updates for 24.2

files/galaxy/config/datatypes_conf.xml

@@ -116,7 +116,11 @@
     <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
     <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="false"/>
     <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="false"/>
-    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
+    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true">
+        <upload_warning>
+          SOLID Color-Space sequence data is a rare data type. Consider selecting fasta instead.
+        </upload_warning>
+    </datatype>
     <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
     <datatype extension="gz" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
@@ -150,6 +154,9 @@
     </datatype>
     <datatype extension="fastqsolexa" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="Solexa variant of the FASTQ format: solexa+64" description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+      <upload_warning>
+        Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
     </datatype>
     <datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true" description="sequence in in color space phred scored quality values 0:93 represented by ASCII 33:126">
       <upload_warning>
@@ -159,6 +166,9 @@
     </datatype>
     <datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true" description="Sanger variant of the FASTQ format: phred+64">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+      <upload_warning>
+        Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
     </datatype>
     <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
     <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
@@ -184,7 +194,7 @@
     <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
     <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
     <datatype extension="graph_dot" type="galaxy.datatypes.data:Text" subclass="true"/>
-    <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
+    <datatype extension="gtf" auto_compressed_types="gz" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
       <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
       <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <display file="igb/gtf.xml"/>
@@ -198,6 +208,7 @@
     <datatype extension="grib" type="galaxy.datatypes.binary:Grib" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="loom" type="galaxy.datatypes.binary:Loom" description="An HDF5-based Loom File" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="h5ad" type="galaxy.datatypes.binary:Anndata" description="An HDF5-based anndata File" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="h5mu" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="MuData is a format analogous to Anndata for multimodal datasets and is based on HDF5" description_url="https://github.com/scverse/mudata"/>
     <datatype extension="visium.tar.gz" type="galaxy.datatypes.binary:Visium" subclass="true" display_in_upload="true" description="Visium is a tar.gz archive with at least a 'Spatial' subfolder, a filtered h5 file and a raw h5 file." />
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
@@ -286,15 +297,25 @@
       <display file="qiime/qiime2/q2view.xml"/>
     </datatype>
     <datatype extension='qiime2.tabular' type="galaxy.datatypes.qiime2:QIIME2Metadata" display_in_upload="true"/>
-    <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true"/>
+    <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true">
+        <converter file="archive_to_directory.xml" target_datatype="directory" />
+    </datatype>
     <datatype extension="ncbi_genome_dataset.zip" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
-    <datatype extension="tar" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
-      <converter file="tar_to_directory.xml" target_datatype="directory"/>
+    <datatype extension="zarr.zip" type="galaxy.datatypes.binary:CompressedZarrZipArchive" display_in_upload="true">
+        <converter file="archive_to_directory.xml" target_datatype="zarr" />
+    </datatype>
+    <datatype extension="ome_zarr.zip" type="galaxy.datatypes.binary:CompressedOMEZarrZipArchive" display_in_upload="true">
+        <converter file="archive_to_directory.xml" target_datatype="ome_zarr" />
     </datatype>
     <datatype extension="mat" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="true"/>
     <datatype extension="no_unzip.zip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
-    <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
+    <datatype extension="tar" auto_compressed_types="gz,bz2" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
+      <converter file="archive_to_directory.xml" target_datatype="directory"/>
+    </datatype>
+    <datatype extension="directory" type="galaxy.datatypes.data:Directory"/>
+    <datatype extension="zarr" type="galaxy.datatypes.data:ZarrDirectory" />
+    <datatype extension="ome_zarr" type="galaxy.datatypes.images:OMEZarr" />
     <datatype extension="yaml" type="galaxy.datatypes.text:Yaml" display_in_upload="true" />
     <!-- Proteomics Datatypes -->
     <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true"/>
@@ -379,6 +400,7 @@
     <datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>
     <datatype extension="fast5.tar.bz2" type="galaxy.datatypes.binary:Fast5ArchiveBz2" display_in_upload="true"/>
     <datatype extension="fast5.tar.xz" type="galaxy.datatypes.binary:Fast5ArchiveXz" display_in_upload="true"/>
+    <datatype extension="pod5" type="galaxy.datatypes.binary:Pod5" display_in_upload="true"/>
     <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
     <datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true"/>
@@ -983,6 +1005,7 @@
     <datatype extension="gmsh.msh" type="galaxy.datatypes.constructive_solid_geometry:GmshMsh" display_in_upload="true"/>
     <datatype extension="gmsh.geo" type="galaxy.datatypes.constructive_solid_geometry:GmshGeo" display_in_upload="true"/>
     <datatype extension="zset.geof" type="galaxy.datatypes.constructive_solid_geometry:ZsetGeof" display_in_upload="true"/>
+    <datatype extension="vtkxml" type="galaxy.datatypes.constructive_solid_geometry:VtkXml" display_in_upload="true"/>
     <datatype extension="stl" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" description="STL is a file format native to the stereolithography CAD software created by 3D Systems."/>
     <!-- Povray script -->
     <datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
@@ -1015,6 +1038,7 @@
     <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" 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"/>
+    <datatype extension="bcsp" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="Binary format of k-mer hash table which is only compatible with Fairy"/>
   </registration>
   <sniffers>
     <!--
@@ -1041,6 +1065,7 @@
     <sniffer type="galaxy.datatypes.mothur:Axes"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
+    <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkXml"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:NeperTess"/>
@@ -1098,6 +1123,7 @@
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveXz"/>
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>
     <sniffer type="galaxy.datatypes.binary:Fast5Archive"/>
+    <sniffer type="galaxy.datatypes.binary:Pod5"/>
     <sniffer type="galaxy.datatypes.binary:Meryldb" />
     <sniffer type="galaxy.datatypes.binary:Bref3" />
     <sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>
@@ -1114,6 +1140,8 @@
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
+    <sniffer type="galaxy.datatypes.binary:CompressedOMEZarrZipArchive"/>
+    <sniffer type="galaxy.datatypes.binary:CompressedZarrZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:CompressedZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:Pretext"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>

files/galaxy/config/user_preferences_extra_conf.yml

@@ -64,6 +64,19 @@ preferences:
               # store: vault
               required: False
 
+    invenio:
+        description: Your Invenio RDM Integration Settings
+        inputs:
+            - name: token
+              label: Personal Token used to create draft records and to upload files
+              type: secret
+              store: vault # Requires setting up vault_config_file in your galaxy.yml
+              required: False
+            - name: public_name
+              label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used. You can always change this by editing your record directly.
+              type: text
+              required: False
+
     zenodo:
         description: Your Zenodo Integration Settings
         inputs:
@@ -95,13 +108,18 @@ preferences:
         description: Your Onedata account
         inputs:
             - name: onezone_domain
-              label: Domain of the Onezone service (e.g. "demo.onedata.org")
+              label: Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4.
               type: text
               required: False
             - name: access_token
               label: Your access token, suitable for REST API access in a Oneprovider service
               type: password
               required: False
+            - name: disable_tls_certificate_validation
+              label: Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing.
+              type: boolean
+              required: False
+              value: False
 
     distributed_arc_compute:
         description: The URL to your ARC remote HPC compute resource.

group_vars/gxconfig.yml

@@ -234,7 +234,7 @@ base_app_main: &BASE_APP_MAIN
 
   # conda channels to enable by default
   # (https://conda.io/docs/user-guide/tasks/manage-channels.html)
-  conda_ensure_channels: "conda-forge,bioconda"
+  #conda_ensure_channels: conda-forge,bioconda
 
   # Use locally-built conda packages.
   #conda_use_local: false
@@ -245,8 +245,9 @@ base_app_main: &BASE_APP_MAIN
 
   # Set to true to instruct Galaxy to install Conda from the web
   # automatically if it cannot find a local copy and conda_exec is not
-  # configured.
-  #conda_auto_init: true
+  # configured. The default is true if running Galaxy from source, and
+  # false if running from installed packages.
+  #conda_auto_init: false
 
   # You must set this to true if conda_prefix and job_working_directory
   # are not on the same volume, or some conda dependencies will fail to
@@ -377,15 +378,6 @@ base_app_main: &BASE_APP_MAIN
   # 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
@@ -769,8 +761,8 @@ base_app_main: &BASE_APP_MAIN
   # <cache_dir>.
   object_store_cache_path: '/data/jwd02f/s3_object_store_cache'
 
-  # Default cache size for caching object stores if cache not configured
-  # for that object store entry.
+  # Default cache size, in GB, for caching object stores if the cache is
+  # not configured for that object store entry.
   object_store_cache_size: 10000
 
   # Set this to true to indicate in the UI that a user's object store
@@ -1013,11 +1005,24 @@ base_app_main: &BASE_APP_MAIN
   # subdomain. Defaults to "/".
   #interactivetools_base_path: /
 
-  # Map for interactivetool proxy.
+  # Map for the interactivetool proxy. Mappings are stored in a SQLite
+  # database file located on this path. As an alternative, you may also
+  # store them in any other RDBMS supported by SQLAlchemy using the
+  # option ``interactivetoolsproxy_map``, which overrides this one.
   # The value of this option will be resolved with respect to
   # <data_dir>.
   interactivetools_map: "{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite"
 
+  # Use a database supported by SQLAlchemy as map for the
+  # interactivetool proxy. When this option is set, the value of
+  # ``interactivetools_map`` is ignored. The value of this option must
+  # be a `SQLAlchemy database URL
+  # <https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls>`_.
+  # Mappings are written to the table "gxitproxy" within the database.
+  # This value cannot match ``database_connection`` nor
+  # ``install_database_connection``.
+  #interactivetoolsproxy_map: null
+
   # Prefix to use in the formation of the subdomain or path for
   # interactive tools
   #interactivetools_prefix: interactivetool
@@ -2110,10 +2115,6 @@ base_app_main: &BASE_APP_MAIN
   # <config_dir>.
   job_metrics_config_file: "{{ galaxy_config_dir }}/job_metrics_conf.yml"
 
-  # This option allows users to see the job metrics (except for
-  # environment variables).
-  expose_potentially_sensitive_job_metrics: true
-
   # Rather than specifying a job_metrics_config_file, the definition of
   # the metrics to enable can be embedded into Galaxy's config with this
   # option. This has no effect if a job_metrics_config_file is used.
@@ -2126,7 +2127,7 @@ base_app_main: &BASE_APP_MAIN
 
   # This option allows users to see the job metrics (except for
   # environment variables).
-  #expose_potentially_sensitive_job_metrics: false
+  expose_potentially_sensitive_job_metrics: true
 
   # Enable the API for sample tracking
   #enable_legacy_sample_tracking_api: false
@@ -2444,6 +2445,19 @@ base_app_main: &BASE_APP_MAIN
   # <config_dir>.
   workflow_schedulers_config_file: "{{ galaxy_config_dir  }}/workflow_schedulers_conf.xml"
 
+  # Workflows launched with URI/URL inputs that are not marked as
+  # 'deferred' are "materialized" (or undeferred) by the workflow
+  # scheduler. This might be a lengthy process. Setting this to 'True'
+  # will place the invocation back in the queue after materialization
+  # before scheduling the workflow so it is less likely to starve other
+  # workflow scheduling. Ideally, Galaxy would allow more fine grain
+  # control of handlers but until then, this provides a way to tip the
+  # balance between "doing more work" and "being more fair". The default
+  # here is pretty arbitrary - it has been to False to optimize Galaxy
+  # for automated, single user applications where "fairness" is mostly
+  # irrelevant.
+  #workflow_scheduling_separate_materialization_iteration: false
+
   # If using job concurrency limits (configured in job_config_file),
   # several extra database queries must be performed to determine the
   # number of jobs a user has dispatched to a given destination.  By
@@ -2573,6 +2587,13 @@ base_app_main: &BASE_APP_MAIN
   # as threshold (above threshold: regular select fields will be used)
   #select_type_workflow_threshold: -1
 
+  # API key for OpenAI (https://openai.com/) to enable the wizard (or
+  # more?)
+  #openai_api_key: null
+
+  # OpenAI model to enable the wizard.
+  #openai_model: gpt-4o
+
   # Allow the display of tool recommendations in workflow editor and
   # after tool execution. If it is enabled and set to true, please
   # enable 'tool_recommendation_model_path' as well
@@ -2684,6 +2705,21 @@ base_app_main: &BASE_APP_MAIN
   # This requires the help_forum_api_url to be set.
   enable_help_forum_tool_panel_integration: true
 
+  # Directory to store temporary files for file sources. This defaults
+  # to new_file_path if not set.
+  #file_source_temp_dir: null
+
+  # Default value for use_temp_files for webdav plugins that don't
+  # explicitly declare this.
+  #file_source_webdav_use_temp_files: true
+
+  # Number of seconds before file source content listings are refreshed.
+  # Shorter times will result in more queries while browsing a file
+  # sources. Longer times will result in fewer requests to file sources
+  # but outdated contents might be displayed to the user. Currently only
+  # affects s3fs file sources.
+  #file_source_listings_expiry_time: 60
+
   # TODO(hxr): UNDOCUMENTED
   ucsc_build_sites: "{{ galaxy_config_dir }}/ucsc_build_sites.txt"
 

group_vars/sn06/sn06.yml

@@ -323,7 +323,7 @@ galaxy_instance_hostname: usegalaxy.eu
 galaxy_config_style: yaml
 
 galaxy_repo: "https://github.com/usegalaxy-eu/galaxy.git"
-galaxy_commit_id: "release_24.1_europe"
+galaxy_commit_id: "release_24.2_europe"
 galaxy_force_checkout: true # discard any modified files
 #galaxy_admin_email_from: '[email protected]'