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Bring back pre-installed DMs after all
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@afgane
afgane committed Feb 14, 2025
1 parent 9d83c80 commit b4f8766
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154 changes: 151 additions & 3 deletions galaxy/files/configs/shed_tool_data_table_conf.xml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,151 @@
<?xml version='1.0' encoding='utf-8'?>
<table>
</table>
<?xml version="1.0" ?>
<tables>
<table name="all_fasta" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/all_fasta.loc" />
</table>
<table name="__dbkeys__" comment_char="#">
<columns>value, name, len_path</columns>
<file path="/galaxy/server/config/mutable/dbkeys.loc" />
</table>
<table name="bowtie2_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/bowtie2_indices.loc"/>
</table>
<table name="bwa_mem_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/bwa_mem_index.loc"/>
</table>
<table name="twobit" comment_char="#">
<columns>value, path</columns>
<file path="/galaxy/server/config/mutable/twobit.loc"/>
</table>
<table name="lastz_seqs" comment_char="#">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/lastz_seqs.loc" />
</table>
<table name="alignseq_seq" comment_char="#">
<columns>type, value, path</columns>
<file path="/galaxy/server/config/mutable/alignseq.loc"/>
</table>
<table name="picard_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/picard_index.loc"/>
</table>
<table name="fasta_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/fasta_indexes.loc"/>
</table>
<table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/hisat2_indexes.loc"/>
</table>
<table name="rnastar_index2x_versioned" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path, with_gene_model, version</columns>
<file path="/galaxy/server/config/mutable/rnastar_index2x_versioned.loc"/>
</table>
<table name="bowtie_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/bowtie_indices.loc"/>
</table>
<table name="kallisto_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/kallisto_indexes.loc"/>
</table>
<table name="snpeffv_genomedb" comment_char="#" allow_duplicate_entries="False">
<columns>key, version, value, name, path</columns>
<file path="/galaxy/server/config/mutable/snpeffv_genomedb.loc"/>
</table>
<table name="snpeffv_regulationdb" comment_char="#" allow_duplicate_entries="False">
<columns>key, version, genome, value, name</columns>
<file path="/galaxy/server/config/mutable/snpeffv_regulationdb.loc"/>
</table>
<table name="snpeffv_databases" comment_char="#" allow_duplicate_entries="False">
<columns>key, version, value, name</columns>
<file path="/galaxy/server/config/mutable/snpeffv_databases.loc"/>
</table>
<table name="plant_tribes_scaffolds" comment_char="#">
<columns>value, name, path, description</columns>
<file path="/galaxy/server/config/mutable/plant_tribes_scaffolds.loc"/>
</table>
<table name="ncbi_taxonomy" comment_char="#">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/ncbi_taxonomy.loc"/>
</table>
<table name="ncbi_accession2taxid" comment_char="#">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/ncbi_accession2taxid.loc"/>
</table>
<table name="gemini_versioned_databases" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, version, name, path</columns>
<file path="/galaxy/server/config/mutable/gemini_versioned_databases.loc"/>
</table>
<table name="kraken2_databases" comment_char="#">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/kraken2_databases.loc"/>
</table>
<table name="bracken_databases" comment_char="#">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/bracken_databases.loc"/>
</table>
<table name="plasmidfinder_database" comment_char="#">
<columns>value, name, date, path</columns>
<file path="/galaxy/server/config/mutable/plasmidfinder_database.loc"/>
</table>
<table name="primer_scheme_bedfiles" comment_char="#">
<columns>value, description, path</columns>
<file path="/galaxy/server/config/mutable/primer_scheme_bedfiles.loc"/>
</table>
<table name="all_gff" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/all_gff.loc"/>
</table>
<table name="adapters" comment_char="#" allow_duplicate_entries="False">
<columns>value, name</columns>
<file path="/galaxy/server/config/mutable/adapters.loc"/>
</table>
<table name="bwameth_indexes" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/bwameth_indexes.loc"/>
</table>
<table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path, version</columns>
<file path="/galaxy/server/config/mutable/salmon_indexes_versioned.loc"/>
</table>
<table name="sailfish_indexes" comment_char="#">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/sailfish_indexes.loc"/>
</table>
<table name="gene_sets" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/gene_sets.loc"/>
</table>
<table name="sam_fa_indexes" comment_char="#">
<columns>line_type, value, path</columns>
<file path="/galaxy/server/config/mutable/sam_fa_indices.loc"/>
</table>
<table name="snpeff_msigdb_database" comment_char="#" allow_duplicate_entries="False">
<columns>value, name, path</columns>
<file path="/galaxy/server/config/mutable/snpeff_msigdb_database.loc"/>
</table>
<table name="snpsift_dbnsfps" comment_char="#" allow_duplicate_entries="False">
<columns>key, build, name, value, annotations</columns>
<file path="/galaxy/server/config/mutable/snpsift_dbnsfp.loc"/>
</table>
<table name="snpeffv_genomedb" comment_char="#" allow_duplicate_entries="False">
<columns>key, version, value, name, path</columns>
<file path="/galaxy/server/config/mutable/snpeffv_genomedb.loc"/>
</table>
<table name="snpeffv_regulationdb" comment_char="#" allow_duplicate_entries="False">
<columns>key, version, genome, value, name</columns>
<file path="/galaxy/server/config/mutable/snpeffv_regulationdb.loc"/>
</table>
<table name="featurecounts_anno" comment_char="#">
<columns>value, dbkey</columns>
<file path="/galaxy/server/config/mutable/featurecounts_anno.loc"/>
</table>
<table name="gemini_databases" comment_char="#" allow_duplicate_entries="False">
<columns>value, dbkey, name, path</columns>
<file path="/galaxy/server/config/mutable/gemini_databases.loc"/>
</table>
</tables>
1 change: 1 addition & 0 deletions galaxy/values.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -549,6 +549,7 @@ configs:
containers_resolvers_config_file: "/galaxy/server/config/container_resolvers_conf.xml"
workflow_schedulers_config_file: "/galaxy/server/config/workflow_schedulers_conf.xml"
build_sites_config_file: "/galaxy/server/config/build_sites.yml"
data_manager_config_file: "{{if .Values.setupJob.downloadToolConfs.enabled }}{{ .Values.setupJob.downloadToolConfs.volume.mountPath }}/config/shed_data_manager_conf.xml{{ else }}/galaxy/server/config/data_manager_conf.xml.sample{{ end }}"
shed_data_manager_config_file: "/galaxy/server/config/mutable/shed_data_manager_conf.xml"
shed_tool_data_table_config: "/galaxy/server/config/mutable/shed_tool_data_table_conf.xml"
enable_data_manager_user_view: true
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