/galaxy/config/file_source_templates/production_s3fs.yml
@@ -0,0 +1,57 @@
+- id: s3fs
+  version: 0
+  name: S3 Compatible Storage with Credentials
+  description: |
+    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
+    of an unofficial standard for cloud storage across a variety of vendors and services.
+    Many vendors offer storage APIs compatible with S3. This template configuration allows
+    using such service as a Galaxy storage location as long as you are able to find the
+    connection details and have the relevant credentials.
+
+    Given the amount of information needed to connect to such a service, this is a bit of an
+    advanced template and probably should not be used to connect to a service if a more
+    specific template is available.
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        The less secure part of your access tokens or access keys that describe the user
+        that is accessing the data. The [Amazon documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/security-creds.html)
+        calls these an "access key ID", the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_access_key_id``.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        store your datasets in. How to setup buckets for your storage will vary from service to service
+        but all S3 compatible storage services should have the concept of a bucket to namespace
+        a grouping of your data together with.
+    endpoint_url:
+      label: S3-Compatible API Endpoint
+      type: string
+      help: |
+        If the documentation for your storage service has something called an ``endpoint_url``,
+        For instance, the CloudFlare documentation describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
+        you would substitute your CloudFlare account ID into the endpoint url and use that value.
+        So if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
+        The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
+        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``,
+        this value would be entered here.
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        The secret key used to connect to the S3 compatible storage with for the given access key.
+
+        The [Amazon documentation] calls these an "secret access key" and
+        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
+        this the ``secret_key``.
+  configuration:
+    type: s3fs
+    endpoint_url: '{{ variables.endpoint_url }}'
+    key: '{{ variables.access_key }}'
+    secret: '{{ secrets.secret_key }}'
+    bucket: '{{ variables.bucket }}'
diff --git a/files/galaxy/config/object_store_templates/production_aws_s3.yml b/files/galaxy/config/object_store_templates/production_aws_s3.yml
new file mode 100644
index 000000000..c87026d10
--- /dev/null
+++ b/files/galaxy/config/object_store_templates/production_aws_s3.yml
@@ -0,0 +1,35 @@
+- id: aws_s3
+  version: 0
+  name: Amazon Web Services S3 Storage
+  description: |
+    Amazon's Simple Storage Service (S3) is Amazon's primary cloud storage service.
+    More information on S3 can be found in [Amazon's documentation](https://aws.amazon.com/s3/).
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        A security credential for interacting with AWS services can be created from your
+        AWS web console. Creating an "Access Key" creates a pair of keys used to identify
+        and authenticate access to your AWS account - the first part of the pair  is
+        "Access Key ID" and should be entered here. The second part of your key is the secret
+        part called the "Secret Access Key". Place that in the secure part of this form below.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [AWS S3 Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        store your datasets in. You will need to create a bucket to use in your AWS web console before
+        using this form.
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        See the documentation above used "Access Key ID" for information about access key pairs.
+  configuration:
+    type: boto3
+    auth:
+      access_key: '{{ variables.access_key }}'
+      secret_key: '{{ secrets.secret_key }}'
+    bucket:
+      name: '{{ variables.bucket }}'
diff --git a/files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml b/files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml
new file mode 100644
index 000000000..1a3730897
--- /dev/null
+++ b/files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml
@@ -0,0 +1,36 @@
+- id: aws_s3_legacy
+  version: 0
+  name: Amazon Web Services S3 Storage (Legacy)
+  description: |
+    Amazon's Simple Storage Service (S3) is Amazon's primary cloud storage service.
+    More information on S3 can be found in [Amazon's documentation](https://aws.amazon.com/s3/).
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        A security credential for interacting with AWS services can be created from your
+        AWS web console. Creating an "Access Key" creates a pair of keys used to identify
+        and authenticate access to your AWS account - the first part of the pair  is
+        "Access Key ID" and should be entered here. The second part of your key is the secret
+        part called the "Secret Access Key". Place that in the secure part of this form below.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [AWS S3 Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        store your datasets in. You will need to create a bucket to use in your AWS web console before
+        using this form.
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        See the documentation above used "Access Key ID" for information about access key pairs.
+
+  configuration:
+    type: aws_s3
+    auth:
+      access_key: '{{ variables.access_key }}'
+      secret_key: '{{ secrets.secret_key }}'
+    bucket:
+      name: '{{ variables.bucket }}'
diff --git a/files/galaxy/config/object_store_templates/production_azure_blob.yml b/files/galaxy/config/object_store_templates/production_azure_blob.yml
new file mode 100644
index 000000000..ee57eaf74
--- /dev/null
+++ b/files/galaxy/config/object_store_templates/production_azure_blob.yml
@@ -0,0 +1,31 @@
+- id: azure
+  version: 0
+  name: Azure Blob Storage
+  description: |
+    This template allows storing dataset in [Azure Blob Storage](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction).
+  configuration:
+    type: azure_blob
+    auth:
+      account_name: '{{ variables.account_name }}'
+      account_key: '{{ secrets.account_key}}'
+    container:
+      name: '{{ variables.container_name }}'
+  variables:
+    container_name:
+      label: Container Name
+      type: string
+      help: |
+        The name of your Azure Blob Storage container. More information on containers can be found
+        in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction#containers).
+    account_name:
+      label: Storage Account Name
+      type: string
+      help: |
+        The name of your Azure Blob Storage account. More information on containers can be found in the
+        [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-overview).
+  secrets:
+    account_key:
+      label: Account Key
+      help: |
+        The Azure Blob Storage account key to use to access your Azure Blob Storage data. More information
+        on account keys can be found in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-keys-manage).
diff --git a/files/galaxy/config/object_store_templates/production_gcp_s3.yml b/files/galaxy/config/object_store_templates/production_gcp_s3.yml
new file mode 100644
index 000000000..95a14a634
--- /dev/null
+++ b/files/galaxy/config/object_store_templates/production_gcp_s3.yml
@@ -0,0 +1,41 @@
+# https://cloud.google.com/storage/docs/aws-simple-migration
+- id: gcp_s3_interop
+  version: 0
+  name: Google Cloud Storage
+  description: |
+    This template can be used to connect to your [Google Cloud Storage](https://cloud.google.com/storage).
+    To use these templates you will need to generate
+    [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys) - these
+    can be linked to your user or a service account. Additionally, you will need to defined
+    a [default Google cloud project](https://cloud.google.com/storage/docs/aws-simple-migration#defaultproj)
+    to allow Galaxy to access your Google Cloud Storage via the interfaces
+    described by this template.
+  variables:
+    access_key:
+      label: Access ID
+      type: string
+      help: |
+        This will be given to you by Google when you generate [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys)
+        to use your storage.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The name of a [bucket](https://cloud.google.com/storage/docs/buckets) you've created to store your Galaxy data. Documentation for how to create buckets
+        can be found in [this part of the Google Cloud Storage documentation](https://cloud.google.com/storage/docs/creating-buckets).
+  secrets:
+    secret_key:
+      label: Secret Key
+      help: |
+        This will be given to you by Google when you generate [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys)
+        to use your storage. It should be 40 characters long and look something like the example used
+        the Google documentation - `bGoa+V7g/yqDXvKRqq+JTFn4uQZbPiQJo4pf9RzJ`.
+  configuration:
+    type: boto3
+    auth:
+      access_key: '{{ variables.access_key }}'
+      secret_key: '{{ secrets.secret_key }}'
+    bucket:
+      name: '{{ variables.bucket }}'
+    connection:
+      endpoint_url: 'https://storage.googleapis.com/'
diff --git a/files/galaxy/config/object_store_templates/production_generic_s3.yml b/files/galaxy/config/object_store_templates/production_generic_s3.yml
new file mode 100644
index 000000000..8a9c02e37
--- /dev/null
+++ b/files/galaxy/config/object_store_templates/production_generic_s3.yml
@@ -0,0 +1,61 @@
+- id: generic_s3
+  version: 0
+  name: Any S3 Compatible Storage
+  description: |
+    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
+    of an unofficial standard for cloud storage across a variety of vendors and services.
+    Many vendors offer storage APIs compatible with S3 - Galaxy calls these ``generic_s3``
+    storage locations. This template configuration allows using such service as a Galaxy storage
+    location as long as you are able to find the connection details and have the relevant credentials.
+
+    Given the amount of information needed to connect to such a service, this is a bit of an
+    advanced template and probably should not be used to connect to a service if a more
+    specific template is available.
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        The less secure part of your access tokens or access keys that describe the user
+        that is accessing the data. The [Amazon documentation] calls these an "access key ID",
+        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_access_key_id``. Internally to Galaxy, we often just call
+        this the ``access_key``.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        store your datasets in. How to setup buckets for your storage will vary from service to service
+        but all S3 compatible storage services should have the concept of a bucket to namespace
+        a grouping of your data together with.
+    endpoint_url:
+      label: S3-Compatible API Endpoint
+      type: string
+      help: |
+        If the documentation for your storage service has something called an ``endpoint_url``,
+        For instance, the CloudFlare documentation describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
+        you would substitute your CloudFlare account ID into the endpoint url and use that value.
+        So if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
+        The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
+        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``,
+        this whole value would be entered here.
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        The secret key used to connect to the S3 compatible storage with for the given access key.
+
+        The [Amazon documentation] calls these an "secret access key" and
+        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
+        this the ``secret_key``.
+  configuration:
+    type: boto3
+    auth:
+      access_key: '{{ variables.access_key }}'
+      secret_key: '{{ secrets.secret_key }}'
+    bucket:
+      name: '{{ variables.bucket }}'
+    connection:
+      endpoint_url: '{{ variables.endpoint_url }}'
diff --git a/files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml b/files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml
new file mode 100644
index 000000000..0894205b3
--- /dev/null
+++ b/files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml
@@ -0,0 +1,97 @@
+- id: generic_s3_legacy
+  version: 0
+  name: Any S3 Compatible Storage (Legacy)
+  description: |
+    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
+    of an unofficial standard for cloud storage across a variety of vendors and services.
+    Many vendors offer storage APIs compatible with S3 - Galaxy calls these ``generic_s3``
+    storage locations. This template configuration allows using such service as a Galaxy storage
+    location as long as you are able to find the connection details and have the relevant credentials.
+
+    Given the amount of information needed to connect to such a service, this is a bit of an
+    advanced template and probably should not be used to connect to a service if a more
+    specific template is available.
+  variables:
+    access_key:
+      label: Access Key ID
+      type: string
+      help: |
+        The less secure part of your access tokens or access keys that describe the user
+        that is accessing the data. The [Amazon documentation] calls these an "access key ID",
+        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_access_key_id``. Internally to Galaxy, we often just call
+        this the ``access_key``.
+    bucket:
+      label: Bucket
+      type: string
+      help: |
+        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
+        store your datasets in. How to setup buckets for your storage will vary from service to service
+        but all S3 compatible storage services should have the concept of a bucket to namespace
+        a grouping of your data together with.
+    host:
+      label: Connection Host
+      type: string
+      help: |
+        The [hostname](https://en.wikipedia.org/wiki/Hostname) used to connect to the target
+        S3 compatible service.
+
+        If the documentation for your storage service has something called an ``endpoint_url``,
+        this can be used to determine this value. For instance, the CloudFlare documentation
+        describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
+        you would substitute your CloudFlare account ID into the endpoint and shave off the ``https://``,
+        so if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
+    port:
+      label: Connection Port
+      type: integer
+      default: 443
+      help: |
+        The [port](https://en.wikipedia.org/wiki/Port_(computer_networking)) used to connect
+        to the target S3 compatible service. This might be ``443`` if you cannot find a relevant
+        port - this is the default for secure HTTP connections.
+
+        If the documentation for your storage service has something called an ``endpoint_url``,
+        this can be used to determine this value. The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
+        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``.
+        The ``:9000`` here indicates this port should be specified as ``9000``. Alternatively, the
+        CloudFlare documentation describes its endpoints ``https://<accountid>.r2.cloudflarestorage.com``.
+        Here there is no number at the end of the URL so the port is ``443`` as long the URL starts
+        with ``https``.
+    connection_path:
+      label: Connection Path
+      type: string
+      default: ""
+      help: |
+        This is an advanced configuration option and it is very likely best to just keep this empty
+        for most storage services. If specified, it will be the prefix in the URL for the S3 compatible
+        API after the host and port to reach the target API.
+    secure:
+      label: Use HTTPS?
+      type: boolean
+      default: true
+      help: |
+        This is an advanced configuration option and if this option is not checked, you should not assume
+        your data is secure at all. This should only ever be unchecked during testing new or experimental
+        services with data and keys you do not care about.
+  secrets:
+    secret_key:
+      label: Secret Access Key
+      help: |
+        The secret key used to connect to the S3 compatible storage with for the given access key.
+
+        The [Amazon documentation] calls these an "secret access key" and
+        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
+        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
+        this the ``secret_key``.
+  configuration:
+    type: generic_s3
+    auth:
+      access_key: '{{ variables.access_key }}'
+      secret_key: '{{ secrets.secret_key }}'
+    bucket:
+      name: '{{ variables.bucket }}'
+    connection:
+      host: '{{ variables.host }}'
+      port: '{{ variables.port  }}'
+      is_secure: '{{ variables.secure }}'
+      conn_path: '{{ variables.connection_path }}'
diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml
index 31b6709a0..4b46067c0 100644
--- a/group_vars/gxconfig.yml
+++ b/group_vars/gxconfig.yml
@@ -363,7 +363,7 @@ base_app_main: &BASE_APP_MAIN
   # Configured Object Store templates configuration file.
   # The value of this option will be resolved with respect to
   # <config_dir>.
-  #object_store_templates_config_file: object_store_templates.yml
+  object_store_templates_config_file: '{{ galaxy_config_dir }}/object_store_templates.yml'
 
   # Configured Object Store templates embedded into Galaxy's config.
   #object_store_templates: null
@@ -371,7 +371,7 @@ base_app_main: &BASE_APP_MAIN
   # Configured user file source templates configuration file.
   # The value of this option will be resolved with respect to
   # <config_dir>.
-  #file_source_templates_config_file: file_source_templates.yml
+  file_source_templates_config_file: '{{ galaxy_config_dir }}/file_source_templates.yml'
 
   # Configured user file source templates embedded into Galaxy's config.
   #file_source_templates: null
diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml
index 58de5f569..00b4fbd2b 100644
--- a/group_vars/sn06.yml
+++ b/group_vars/sn06.yml
@@ -292,6 +292,8 @@ galaxy_config_dir: "{{ galaxy_root }}/config"
 galaxy_venv_dir: "{{ galaxy_root }}/venv"
 galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}"
 ucsc_build_sites:
+galaxy_file_source_templates_dir: "{{ galaxy_mutable_config_dir }}/file_source_templates"
+galaxy_object_store_templates_dir: "{{ galaxy_mutable_config_dir }}/object_store_templates"
 
 galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies"
 #galaxy_virtualenv_python: "python3.6"
@@ -317,6 +319,8 @@ galaxy_dirs:
   - "{{ galaxy_log_dir }}"
   - "{{ galaxy_config_dir }}/total_perspective_vortex"
   - "{{ tpv_mutable_dir }}"
+  - "{{ galaxy_file_source_templates_dir }}"
+  - "{{ galaxy_object_store_templates_dir }}"
 
 galaxy_instance_hostname: usegalaxy.eu
 galaxy_config_style: yaml
@@ -421,6 +425,28 @@ galaxy_config_files:
     dest: "{{ tpv_mutable_dir }}/interactive_tools.yml"
   - src: "{{ galaxy_config_file_src_dir }}/tpv/users.yml"
     dest: "{{ tpv_mutable_dir }}/users.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_aws_private_bucket.yml"
+    dest: "{{ galaxy_file_source_templates_dir }}/production_aws_private_bucket.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_aws_public_bucket.yml"
+    dest: "{{ galaxy_file_source_templates_dir }}/production_aws_public_bucket.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_azure.yml"
+    dest: "{{ galaxy_file_source_templates_dir }}/production_azure.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_ftp.yml"
+    dest: "{{ galaxy_file_source_templates_dir }}/production_ftp.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_s3fs.yml"
+    dest: "{{ galaxy_file_source_templates_dir }}/production_s3fs.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_aws_s3_legacy.yml"
+    dest: "{{ galaxy_object_store_templates_dir }}/production_aws_s3_legacy.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_aws_s3.yml"
+    dest: "{{ galaxy_object_store_templates_dir }}/production_aws_s3.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_azure_blob.yml"
+    dest: "{{ galaxy_object_store_templates_dir }}/production_azure_blob.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_gcp_s3.yml"
+    dest: "{{ galaxy_object_store_templates_dir }}/production_gcp_s3.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_generic_s3_legacy.yml"
+    dest: "{{ galaxy_object_store_templates_dir }}/production_generic_s3_legacy.yml"
+  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_generic_s3.yml"
+    dest: "{{ galaxy_object_store_templates_dir }}/production_generic_s3.yml"
 
   #- src: files/galaxy/config/job_resource_params_conf.xml
   #dest: "{{ galaxy_config['app:main']['job_resource_params_file'] }}"
@@ -467,3 +493,7 @@ galaxy_config_templates:
     dest: "{{ tpv_mutable_dir }}/destinations.yml"
   - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2'
     dest: '{{ galaxy_config_dir }}/vault_conf.yml'
+  - src: "{{ galaxy_config_template_src_dir }}/config/file_source_templates.yml.j2"
+    dest: "{{ galaxy_config['galaxy']['file_source_templates_config_file'] }}"
+  - src: "{{ galaxy_config_template_src_dir }}/config/object_store_templates.yml.j2"
+    dest: "{{ galaxy_config['galaxy']['object_store_templates_config_file'] }}"
diff --git a/templates/galaxy/config/file_source_templates.yml.j2 b/templates/galaxy/config/file_source_templates.yml.j2
new file mode 100644
index 000000000..839a55db6
--- /dev/null
+++ b/templates/galaxy/config/file_source_templates.yml.j2
@@ -0,0 +1,5 @@
+- include: "{{ galaxy_file_source_templates_dir }}/production_azure.yml"
+- include: "{{ galaxy_file_source_templates_dir }}/production_ftp.yml"
+- include: "{{ galaxy_file_source_templates_dir }}/production_s3fs.yml"
+- include: "{{ galaxy_file_source_templates_dir }}/production_aws_private_bucket.yml"
+- include: "{{ galaxy_file_source_templates_dir }}/production_aws_public_bucket.yml"
diff --git a/templates/galaxy/config/object_store_templates.yml.j2 b/templates/galaxy/config/object_store_templates.yml.j2
new file mode 100644
index 000000000..c73ca87e1
--- /dev/null
+++ b/templates/galaxy/config/object_store_templates.yml.j2
@@ -0,0 +1,6 @@
+- include: "{{ galaxy_object_store_templates_dir }}/production_azure_blob.yml"
+- include: "{{ galaxy_object_store_templates_dir }}/production_aws_s3.yml"
+- include: "{{ galaxy_object_store_templates_dir }}/production_aws_s3_legacy.yml"
+- include: "{{ galaxy_object_store_templates_dir }}/production_generic_s3.yml"
+- include: "{{ galaxy_object_store_templates_dir }}/production_generic_s3_legacy.yml"
+- include: "{{ galaxy_object_store_templates_dir }}/production_gcp_s3.yml"

From 0b49201926c76bc24a96c2e157861b28b7bb5237 Mon Sep 17 00:00:00 2001
From: Sanjay Kumar Srikakulam <sanjaysrikakulam@gmail.com>
Date: Fri, 5 Jul 2024 08:47:48 +0000
Subject: [PATCH 4/6] Update galaxy commit id to 24.1 release

---
 group_vars/sn06.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml
index 00b4fbd2b..9c366b288 100644
--- a/group_vars/sn06.yml
+++ b/group_vars/sn06.yml
@@ -326,7 +326,7 @@ galaxy_instance_hostname: usegalaxy.eu
 galaxy_config_style: yaml
 
 galaxy_repo: "https://github.com/usegalaxy-eu/galaxy.git"
-galaxy_commit_id: "release_24.0_europe"
+galaxy_commit_id: "release_24.1_europe"
 galaxy_force_checkout: true # discard any modified files
 #galaxy_admin_email_from: 'noreply@usegalaxy.eu'
 

From 246db7260cef23247ae9dd24b949b76832a51bbc Mon Sep 17 00:00:00 2001
From: Sanjay Kumar Srikakulam <sanjaysrikakulam@gmail.com>
Date: Tue, 9 Jul 2024 11:55:07 +0000
Subject: [PATCH 5/6] Disable file source and object store config for now in
 24.1 rollout

---
 group_vars/gxconfig.yml | 4 ++--
 group_vars/sn06.yml     | 9 +++++----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml
index 4b46067c0..a7c975234 100644
--- a/group_vars/gxconfig.yml
+++ b/group_vars/gxconfig.yml
@@ -363,7 +363,7 @@ base_app_main: &BASE_APP_MAIN
   # Configured Object Store templates configuration file.
   # The value of this option will be resolved with respect to
   # <config_dir>.
-  object_store_templates_config_file: '{{ galaxy_config_dir }}/object_store_templates.yml'
+  # object_store_templates_config_file: '{{ galaxy_config_dir }}/object_store_templates.yml'
 
   # Configured Object Store templates embedded into Galaxy's config.
   #object_store_templates: null
@@ -371,7 +371,7 @@ base_app_main: &BASE_APP_MAIN
   # Configured user file source templates configuration file.
   # The value of this option will be resolved with respect to
   # <config_dir>.
-  file_source_templates_config_file: '{{ galaxy_config_dir }}/file_source_templates.yml'
+  # file_source_templates_config_file: '{{ galaxy_config_dir }}/file_source_templates.yml'
 
   # Configured user file source templates embedded into Galaxy's config.
   #file_source_templates: null
diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml
index 9c366b288..d71520753 100644
--- a/group_vars/sn06.yml
+++ b/group_vars/sn06.yml
@@ -493,7 +493,8 @@ galaxy_config_templates:
     dest: "{{ tpv_mutable_dir }}/destinations.yml"
   - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2'
     dest: '{{ galaxy_config_dir }}/vault_conf.yml'
-  - src: "{{ galaxy_config_template_src_dir }}/config/file_source_templates.yml.j2"
-    dest: "{{ galaxy_config['galaxy']['file_source_templates_config_file'] }}"
-  - src: "{{ galaxy_config_template_src_dir }}/config/object_store_templates.yml.j2"
-    dest: "{{ galaxy_config['galaxy']['object_store_templates_config_file'] }}"
+    # 9/7/24: Uncomment these when deploying object store and update the galaxy config
+  # - src: "{{ galaxy_config_template_src_dir }}/config/file_source_templates.yml.j2"
+  #   dest: "{{ galaxy_config['galaxy']['file_source_templates_config_file'] }}"
+  # - src: "{{ galaxy_config_template_src_dir }}/config/object_store_templates.yml.j2"
+  #   dest: "{{ galaxy_config['galaxy']['object_store_templates_config_file'] }}"

From 605cde481254eb640cba2430836a225e8982984c Mon Sep 17 00:00:00 2001
From: Sanjay Kumar Srikakulam <sanjaysrikakulam@gmail.com>
Date: Wed, 10 Jul 2024 14:30:31 +0000
Subject: [PATCH 6/6] Undo the commit bb01c94ca30589914217ea6cfb6941bdce6273fc

Removes all the user file sources and object store conf along with the catalog, templates and ansible copy stuff for now. This can be added when this feature is going to be rolled out.
---
 bin/diff-before-update                        | 16 ---
 .../production_aws_private_bucket.yml         | 31 ------
 .../production_aws_public_bucket.yml          | 16 ---
 .../production_azure.yml                      | 44 ---------
 .../file_source_templates/production_ftp.yml  | 39 --------
 .../file_source_templates/production_s3fs.yml | 57 -----------
 .../production_aws_s3.yml                     | 35 -------
 .../production_aws_s3_legacy.yml              | 36 -------
 .../production_azure_blob.yml                 | 31 ------
 .../production_gcp_s3.yml                     | 41 --------
 .../production_generic_s3.yml                 | 61 ------------
 .../production_generic_s3_legacy.yml          | 97 -------------------
 group_vars/gxconfig.yml                       |  4 +-
 group_vars/sn06.yml                           | 31 ------
 .../config/file_source_templates.yml.j2       |  5 -
 .../config/object_store_templates.yml.j2      |  6 --
 16 files changed, 2 insertions(+), 548 deletions(-)
 delete mode 100644 files/galaxy/config/file_source_templates/production_aws_private_bucket.yml
 delete mode 100644 files/galaxy/config/file_source_templates/production_aws_public_bucket.yml
 delete mode 100644 files/galaxy/config/file_source_templates/production_azure.yml
 delete mode 100644 files/galaxy/config/file_source_templates/production_ftp.yml
 delete mode 100644 files/galaxy/config/file_source_templates/production_s3fs.yml
 delete mode 100644 files/galaxy/config/object_store_templates/production_aws_s3.yml
 delete mode 100644 files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml
 delete mode 100644 files/galaxy/config/object_store_templates/production_azure_blob.yml
 delete mode 100644 files/galaxy/config/object_store_templates/production_gcp_s3.yml
 delete mode 100644 files/galaxy/config/object_store_templates/production_generic_s3.yml
 delete mode 100644 files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml
 delete mode 100644 templates/galaxy/config/file_source_templates.yml.j2
 delete mode 100644 templates/galaxy/config/object_store_templates.yml.j2

diff --git a/bin/diff-before-update b/bin/diff-before-update
index 37ab31674..f62904b5e 100755
--- a/bin/diff-before-update
+++ b/bin/diff-before-update
@@ -51,19 +51,3 @@ compare files/$folder/config/user_preferences_extra_conf.yml	$GALAXY/config/user
 #compare templates/$folder/config/build_sites.yml.j2	$GALAXY/config/build_sites.yml.sample.sample
 
 compare group_vars/gxconfig${ext}.yml	$GALAXY/config/galaxy.yml.sample
-
-# Compare file source templates
-compare files/$folder/config/file_source_templates/production_aws_private_bucket.yml	$GALAXY/files/templates/examples/production_aws_private_bucket.yml
-compare files/$folder/config/file_source_templates/production_aws_public_bucket.yml	$GALAXY/files/templates/examples/production_aws_public_bucket.yml
-compare files/$folder/config/file_source_templates/production_azure.yml	$GALAXY/files/templates/examples/production_azure.yml
-compare files/$folder/config/file_source_templates/production_ftp.yml	$GALAXY/files/templates/examples/production_ftp.yml
-compare files/$folder/config/file_source_templates/production_s3fs.yml	$GALAXY/files/templates/examples/production_s3fs.yml
-
-# Compare object store templates
-compare files/$folder/config/object_store_templates/production_aws_s3_legacy.yml	$GALAXY/objectstore/templates/examples/production_aws_s3_legacy.yml
-compare files/$folder/config/object_store_templates/production_aws_s3.yml	$GALAXY/objectstore/templates/examples/production_aws_s3.yml
-compare files/$folder/config/object_store_templates/production_azure_blob.yml	$GALAXY/objectstore/templates/examples/production_azure_blob.yml
-compare files/$folder/config/object_store_templates/production_gcp_s3.yml	$GALAXY/objectstore/templates/examples/production_gcp_s3.yml
-compare files/$folder/config/object_store_templates/production_generic_s3_legacy.yml	$GALAXY/objectstore/templates/examples/production_generic_s3_legacy.yml
-compare files/$folder/config/object_store_templates/production_generic_s3.yml	$GALAXY/objectstore/templates/examples/production_generic_s3.yml
-compare files/$folder/config/object_store_templates/minio_example.yml	$GALAXY/objectstore/templates/examples/minio_example.yml
diff --git a/files/galaxy/config/file_source_templates/production_aws_private_bucket.yml b/files/galaxy/config/file_source_templates/production_aws_private_bucket.yml
deleted file mode 100644
index 2770bfa1f..000000000
--- a/files/galaxy/config/file_source_templates/production_aws_private_bucket.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- id: aws_private
-  version: 0
-  name: Amazon Web Services Private Bucket
-  description: Setup access to a private AWS bucket using a secret access key.
-  configuration:
-    type: s3fs
-    bucket: '{{ bucket }}'
-    writable: '{{ writable }}'
-    secret: '{{ secret_key }}'
-    key: '{{ access_key }}'
-  variables:
-    access_key:
-      label: Access Key ID
-      type: string
-      help: |
-        The "access key ID" as defined in the [Amazon Documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html).
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [Amazon Web Services Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        access. This should be a bucket the user described by the Access Key ID has access to.
-    writable:
-      label: Writable?
-      type: boolean
-      help: Is this a bucket you have permission to write to?
-  secrets:
-    secret_key:
-      label: Secret Access Key
-      help: |
-        The "secret access key" as defined in the [Amazon Documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_access-keys.html).
diff --git a/files/galaxy/config/file_source_templates/production_aws_public_bucket.yml b/files/galaxy/config/file_source_templates/production_aws_public_bucket.yml
deleted file mode 100644
index fc55847ba..000000000
--- a/files/galaxy/config/file_source_templates/production_aws_public_bucket.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- id: aws_public
-  version: 0
-  name: Amazon Web Services Public Bucket
-  description: Setup anonymous access to a public AWS bucket.
-  configuration:
-    type: s3fs
-    bucket: '{{ variables.bucket }}'
-    writable: false
-    anon: true
-  variables:
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [Amazon Web Services Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        anonymously access.
diff --git a/files/galaxy/config/file_source_templates/production_azure.yml b/files/galaxy/config/file_source_templates/production_azure.yml
deleted file mode 100644
index 81437b91b..000000000
--- a/files/galaxy/config/file_source_templates/production_azure.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-- id: azure
-  version: 0
-  name: Azure Blob Storage
-  description: |
-    This template allows connecting to [Azure Blob Storage](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction).
-  configuration:
-    type: azure
-    container_name: '{{ variables.container_name }}'
-    account_name: '{{ variables.account_name }}'
-    account_key: '{{ secrets.account_key }}'
-    namespace_type: "{{ 'hierarchical' if variables.hierarchical else 'flat' }}"
-    writable: '{{ variables.writable }}'
-  variables:
-    container_name:
-      label: Container Name
-      type: string
-      help: |
-        The name of your Azure Blob Storage container. More information on containers can be found
-        in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction#containers).
-    account_name:
-      label: Storage Account Name
-      type: string
-      help: |
-        The name of your Azure Blob Storage account. More information on containers can be found in the
-        [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-overview).
-    hierarchical:
-      label: Hierarchical?
-      type: boolean
-      default: true
-      help: |
-        Is this storage hierarchical (e.g. does it use a Azure Data Lake Storage Gen2 hierarchical namespace)?
-        More information on Data Lake Storage namespaces can be found in the
-        [Azure Blob Storage documentation](https://learn.microsoft.com/en-us/azure/storage/blobs/data-lake-storage-namespace).
-    writable:
-      label: Writable?
-      type: boolean
-      default: true
-      help: Allow Galaxy to write data to this Azure Blob Storage container.
-  secrets:
-    account_key:
-      label: Account Key
-      help: |
-        The Azure Blob Storage account key to use to access your Azure Blob Storage data. More information
-        on account keys can be found in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-keys-manage).
diff --git a/files/galaxy/config/file_source_templates/production_ftp.yml b/files/galaxy/config/file_source_templates/production_ftp.yml
deleted file mode 100644
index 04e334718..000000000
--- a/files/galaxy/config/file_source_templates/production_ftp.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-- id: ftp
-  version: 0
-  name: An FTP Server
-  description: |
-    This template allows connecting to FTP servers. This file source plugin should
-    support FTP and FTPS servers.
-  configuration:
-    type: ftp
-    host: '{{ variables.host }}'
-    user: '{{ variables.user }}'
-    port: '{{ variables.port }}'
-    passwd: '{{ secrets.password }}'
-    writable: '{{ variables.writable }}'
-  variables:
-    host:
-      label: FTP Host
-      type: string
-      help: Host of FTP Server to connect to.
-    user:
-      label: FTP User
-      type: string
-      help: |
-        Username to connect with. Leave this blank to connect to the server
-        anonymously (if allowed by target server).
-    writable:
-      label: Writable?
-      type: boolean
-      help: Is this an FTP server you have permission to write to?
-    port:
-      label: FTP Port
-      type: integer
-      help: Port used to connect to the FTP server.
-      default: 21
-  secrets:
-    password:
-      label: FTP Password
-      help: |
-        Password to connect to FTP server with. Leave this blank to connect
-        to the server anonymously (if allowed by target server).
diff --git a/files/galaxy/config/file_source_templates/production_s3fs.yml b/files/galaxy/config/file_source_templates/production_s3fs.yml
deleted file mode 100644
index dbe1c2323..000000000
--- a/files/galaxy/config/file_source_templates/production_s3fs.yml
+++ /dev/null
@@ -1,57 +0,0 @@
-- id: s3fs
-  version: 0
-  name: S3 Compatible Storage with Credentials
-  description: |
-    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
-    of an unofficial standard for cloud storage across a variety of vendors and services.
-    Many vendors offer storage APIs compatible with S3. This template configuration allows
-    using such service as a Galaxy storage location as long as you are able to find the
-    connection details and have the relevant credentials.
-
-    Given the amount of information needed to connect to such a service, this is a bit of an
-    advanced template and probably should not be used to connect to a service if a more
-    specific template is available.
-  variables:
-    access_key:
-      label: Access Key ID
-      type: string
-      help: |
-        The less secure part of your access tokens or access keys that describe the user
-        that is accessing the data. The [Amazon documentation](https://docs.aws.amazon.com/IAM/latest/UserGuide/security-creds.html)
-        calls these an "access key ID", the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
-        describes these as ``aws_access_key_id``.
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        store your datasets in. How to setup buckets for your storage will vary from service to service
-        but all S3 compatible storage services should have the concept of a bucket to namespace
-        a grouping of your data together with.
-    endpoint_url:
-      label: S3-Compatible API Endpoint
-      type: string
-      help: |
-        If the documentation for your storage service has something called an ``endpoint_url``,
-        For instance, the CloudFlare documentation describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
-        you would substitute your CloudFlare account ID into the endpoint url and use that value.
-        So if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
-        The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
-        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``,
-        this value would be entered here.
-  secrets:
-    secret_key:
-      label: Secret Access Key
-      help: |
-        The secret key used to connect to the S3 compatible storage with for the given access key.
-
-        The [Amazon documentation] calls these an "secret access key" and
-        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
-        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
-        this the ``secret_key``.
-  configuration:
-    type: s3fs
-    endpoint_url: '{{ variables.endpoint_url }}'
-    key: '{{ variables.access_key }}'
-    secret: '{{ secrets.secret_key }}'
-    bucket: '{{ variables.bucket }}'
diff --git a/files/galaxy/config/object_store_templates/production_aws_s3.yml b/files/galaxy/config/object_store_templates/production_aws_s3.yml
deleted file mode 100644
index c87026d10..000000000
--- a/files/galaxy/config/object_store_templates/production_aws_s3.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-- id: aws_s3
-  version: 0
-  name: Amazon Web Services S3 Storage
-  description: |
-    Amazon's Simple Storage Service (S3) is Amazon's primary cloud storage service.
-    More information on S3 can be found in [Amazon's documentation](https://aws.amazon.com/s3/).
-  variables:
-    access_key:
-      label: Access Key ID
-      type: string
-      help: |
-        A security credential for interacting with AWS services can be created from your
-        AWS web console. Creating an "Access Key" creates a pair of keys used to identify
-        and authenticate access to your AWS account - the first part of the pair  is
-        "Access Key ID" and should be entered here. The second part of your key is the secret
-        part called the "Secret Access Key". Place that in the secure part of this form below.
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [AWS S3 Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        store your datasets in. You will need to create a bucket to use in your AWS web console before
-        using this form.
-  secrets:
-    secret_key:
-      label: Secret Access Key
-      help: |
-        See the documentation above used "Access Key ID" for information about access key pairs.
-  configuration:
-    type: boto3
-    auth:
-      access_key: '{{ variables.access_key }}'
-      secret_key: '{{ secrets.secret_key }}'
-    bucket:
-      name: '{{ variables.bucket }}'
diff --git a/files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml b/files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml
deleted file mode 100644
index 1a3730897..000000000
--- a/files/galaxy/config/object_store_templates/production_aws_s3_legacy.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-- id: aws_s3_legacy
-  version: 0
-  name: Amazon Web Services S3 Storage (Legacy)
-  description: |
-    Amazon's Simple Storage Service (S3) is Amazon's primary cloud storage service.
-    More information on S3 can be found in [Amazon's documentation](https://aws.amazon.com/s3/).
-  variables:
-    access_key:
-      label: Access Key ID
-      type: string
-      help: |
-        A security credential for interacting with AWS services can be created from your
-        AWS web console. Creating an "Access Key" creates a pair of keys used to identify
-        and authenticate access to your AWS account - the first part of the pair  is
-        "Access Key ID" and should be entered here. The second part of your key is the secret
-        part called the "Secret Access Key". Place that in the secure part of this form below.
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [AWS S3 Bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        store your datasets in. You will need to create a bucket to use in your AWS web console before
-        using this form.
-  secrets:
-    secret_key:
-      label: Secret Access Key
-      help: |
-        See the documentation above used "Access Key ID" for information about access key pairs.
-
-  configuration:
-    type: aws_s3
-    auth:
-      access_key: '{{ variables.access_key }}'
-      secret_key: '{{ secrets.secret_key }}'
-    bucket:
-      name: '{{ variables.bucket }}'
diff --git a/files/galaxy/config/object_store_templates/production_azure_blob.yml b/files/galaxy/config/object_store_templates/production_azure_blob.yml
deleted file mode 100644
index ee57eaf74..000000000
--- a/files/galaxy/config/object_store_templates/production_azure_blob.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- id: azure
-  version: 0
-  name: Azure Blob Storage
-  description: |
-    This template allows storing dataset in [Azure Blob Storage](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction).
-  configuration:
-    type: azure_blob
-    auth:
-      account_name: '{{ variables.account_name }}'
-      account_key: '{{ secrets.account_key}}'
-    container:
-      name: '{{ variables.container_name }}'
-  variables:
-    container_name:
-      label: Container Name
-      type: string
-      help: |
-        The name of your Azure Blob Storage container. More information on containers can be found
-        in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/blobs/storage-blobs-introduction#containers).
-    account_name:
-      label: Storage Account Name
-      type: string
-      help: |
-        The name of your Azure Blob Storage account. More information on containers can be found in the
-        [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-overview).
-  secrets:
-    account_key:
-      label: Account Key
-      help: |
-        The Azure Blob Storage account key to use to access your Azure Blob Storage data. More information
-        on account keys can be found in the [Azure Storage documentation](https://learn.microsoft.com/en-us/azure/storage/common/storage-account-keys-manage).
diff --git a/files/galaxy/config/object_store_templates/production_gcp_s3.yml b/files/galaxy/config/object_store_templates/production_gcp_s3.yml
deleted file mode 100644
index 95a14a634..000000000
--- a/files/galaxy/config/object_store_templates/production_gcp_s3.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-# https://cloud.google.com/storage/docs/aws-simple-migration
-- id: gcp_s3_interop
-  version: 0
-  name: Google Cloud Storage
-  description: |
-    This template can be used to connect to your [Google Cloud Storage](https://cloud.google.com/storage).
-    To use these templates you will need to generate
-    [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys) - these
-    can be linked to your user or a service account. Additionally, you will need to defined
-    a [default Google cloud project](https://cloud.google.com/storage/docs/aws-simple-migration#defaultproj)
-    to allow Galaxy to access your Google Cloud Storage via the interfaces
-    described by this template.
-  variables:
-    access_key:
-      label: Access ID
-      type: string
-      help: |
-        This will be given to you by Google when you generate [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys)
-        to use your storage.
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The name of a [bucket](https://cloud.google.com/storage/docs/buckets) you've created to store your Galaxy data. Documentation for how to create buckets
-        can be found in [this part of the Google Cloud Storage documentation](https://cloud.google.com/storage/docs/creating-buckets).
-  secrets:
-    secret_key:
-      label: Secret Key
-      help: |
-        This will be given to you by Google when you generate [HMAC Keys](https://cloud.google.com/storage/docs/authentication/hmackeys)
-        to use your storage. It should be 40 characters long and look something like the example used
-        the Google documentation - `bGoa+V7g/yqDXvKRqq+JTFn4uQZbPiQJo4pf9RzJ`.
-  configuration:
-    type: boto3
-    auth:
-      access_key: '{{ variables.access_key }}'
-      secret_key: '{{ secrets.secret_key }}'
-    bucket:
-      name: '{{ variables.bucket }}'
-    connection:
-      endpoint_url: 'https://storage.googleapis.com/'
diff --git a/files/galaxy/config/object_store_templates/production_generic_s3.yml b/files/galaxy/config/object_store_templates/production_generic_s3.yml
deleted file mode 100644
index 8a9c02e37..000000000
--- a/files/galaxy/config/object_store_templates/production_generic_s3.yml
+++ /dev/null
@@ -1,61 +0,0 @@
-- id: generic_s3
-  version: 0
-  name: Any S3 Compatible Storage
-  description: |
-    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
-    of an unofficial standard for cloud storage across a variety of vendors and services.
-    Many vendors offer storage APIs compatible with S3 - Galaxy calls these ``generic_s3``
-    storage locations. This template configuration allows using such service as a Galaxy storage
-    location as long as you are able to find the connection details and have the relevant credentials.
-
-    Given the amount of information needed to connect to such a service, this is a bit of an
-    advanced template and probably should not be used to connect to a service if a more
-    specific template is available.
-  variables:
-    access_key:
-      label: Access Key ID
-      type: string
-      help: |
-        The less secure part of your access tokens or access keys that describe the user
-        that is accessing the data. The [Amazon documentation] calls these an "access key ID",
-        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
-        describes these as ``aws_access_key_id``. Internally to Galaxy, we often just call
-        this the ``access_key``.
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        store your datasets in. How to setup buckets for your storage will vary from service to service
-        but all S3 compatible storage services should have the concept of a bucket to namespace
-        a grouping of your data together with.
-    endpoint_url:
-      label: S3-Compatible API Endpoint
-      type: string
-      help: |
-        If the documentation for your storage service has something called an ``endpoint_url``,
-        For instance, the CloudFlare documentation describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
-        you would substitute your CloudFlare account ID into the endpoint url and use that value.
-        So if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
-        The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
-        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``,
-        this whole value would be entered here.
-  secrets:
-    secret_key:
-      label: Secret Access Key
-      help: |
-        The secret key used to connect to the S3 compatible storage with for the given access key.
-
-        The [Amazon documentation] calls these an "secret access key" and
-        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
-        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
-        this the ``secret_key``.
-  configuration:
-    type: boto3
-    auth:
-      access_key: '{{ variables.access_key }}'
-      secret_key: '{{ secrets.secret_key }}'
-    bucket:
-      name: '{{ variables.bucket }}'
-    connection:
-      endpoint_url: '{{ variables.endpoint_url }}'
diff --git a/files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml b/files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml
deleted file mode 100644
index 0894205b3..000000000
--- a/files/galaxy/config/object_store_templates/production_generic_s3_legacy.yml
+++ /dev/null
@@ -1,97 +0,0 @@
-- id: generic_s3_legacy
-  version: 0
-  name: Any S3 Compatible Storage (Legacy)
-  description: |
-    The APIs used to connect to Amazon's S3 (Simple Storage Service) have become something
-    of an unofficial standard for cloud storage across a variety of vendors and services.
-    Many vendors offer storage APIs compatible with S3 - Galaxy calls these ``generic_s3``
-    storage locations. This template configuration allows using such service as a Galaxy storage
-    location as long as you are able to find the connection details and have the relevant credentials.
-
-    Given the amount of information needed to connect to such a service, this is a bit of an
-    advanced template and probably should not be used to connect to a service if a more
-    specific template is available.
-  variables:
-    access_key:
-      label: Access Key ID
-      type: string
-      help: |
-        The less secure part of your access tokens or access keys that describe the user
-        that is accessing the data. The [Amazon documentation] calls these an "access key ID",
-        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
-        describes these as ``aws_access_key_id``. Internally to Galaxy, we often just call
-        this the ``access_key``.
-    bucket:
-      label: Bucket
-      type: string
-      help: |
-        The [bucket](https://docs.aws.amazon.com/AmazonS3/latest/userguide/UsingBucket.html) to
-        store your datasets in. How to setup buckets for your storage will vary from service to service
-        but all S3 compatible storage services should have the concept of a bucket to namespace
-        a grouping of your data together with.
-    host:
-      label: Connection Host
-      type: string
-      help: |
-        The [hostname](https://en.wikipedia.org/wiki/Hostname) used to connect to the target
-        S3 compatible service.
-
-        If the documentation for your storage service has something called an ``endpoint_url``,
-        this can be used to determine this value. For instance, the CloudFlare documentation
-        describes its endpoints as ``https://<accountid>.r2.cloudflarestorage.com``. Here
-        you would substitute your CloudFlare account ID into the endpoint and shave off the ``https://``,
-        so if your account ID was ``galactian``, you would enter ``galactian.r2.cloudflarestorage.com``.
-    port:
-      label: Connection Port
-      type: integer
-      default: 443
-      help: |
-        The [port](https://en.wikipedia.org/wiki/Port_(computer_networking)) used to connect
-        to the target S3 compatible service. This might be ``443`` if you cannot find a relevant
-        port - this is the default for secure HTTP connections.
-
-        If the documentation for your storage service has something called an ``endpoint_url``,
-        this can be used to determine this value. The [MinIO](https://min.io/docs/minio/linux/integrations/aws-cli-with-minio.html)
-        documentation describes the endpoint URL for its Play service as ``https://play.min.io:9000``.
-        The ``:9000`` here indicates this port should be specified as ``9000``. Alternatively, the
-        CloudFlare documentation describes its endpoints ``https://<accountid>.r2.cloudflarestorage.com``.
-        Here there is no number at the end of the URL so the port is ``443`` as long the URL starts
-        with ``https``.
-    connection_path:
-      label: Connection Path
-      type: string
-      default: ""
-      help: |
-        This is an advanced configuration option and it is very likely best to just keep this empty
-        for most storage services. If specified, it will be the prefix in the URL for the S3 compatible
-        API after the host and port to reach the target API.
-    secure:
-      label: Use HTTPS?
-      type: boolean
-      default: true
-      help: |
-        This is an advanced configuration option and if this option is not checked, you should not assume
-        your data is secure at all. This should only ever be unchecked during testing new or experimental
-        services with data and keys you do not care about.
-  secrets:
-    secret_key:
-      label: Secret Access Key
-      help: |
-        The secret key used to connect to the S3 compatible storage with for the given access key.
-
-        The [Amazon documentation] calls these an "secret access key" and
-        the [CloudFlare documentation](https://developers.cloudflare.com/r2/examples/aws/boto3/)
-        describes these as ``aws_secret_access_key``. Internally to Galaxy, we often just call
-        this the ``secret_key``.
-  configuration:
-    type: generic_s3
-    auth:
-      access_key: '{{ variables.access_key }}'
-      secret_key: '{{ secrets.secret_key }}'
-    bucket:
-      name: '{{ variables.bucket }}'
-    connection:
-      host: '{{ variables.host }}'
-      port: '{{ variables.port  }}'
-      is_secure: '{{ variables.secure }}'
-      conn_path: '{{ variables.connection_path }}'
diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml
index a7c975234..e3c7f5e11 100644
--- a/group_vars/gxconfig.yml
+++ b/group_vars/gxconfig.yml
@@ -363,7 +363,7 @@ base_app_main: &BASE_APP_MAIN
   # Configured Object Store templates configuration file.
   # The value of this option will be resolved with respect to
   # <config_dir>.
-  # object_store_templates_config_file: '{{ galaxy_config_dir }}/object_store_templates.yml'
+  # object_store_templates_config_file: 'object_store_templates.yml'
 
   # Configured Object Store templates embedded into Galaxy's config.
   #object_store_templates: null
@@ -371,7 +371,7 @@ base_app_main: &BASE_APP_MAIN
   # Configured user file source templates configuration file.
   # The value of this option will be resolved with respect to
   # <config_dir>.
-  # file_source_templates_config_file: '{{ galaxy_config_dir }}/file_source_templates.yml'
+  # file_source_templates_config_file: 'file_source_templates.yml'
 
   # Configured user file source templates embedded into Galaxy's config.
   #file_source_templates: null
diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml
index d71520753..5ac37da52 100644
--- a/group_vars/sn06.yml
+++ b/group_vars/sn06.yml
@@ -292,8 +292,6 @@ galaxy_config_dir: "{{ galaxy_root }}/config"
 galaxy_venv_dir: "{{ galaxy_root }}/venv"
 galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}"
 ucsc_build_sites:
-galaxy_file_source_templates_dir: "{{ galaxy_mutable_config_dir }}/file_source_templates"
-galaxy_object_store_templates_dir: "{{ galaxy_mutable_config_dir }}/object_store_templates"
 
 galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies"
 #galaxy_virtualenv_python: "python3.6"
@@ -319,8 +317,6 @@ galaxy_dirs:
   - "{{ galaxy_log_dir }}"
   - "{{ galaxy_config_dir }}/total_perspective_vortex"
   - "{{ tpv_mutable_dir }}"
-  - "{{ galaxy_file_source_templates_dir }}"
-  - "{{ galaxy_object_store_templates_dir }}"
 
 galaxy_instance_hostname: usegalaxy.eu
 galaxy_config_style: yaml
@@ -425,28 +421,6 @@ galaxy_config_files:
     dest: "{{ tpv_mutable_dir }}/interactive_tools.yml"
   - src: "{{ galaxy_config_file_src_dir }}/tpv/users.yml"
     dest: "{{ tpv_mutable_dir }}/users.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_aws_private_bucket.yml"
-    dest: "{{ galaxy_file_source_templates_dir }}/production_aws_private_bucket.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_aws_public_bucket.yml"
-    dest: "{{ galaxy_file_source_templates_dir }}/production_aws_public_bucket.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_azure.yml"
-    dest: "{{ galaxy_file_source_templates_dir }}/production_azure.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_ftp.yml"
-    dest: "{{ galaxy_file_source_templates_dir }}/production_ftp.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_s3fs.yml"
-    dest: "{{ galaxy_file_source_templates_dir }}/production_s3fs.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_aws_s3_legacy.yml"
-    dest: "{{ galaxy_object_store_templates_dir }}/production_aws_s3_legacy.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_aws_s3.yml"
-    dest: "{{ galaxy_object_store_templates_dir }}/production_aws_s3.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_azure_blob.yml"
-    dest: "{{ galaxy_object_store_templates_dir }}/production_azure_blob.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_gcp_s3.yml"
-    dest: "{{ galaxy_object_store_templates_dir }}/production_gcp_s3.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_generic_s3_legacy.yml"
-    dest: "{{ galaxy_object_store_templates_dir }}/production_generic_s3_legacy.yml"
-  - src: "{{ galaxy_config_file_src_dir }}/config/object_store_templates/production_generic_s3.yml"
-    dest: "{{ galaxy_object_store_templates_dir }}/production_generic_s3.yml"
 
   #- src: files/galaxy/config/job_resource_params_conf.xml
   #dest: "{{ galaxy_config['app:main']['job_resource_params_file'] }}"
@@ -493,8 +467,3 @@ galaxy_config_templates:
     dest: "{{ tpv_mutable_dir }}/destinations.yml"
   - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2'
     dest: '{{ galaxy_config_dir }}/vault_conf.yml'
-    # 9/7/24: Uncomment these when deploying object store and update the galaxy config
-  # - src: "{{ galaxy_config_template_src_dir }}/config/file_source_templates.yml.j2"
-  #   dest: "{{ galaxy_config['galaxy']['file_source_templates_config_file'] }}"
-  # - src: "{{ galaxy_config_template_src_dir }}/config/object_store_templates.yml.j2"
-  #   dest: "{{ galaxy_config['galaxy']['object_store_templates_config_file'] }}"
diff --git a/templates/galaxy/config/file_source_templates.yml.j2 b/templates/galaxy/config/file_source_templates.yml.j2
deleted file mode 100644
index 839a55db6..000000000
--- a/templates/galaxy/config/file_source_templates.yml.j2
+++ /dev/null
@@ -1,5 +0,0 @@
-- include: "{{ galaxy_file_source_templates_dir }}/production_azure.yml"
-- include: "{{ galaxy_file_source_templates_dir }}/production_ftp.yml"
-- include: "{{ galaxy_file_source_templates_dir }}/production_s3fs.yml"
-- include: "{{ galaxy_file_source_templates_dir }}/production_aws_private_bucket.yml"
-- include: "{{ galaxy_file_source_templates_dir }}/production_aws_public_bucket.yml"
diff --git a/templates/galaxy/config/object_store_templates.yml.j2 b/templates/galaxy/config/object_store_templates.yml.j2
deleted file mode 100644
index c73ca87e1..000000000
--- a/templates/galaxy/config/object_store_templates.yml.j2
+++ /dev/null
@@ -1,6 +0,0 @@
-- include: "{{ galaxy_object_store_templates_dir }}/production_azure_blob.yml"
-- include: "{{ galaxy_object_store_templates_dir }}/production_aws_s3.yml"
-- include: "{{ galaxy_object_store_templates_dir }}/production_aws_s3_legacy.yml"
-- include: "{{ galaxy_object_store_templates_dir }}/production_generic_s3.yml"
-- include: "{{ galaxy_object_store_templates_dir }}/production_generic_s3_legacy.yml"
-- include: "{{ galaxy_object_store_templates_dir }}/production_gcp_s3.yml"