Catalog¶
What has been requested from the IDC, and which data managers requests can use.
The page is generated from the repository (scripts/site_catalog.py) whenever
the site is built.
A request here isn't necessarily published yet. Each table below links to the data table on test.galaxyproject.org, which shows what is actually available, and Checking on a request explains how to follow one.
Versioned reference data¶
12 request(s) in 8 data table(s). Each version links to its request file under data-managers/; see Requesting reference data to add one.
all_fasta¶
Served entries on test.galaxyproject.org: /api/tool_data/all_fasta
| version | description | data manager | built from |
|---|---|---|---|
hg38canon |
Human hg38 (UCSC), canonical chromosomes chr1-22, X, Y, M only | devteam/data_manager_fetch_genome_dbkeys_all_fasta 0.0.6 |
fasta_indexes¶
Served entries on test.galaxyproject.org: /api/tool_data/fasta_indexes
| version | description | data manager | built from |
|---|---|---|---|
hg38canon |
Fasta index of human hg38, canonical chromosomes only (hg38canon) | devteam/data_manager_sam_fasta_index_builder 1.21+galaxy1 | all_fasta hg38canon |
gemini_versioned_databases¶
Served entries on test.galaxyproject.org: /api/tool_data/gemini_versioned_databases
| version | description | data manager | built from |
|---|---|---|---|
200 |
Full GEMINI 0.20.1 hg19 annotations with CADD and base-pair GERP (compatibility version 200). (doi:10.1371/journal.pcbi.1003153) | iuc/data_manager_gemini_database_downloader 0.20.1+galaxy1 |
metaphlan_database_versioned¶
Served entries on test.galaxyproject.org: /api/tool_data/metaphlan_database_versioned
| version | description | data manager | built from |
|---|---|---|---|
mpa_vJan21_CHOCOPhlAnSGB_202103 |
MetaPhlAn clade-specific marker genes (mpa_vJan21_CHOCOPhlAnSGB_202103) (doi:10.1101/2020.11.19.388223) | iuc/data_manager_metaphlan_database_downloader 4.0.6+galaxy5 | |
mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 |
MetaPhlAn TOY/demo marker database for tests (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103) (doi:10.1101/2020.11.19.388223) | iuc/data_manager_metaphlan_database_downloader 4.0.6+galaxy5 |
motus_db_versioned¶
Served entries on test.galaxyproject.org: /api/tool_data/motus_db_versioned
| version | description | data manager | built from |
|---|---|---|---|
3.1.0 |
mOTUs profiler database, version 3.1.0 | bgruening/data_manager_motus 3.1.0+galaxy2 |
repeatmasker_famdb¶
Served entries on test.galaxyproject.org: /api/tool_data/repeatmasker_famdb
| version | description | data manager | built from |
|---|---|---|---|
dfam_4.0_curated_consensus |
Dfam 4.0 repeat library in FamDB format (root partition and curated consensus sequences) for RepeatMasker | iuc/data_manager_repeatmasker 4.0+galaxy0 | |
dfam_4.0_curated_uncurated_consensus |
Dfam 4.0 repeat library in FamDB format (root partition, curated and uncurated consensus sequences) for RepeatMasker | iuc/data_manager_repeatmasker 4.0+galaxy0 |
rnastar_index2x_versioned¶
Served entries on test.galaxyproject.org: /api/tool_data/rnastar_index2x_versioned
| version | description | data manager | built from |
|---|---|---|---|
hg38canon |
STAR 2.7.4a index of human hg38, canonical chromosomes only (hg38canon) | iuc/data_manager_star_index_builder 2.7.4a+galaxy3 | all_fasta hg38canon |
samestr_db¶
Served entries on test.galaxyproject.org: /api/tool_data/samestr_db
| version | description | data manager | built from |
|---|---|---|---|
marker_db_motus_3.1.0 |
SameStr marker database derived from mOTUs 3.1.0 | iuc/data_manager_samestr 1.2025.111+galaxy4 | motus_db_versioned 3.1.0 |
marker_db_mpa_vJan21 |
SameStr marker database derived from MetaPhlAn mpa_vJan21_CHOCOPhlAnSGB_202103 | iuc/data_manager_samestr 1.2025.111+galaxy3 | metaphlan_database_versioned mpa_vJan21_CHOCOPhlAnSGB_202103 |
marker_db_mpa_vJan21_TOY |
SameStr marker database derived from MetaPhlAn mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 (for tests) | iuc/data_manager_samestr 1.2025.111+galaxy5 | metaphlan_database_versioned mpa_vJan21_TOY_CHOCOPhlAnSGB_202103 |
Data tables¶
The 26 data tables defined in config/tool_data_table_conf.xml, which Galaxy servers load from /cvmfs/idc.galaxyproject.org/config/tool_data_table_conf.xml (see Using IDC data in Galaxy). The .loc files are in /cvmfs/idc.galaxyproject.org/config/.
| table | columns | .loc file |
|---|---|---|
__dbkeys__ |
value, name, len_path | dbkeys.loc |
alignseq_seq |
type, value, path | alignseq.loc |
all_fasta |
value, dbkey, name, path | all_fasta.loc |
bowtie2_indexes |
value, dbkey, name, path | bowtie2_indices.loc |
bowtie_indexes |
value, dbkey, name, path | bowtie_indices.loc |
bracken_databases |
value, name, path | bracken_databases.loc |
bwa_mem_indexes |
value, dbkey, name, path | bwa_mem_index.loc |
fasta_indexes |
value, dbkey, name, path | fasta_indexes.loc |
gemini_versioned_databases |
value, dbkey, version, name, path | gemini_versioned_databases.loc |
hisat2_indexes |
value, dbkey, name, path | hisat2_indexes.loc |
kallisto_indexes |
value, dbkey, name, path | kallisto_indexes.loc |
kraken2_databases |
value, name, path | kraken2_databases.loc |
lastz_seqs |
value, name, path | lastz_seqs.loc |
metaphlan_database_versioned |
value, name, dbkey, path, db_version | metaphlan_database_versioned.loc |
motus_db_versioned |
value, version, name, path | motus_db_versioned.loc |
ncbi_accession2taxid |
value, name, path | ncbi_accession2taxid.loc |
ncbi_taxonomy |
value, name, path | ncbi_taxonomy.loc |
picard_indexes |
value, dbkey, name, path | picard_index.loc |
plant_tribes_scaffolds |
value, name, path, description | plant_tribes_scaffolds.loc |
repeatmasker_famdb |
value, name, version, components, engines, path | repeatmasker_famdb.loc |
rnastar_index2x_versioned |
value, dbkey, name, path, with_gene_model, version | rnastar_index2x_versioned.loc |
samestr_db |
value, name, path, version_file, samestr_version | samestr_db.loc |
snpeffv_databases |
key, version, value, name | snpeffv_databases.loc |
snpeffv_genomedb |
key, version, value, name, path | snpeffv_genomedb.loc |
snpeffv_regulationdb |
key, version, genome, value, name | snpeffv_regulationdb.loc |
twobit |
value, path | twobit.loc |
Data managers available for requests¶
The 93 data manager repositories installed on test.galaxyproject.org, the build Galaxy (from schemas/data_managers.yml, which is resolved from usegalaxy-tools' data_managers.yml). A request can use any of these tools; anything else has to be installed first.
| repository | tool id(s) at the installed revision | requested |
|---|---|---|
| bgruening/data_manager_diamond_database_builder | diamond_database_builder 0.0.5 |
|
| bgruening/data_manager_motus | motus_db_fetcher 3.1.0+galaxy2 |
yes |
| bgruening/data_manager_sylph_database | data_manager_sylph_database 0.8.1+galaxy0 |
|
| bgruening/data_manager_sylph_tax_database | data_manager_sylph_tax_database 1.9.1+galaxy0 |
|
| bgruening/kmetashot_build_database | kmetashot_build_database 2.0+galaxy3 |
|
| bgruening/mirge3_build_database | mirge3_build_database 0.1.4+galaxy1 |
|
| dave/data_manager_fetch_index_maf | data_manager_fetch_and_index_maf 1.1.0 |
|
| devteam/data_manager_bowtie2_index_builder | bowtie2_index_builder_data_manager 2.5.4+galaxy1 |
|
| devteam/data_manager_build_kraken_database | kraken_database_builder 1.1.2 |
|
| devteam/data_manager_bwa_mem_index_builder | bwa_mem_index_builder_data_manager 0.7.18+galaxy1 |
|
| devteam/data_manager_fetch_genome_dbkeys_all_fasta | data_manager_fetch_genome_all_fasta_dbkey 0.0.6 |
yes |
| devteam/data_manager_fetch_ncbi_taxonomy | ncbi_taxonomy_fetcher 1.1 |
|
| devteam/data_manager_gatk_picard_index_builder | gatk_picard_index_builder 0.0.2 |
|
| devteam/data_manager_picard_index_builder | picard_index_builder_data_manager 2.7.1+galaxy1 |
|
| devteam/data_manager_rsync_g2 | data_manager_rsync_g2 0.0.3 |
|
| devteam/data_manager_sam_fasta_index_builder | sam_fasta_index_builder 1.21+galaxy1 |
yes |
| devteam/data_manager_twobit_builder | twobit_builder_data_manager 0.0.4 |
|
| galaxyp/custom_pro_db_annotation_data_manager | custom_pro_db_annotation_data_manager 1.16.1.0 |
|
| galaxyp/data_manager_eggnog_mapper_abspath | data_manager_eggnog_abspath 2.1.8+galaxy2.1.8 |
|
| iuc/amrfinderplus_data_manager_build | data_manager_build_amrfinderplus 4.2.7+galaxy0 |
|
| iuc/bmtagger_index_builder_data_manager | bmtagger_index_builder_data_manager 3.101+galaxy0 |
|
| iuc/checkm2_build_database | checkm2_build_database 1.1.0+galaxy1 |
|
| iuc/data_manager_bakta | bakta_build_database 1.12.1+galaxy0 |
|
| iuc/data_manager_bowtie_index_builder | bowtie_index_builder_data_manager 1.3.1+galaxy1 |
|
| iuc/data_manager_build_coreprofiler | data_manager_build_coreprofiler 2.0.0+galaxy4 |
|
| iuc/data_manager_build_kma_index | kma_build_index 1.6.6+galaxy0 |
|
| iuc/data_manager_build_kraken2_database | kraken2_build_database 2.17.2+galaxy0 |
|
| iuc/data_manager_build_staramr | data_manager_build_staramr 0.11.0+galaxy1 |
|
| iuc/data_manager_bwa_mem2_index_builder | bwa_mem2_index_builder_data_manager 2.2.1+galaxy2 |
|
| iuc/data_manager_bwameth_index_builder | bwameth_index_builder_data_manager 1.0.0.3 |
|
| iuc/data_manager_cat | data_manager_cat 5.0.3.1 |
|
| iuc/data_manager_celltypist_models | data_manager_celltypist_models 0.0.2 |
|
| iuc/data_manager_clair3_models | data_manager_clair3_models 0.0.1 |
|
| iuc/data_manager_dada2 | dada2_fetcher 0.1.4 |
|
| iuc/data_manager_deeparg | data_manager_deeparg 1.0.4+galaxy1 |
|
| iuc/data_manager_dram_database_downloader | data_manager_dram_download 1.3.5+galaxy1 |
|
| iuc/data_manager_fetch_busco | busco_fetcher 6.1.0+galaxy0 |
|
| iuc/data_manager_fetch_busco_options | busco_fetcher_options 6.0.0+galaxy0 |
|
| iuc/data_manager_fetch_index_maf | data_manager_fetch_and_index_maf 1.0.0 |
|
| iuc/data_manager_fetch_plasmidfinder | data_manager_fetch_plasmidfinder 2.1.6+galaxy2 |
|
| iuc/data_manager_fetch_refseq | data_manager_fetch_refseq 0.0.20 |
|
| iuc/data_manager_funannotate | data_manager_funannotate_options 1.8.15+galaxy0 |
|
| iuc/data_manager_funannotate_options | data_manager_funannotate_options 1.8.15+galaxy0 |
|
| iuc/data_manager_gemini_database_downloader | data_manager_gemini_download 0.20.1+galaxy1 |
yes |
| iuc/data_manager_genomic_super_signature_ravmodels | data_manager_genomic_super_signature_ravmodels 0.0.1 |
|
| iuc/data_manager_groot_database_downloader | groot_database_downloader 1.1.2+galaxy1 |
|
| iuc/data_manager_gtdbtk_database_installer | gtdbtk_database_installer 232+galaxy0 |
|
| iuc/data_manager_hisat2_index_builder | hisat2_index_builder_data_manager 2.2.1+galaxy2 |
|
| iuc/data_manager_homer_preparse | homer_genome_preparse_data_manager 4.11homer_install_promoters_data_manager 4.11 |
|
| iuc/data_manager_humann2_database_downloader | data_manager_humann2_download 0.11.1.0 |
|
| iuc/data_manager_humann_database_downloader | data_manager_humann_download 3.9+galaxy0 |
|
| iuc/data_manager_interproscan | data_manager_interproscan 0.0.3 |
|
| iuc/data_manager_kaiju | kaiju_data_manager 1.10.1+galaxy0 |
|
| iuc/data_manager_kallisto_index_builder | kallisto_index_builder_data_manager 0.43.2 |
|
| iuc/data_manager_liana_resources | data_manager_fetch_liana_resources 1.0+galaxy0 |
|
| iuc/data_manager_malt_index_builder | data_manager_malt_index_builder 0.5.3+galaxy0 |
|
| iuc/data_manager_manual | data_manager_manual 0.0.3 |
|
| iuc/data_manager_mash_sketch_builder | mash_sketch_builder 2.1+galaxy0 |
|
| iuc/data_manager_metaphlan_database_downloader | data_manager_metaphlan_download 4.0.6+galaxy5 |
yes |
| iuc/data_manager_minibwa_index_builder | minibwa_index_builder_data_manager 0.5+galaxy0 |
|
| iuc/data_manager_mitos | data_manager_mitos 0.0.3 |
|
| iuc/data_manager_mmseqs2_database | data_manager_mmseqs2_download 17-b804f+galaxy0 |
|
| iuc/data_manager_mothur_toolsuite | data_manager_fetch_mothur_reference_data 0.2.2 |
|
| iuc/data_manager_ncbi_fcs_gx_database_downloader | data_manager_ncbi_fcs_gx_database_downloader 0.5.4+galaxy0 |
|
| iuc/data_manager_ncbi_taxonomy_sqlite | data_manager_ncbi_taxonomy_sqlite 1.0.5+galaxy2 |
|
| iuc/data_manager_nextclade | data_manager_nextclade 0.0.1+galaxy0 |
|
| iuc/data_manager_omamer | data_manager_omamer 2.0.2+galaxy2 |
|
| iuc/data_manager_packaged_annotation_data | data_manager_packaged_annotation_data 0.1 |
|
| iuc/data_manager_pangolearn | data_manager_pangolearn 0.0.3+galaxy2 |
|
| iuc/data_manager_pangolin_data | data_manager_pangolin_data 0.0.1+galaxy1 |
|
| iuc/data_manager_pharokka | pharokka_db_fetcher 1.3.2+galaxy0 |
|
| iuc/data_manager_plant_tribes_scaffolds_downloader | data_manager_plant_tribes_scaffolds_download 1.1.2 |
|
| iuc/data_manager_primer_scheme_bedfiles | data_manager_primer_scheme_bedfiles 0.0.13 |
|
| iuc/data_manager_qiime_database_downloader | data_manager_qiime_download 1.9.3 |
|
| iuc/data_manager_repeatmasker | repeatmasker_download 4.0+galaxy0 |
yes |
| iuc/data_manager_salmon_index_builder | salmon_index_builder_data_manager 1.10.1+galaxy1 |
|
| iuc/data_manager_samestr | samestr_db 1.2025.111+galaxy5 |
yes |
| iuc/data_manager_selection_background | data_manager_selection_background 1.0.4 |
|
| iuc/data_manager_semibin | data_manager_semibin 2.0.2+galaxy0 |
|
| iuc/data_manager_snpeff | data_manager_snpeff_databases 5.4.0cdata_manager_snpeff_download 5.4.0c |
|
| iuc/data_manager_snpsift_dbnsfp | data_manager_snpsift_dbnsfp 4.1.1 |
|
| iuc/data_manager_stanza_models | data_manager_stanza_models 1.14.0+galaxy1 |
|
| iuc/data_manager_star_index_builder | rna_star_index_builder_data_manager 2.7.4a+galaxy3 |
yes |
| iuc/data_manager_transvar_annotations | data_manager_transvar_download 2.5.10.20211024+galaxy0 |
|
| iuc/data_manager_vep_cache_downloader | data_manager_vep_cache_download 0.1 |
|
| iuc/data_manager_vsnp_dnaprints | vsnp_dnaprints_fetcher 0.0.8 |
|
| iuc/data_manager_vsnp_excel | vsnp_excel_fetcher 0.0.8 |
|
| iuc/data_manager_vsnp_genbank | vsnp_genbank_fetcher 0.0.8 |
|
| iuc/deacon_build_database | deacon_build_database 0.17.0+galaxy0 |
|
| rnateam/data_manager_sortmerna_database_downloader | data_manager_sortmerna_download 2.1b.1 |
|
| rplanel/data_manager_defense_finder | defense_finder_models_fetcher_data_manager 2.0.0+galaxy4 |
|
| scottx611x/data_manager_fetch_gene_annotation | gene_annotation_fetcher_data_manager 1.0.2 |
|
| ufz/virsorter_build_database | virsorter_build_database 2.2.4+galaxy2 |
Genomes in genomes.yml¶
The 5 genome(s) in genomes.yml, built with the indexers in data_managers.yml by the earlier Jenkins pipeline. New genomes are requested like other data; see Genomes.
| dbkey | description | source | indexers |
|---|---|---|---|
dm6 |
(from UCSC) | ucsc | bowtie2_index_builder, bwa_mem_index_builder, twobit_builder, picard_index_builder, sam_fasta_index_builder, hisat2_index_builder, star_index_builder |
danRer10 |
(from UCSC) | ucsc | bowtie2_index_builder, bwa_mem_index_builder, twobit_builder, picard_index_builder, sam_fasta_index_builder, hisat2_index_builder, star_index_builder |
sacCer3 |
(from UCSC) | ucsc | bowtie2_index_builder, bwa_mem_index_builder, twobit_builder, picard_index_builder, sam_fasta_index_builder, hisat2_index_builder, star_index_builder |
Ecoli-O157-H7-Sakai |
Escherichia coli O157-H7 Sakai | https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/Ecoli-O157_H7-Sakai-chr.fna | bowtie2_index_builder, bwa_mem_index_builder, twobit_builder, picard_index_builder, sam_fasta_index_builder, hisat2_index_builder, star_index_builder |
Salm-enterica-Newport |
Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1 | NC_021902 | bowtie2_index_builder, bwa_mem_index_builder, twobit_builder, picard_index_builder, sam_fasta_index_builder, hisat2_index_builder, star_index_builder |