title = "BioInstaller databases main repo."

[db_oncotator]
source_url = "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/oncotator/oncotator_{{version}}.tar.gz"
version_available = ["v1_ds_April052016"]

[db_srnanalyzer]
source_url = "http://srnanalyzer.systemsbiology.net/downloads/{{version}}.tar.gz"
version_available = ["sRNA_DBs", "MainDBs", "NCBI_NonHuman"]
version_description = ["small RNA Databases", "Human and Exogenous Databases", "NCBI Non-Human Databases"]

[db_cscd]
source_url="http://gb.whu.edu.cn/CSCD/public/static/download/{{version}}.tar.gz"

version_available = ["hg19-cancer-circrna", "hg19-cancer-circrna-mre", "hg19-cancer-circrna-rbp", "hg19-cancer-circrna-orf", "hg19-normal-circrna", "hg19-normal-circrna-mre", "hg19-normal-circrna-rbp", "hg19-normal-circrna-orf", "hg19-common-circrna", "hg19-common-circrna-mre", "hg19-common-circrna-rbp", "hg19-common-circrna-orf", "hg38-cancer-circrna", "hg38-cancer-circrna-mre", "hg38-cancer-circrna-rbp", "hg38-cancer-circrna-orf", "hg38-normal-circrna", "hg38-normal-circrna-mre", "hg38-normal-circrna-rbp", "hg38-normal-circrna-orf", "hg38-common-circrna", "hg38-common-circrna-mre", "hg38-common-circrna-rbp", "hg38-common-circrna-orf"]

[db_differentialnet]
source_url = "http://netbio.bgu.ac.il/diffnet-interactomes/@>@str_replace('{{version}}', '_.*', '')@<@/@>@str_replace('{{version}}', '.*_', '')@<@.tsv"
decompress = false
version_available = ["HPA_Adrenal", "HPA_Appendix", "HPA_Bonemarrow", "HPA_Brain", "HPA_Colon", "HPA_Endometrium", "HPA_Esophagus", "HPA_FallopianTube", "HPA_Fat", "HPA_Gallbladder", "HPA_Heart", "HPA_Kidney", "HPA_Liver", "HPA_Lung", "HPA_LymphNode", "HPA_Ovary", "HPA_Placenta", "HPA_Prostate", "HPA_Rectum", "HPA_SalivaryGland", "HPA_SkeletalMuscle", "HPA_Skin", "HPA_SmallIntestine", "HPA_SmoothMuscle", "HPA_Spleen", "HPA_Stomach", "HPA_Testis", "HPA_Thyroid", "HPA_Tonsil", "GTEx_Adipose - Subcutaneous", "GTEx_Adipose - Visceral (Omentum)", "GTEx_Artery - Aorta", "GTEx_Artery - Coronary", "GTEx_Artery - Tibial", "GTEx_Brain - Amygdala", "GTEx_Brain - Anterior cingulate cortex (BA24)", "GTEx_Brain - Caudate (basal ganglia)", "GTEx_Brain - Cerebellar Hemisphere", "GTEx_Brain - Cerebellum", "GTEx_Brain - Cortex", "GTEx_Brain - Frontal Cortex (BA9)", "GTEx_Brain - Hippocampus", "GTEx_Brain - Hypothalamus", "GTEx_Brain - Nucleus accumbens (basal ganglia)", "GTEx_Brain - Putamen (basal ganglia)", "GTEx_Brain - Spinal cord (cervical c-1)", "GTEx_Brain - Substantia nigra", "GTEx_Breast - Mammary Tissue", "GTEx_Cells - EBV-transformed lymphocytes", "GTEx_Cells - Transformed fibroblasts", "GTEx_Colon - Sigmoid", "GTEx_Esophagus - Gastroesophageal Junction", "GTEx_Esophagus - Mucosa", "GTEx_Esophagus - Muscularis", "GTEx_Heart - Atrial Appendage", "GTEx_Heart - Left Ventricle", "GTEx_Liver", "GTEx_Lung", "GTEx_Minor Salivary Gland", "GTEx_Muscle - Skeletal", "GTEx_Nerve - Tibial", "GTEx_Ovary", "GTEx_Pituitary", "GTEx_Prostate", "GTEx_Skin - Not Sun Exposed (Suprapubic)", "GTEx_Skin - Sun Exposed (Lower leg)", "GTEx_Stomach", "GTEx_Testis", "GTEx_Thyroid", "GTEx_Uterus", "GTEx_Vagina", "GTEx_Whole Blood", "GTEx_Whole Brain"]

[db_seecancer]
source_url = "http://biocc.hrbmu.edu.cn/SEECancer/download/{{version}}.txt"
decompress = false
version_available = ["early_events", "late_events", "relapse_events", "metastasis_events",
                     "drug_resistant_events", "drug_induced_events", "temporal_sequence"]

[db_diseaseenhancer]
source_url = "http://biocc.hrbmu.edu.cn/DiseaseEnhancer/RFunctions/diseaseEnh5.1.txt"
version_available = ["diseaseEnh5.1", "enhInfo", "enh2target"]

[db_pancanqtl]
source_url = "http://bioinfo.life.hust.edu.cn/PancanQTL/static/download/{{version}}.xls"
version_available = ["ACC_tumor.cis_eQTL", "BLCA_tumor.cis_eQTL", "BRCA_tumor.cis_eQTL",
"CESC_tumor.cis_eQTL", "CHOL_tumor.cis_eQTL", "COAD_tumor.cis_eQTL", "DLBC_tumor.cis_eQTL",
"ESCA_tumor.cis_eQTL", "GBM_tumor.cis_eQTL", "HNSC_tumor.cis_eQTL", "KICH_tumor.cis_eQTL",
"KIRC_tumor.cis_eQTL", "KIRP_tumor.cis_eQTL", "LAML_tumor.cis_eQTL", "LGG_tumor.cis_eQTL",
"LIHC_tumor.cis_eQTL", "LUAD_tumor.cis_eQTL", "LUSC_tumor.cis_eQTL", "MESO_tumor.cis_eQTL",
"OV_tumor.cis_eQTL", "PAAD_tumor.cis_eQTL", "PCPG_tumor.cis_eQTL", "PRAD_tumor.cis_eQTL",
"READ_tumor.cis_eQTL", "SARC_tumor.cis_eQTL", "SKCM_tumor.cis_eQTL", "STAD_tumor.cis_eQTL",
"TGCT_tumor.cis_eQTL", "THCA_tumor.cis_eQTL", "THYM_tumor.cis_eQTL", "UCEC_tumor.cis_eQTL",
"UCS_tumor.cis_eQTL", "UVM_tumor.cis_eQTL", "ACC_tumor.trans_eQTL", "BLCA_tumor.trans_eQTL",
"BRCA_tumor.trans_eQTL", "CESC_tumor.trans_eQTL", "CHOL_tumor.trans_eQTL", "COAD_tumor.trans_eQTL",
"DLBC_tumor.trans_eQTL", "ESCA_tumor.trans_eQTL", "GBM_tumor.trans_eQTL", "HNSC_tumor.trans_eQTL",
"KICH_tumor.trans_eQTL", "KIRC_tumor.trans_eQTL", "KIRP_tumor.trans_eQTL", "LAML_tumor.trans_eQTL",
"LGG_tumor.trans_eQTL", "LIHC_tumor.trans_eQTL", "LUAD_tumor.trans_eQTL", "LUSC_tumor.trans_eQTL",
"MESO_tumor.trans_eQTL", "OV_tumor.trans_eQTL", "PAAD_tumor.trans_eQTL", "PCPG_tumor.trans_eQTL",
"PRAD_tumor.trans_eQTL", "READ_tumor.trans_eQTL", "SARC_tumor.trans_eQTL", "SKCM_tumor.trans_eQTL",
"STAD_tumor.trans_eQTL", "TGCT_tumor.trans_eQTL", "THCA_tumor.trans_eQTL", "THYM_tumor.trans_eQTL",
"UCEC_tumor.trans_eQTL", "UCS_tumor.trans_eQTL", "UVM_tumor.trans_eQTL"]

[db_msdd]
source_url = "http://www.bio-bigdata.com/msdd/download/{{version}}.zip"
version_available = "msdd"

[db_mndr]
source_url = "http://www.rna-society.org/mndr/php/download.php?file={{version}}.zip"
version_available = ["All ncRNA-disease", "miRNA-disease", "lncRNA-disease"]

[db_rsnp3]
source_url = "ftp://rv.psych.ac.cn/pub/rsnp3/rSNP_info_{{version}}.tar.gz"
version_available = "all"

[db_ecodrug]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/ecodrug/ECOdrug_{{version}}.csv.gz"
version_available = ["eggnog", "ensembl", "inparanoid", "majority_vote"]

[db_medreaders]
source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/medreader/paper.TF.PWM.tar.gz",
              "http://bioinfo.rjh.com.cn/download/bioinstaller/medreader/paper.TF.summary.xlsx.gz"]
version_available = "newst"

[db_superdrug2]
source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/superdrug2/{{version}}.csv.zip",
              "http://bioinfo.rjh.com.cn/download/bioinstaller/superdrug2/{{version}}.zip"]
url_all_download = false
version_available = ["all_drugs_2D_structures", "all_drugs_3D_structures", "all_drugs_chemical_structure_identifiers", "all_drugs_extlinks", "all_drugs_molecular_properties", "approved_drugs_chemical_structure_identifiers", "approved_drugs_extlinks", "approved_drugs_molecular_properties"]

[db_varcards]
source_url = ["http://159.226.67.237/sun/varcards/resource/download/variant/{{version}}.variant.annotation.xls.gz",
              "http://bioinfo.rjh.com.cn/download/bioinstaller/varcards/{{version}}.variant.annotation.xls.gz"]
url_all_download = false
version_available = ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY"]

[db_civic]
source_url = "https://civic.genome.wustl.edu/downloads/nightly/nightly-{{version}}.tsv"
decompress = false
version_available = ["GeneSummaries", "VariantSummaries", "VariantGroupSummaries", "ClinicalEvidenceSummaries"]

[db_expression_atlas]
source_url = "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/atlas-{{version}}-data.tar.gz"
version_available = "latest"

[db_remap2]
source_url = ["http://tagc.univ-mrs.fr/remap/download/MACS/ReMap2_TF_{{version}}Peaks.tar.gz",
              "http://tagc.univ-mrs.fr/remap/download/MACS/ReMap2_{{version}}Peaks.bed.gz",
              "http://tagc.univ-mrs.fr/remap/download/MACS/ReMap2_{{version}}.bed.gz",
              "@<@if (str_detect('{{version}}', 'hg19')) {str_replace('{{version}}', '_hg19', '');'http://tagc.univ-mrs.fr/remap/download/MACS_lifted_hg19/ReMap2_TF_{{version}}Peaks_hg19.tar.gz'}@<@",
              "@<@if (str_detect('{{version}}', 'hg19')) {str_replace('{{version}}', '_hg19', '');'http://tagc.univ-mrs.fr/remap/download/MACS_lifted_hg19/ReMap2_{{version}}Peaks_hg19.bed.gz'}@<@",
              "@<@if (str_detect('{{version}}', 'hg19')) {str_replace('{{version}}', '_hg19', '');'http://tagc.univ-mrs.fr/remap/download/MACS_lifted_hg19/ReMap2_{{version}}_hg19.bed.gz'}@<@"]

version_available = ["archive_all", "archive_nr",
                     "archive_all_hg19", "archive_nr_hg19",
                     "public_all", "public_crm", "public_nr",
                     "encode_all", "encode_crm", "encode_nr",
                     "all", "crm", "nr"]

[db_remap]
source_url = ["http://tagc.univ-mrs.fr/remap/download/remap1/ReMap2015_TF_{{version}}Peaks.tar.gz",
              "http://tagc.univ-mrs.fr/remap/download/ReMap1_lifted_hg38/{{version}}.bed.gz",
              "http://tagc.univ-mrs.fr/remap/download/remap1/All/{{version}}.bed.gz"]
version_available = ["archive_all", "archive_nr", "filPeaks_public", "filPeaks_all", "nrPeaks_public", "nrPeaks_all",
                     "hg38_allPeaks", "hg38_nrPeaks"]

[db_funcoup]
source_url = "http://funcoup.sbc.su.se/downloads/download.action?type=network&instanceID=7617155&fileName={{version}}.gz"
version_available = ["FC4.0_A.thaliana_full", "FC4.0_B.subtilis_full", "FC4.0_B.taurus_full", "FC4.0_C.elegans_full", "FC4.0_C.familiaris_full", "FC4.0_C.intestinalis_full", "FC4.0_D.melanogaster_full", "FC4.0_D.rerio_full", "FC4.0_E.coli_full", "FC4.0_G.gallus_full", "FC4.0_H.sapiens_full", "FC4.0_M.musculus_full", "FC4.0_O.sativa_full", "FC4.0_P.falciparum_full", "FC4.0_R.norvegicus_full", "FC4.0_S.cerevisiae_full", "FC4.0_S.pombe_full", "FC4.0_A.thaliana_compact", "FC4.0_B.subtilis_compact", "FC4.0_B.taurus_compact", "FC4.0_C.elegans_compact", "FC4.0_C.familiaris_compact", "FC4.0_C.intestinalis_compact", "FC4.0_D.melanogaster_compact", "FC4.0_D.rerio_compact", "FC4.0_E.coli_compact", "FC4.0_G.gallus_compact", "FC4.0_H.sapiens_compact", "FC4.0_M.musculus_compact", "FC4.0_O.sativa_compact", "FC4.0_P.falciparum_compact", "FC4.0_R.norvegicus_compact", "FC4.0_S.cerevisiae_compact", "FC4.0_S.pombe_compact"]

[db_proteinatlas]
source_url = ["https://www.proteinatlas.org/download/{{version}}.tsv.zip",
              "https://www.proteinatlas.org/download/{{version}}.gz",
              "https://www.proteinatlas.org/images_static/{{version}}"]
decompress = [true, true, false]
url_all_download = false
version_available = ["normal_tissue", "pathology", "subcellular_location",
                     "rna_tissue", "transcript_rna_tissue", "transcript_rna_celline",
                     "proteinatlas", "proteinatlas.xml", "proteinatlas.trig", "cell.svg"]

[db_dgidb]
source_url = "http://www.dgidb.org/data/{{version}}"
version_available = ["interactions.tsv", "genes.tsv", "drugs.tsv",
                      "categories.tsv", "data/dGene_04-16-2013_2257.tsv",
                      "data.sql"]

[db_drugbank]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/drugbank/{{version}}.xml.zip"
version_available = "drugbank_all_full_database"

[db_interpro]
source_url = "ftp://ftp.ebi.ac.uk/pub/databases/interpro/{{version}}"
version_available = ["entry.list", "interpro.xml.gz", "match_complete.xml.gz",
                     "uniparc_match.tar.gz", "protein2ipr.dat.gz", "ParentChildTreeFile.txt",
                     "interpro2go", "release_notes.txt"]

[db_inbiomap]
source_url = "https://www.intomics.com/inbio/map/api/get_data?file=InBio_Map_core_{{version}}.tar.gz"
version_available = ["2016_09_12", "2016_05_31", "2016_02_05", "2015_11_02"]

[db_omim_open]
source_url = [
             "https://omim.org/static/omim/data/{{version}}.txt",
             "https://raw.githubusercontent.com/macarthur-lab/omim/master/data/{{version}}.txt"
             ]
version_available = ["mim2gene", "full_omim_table", "gene_symbol_thesaurus", "use_omim_table"]

[db_omim_private]
# {{license}} is omim.org granted
# if you want to download the data using JhuangLab URL and only for academic purpose,
# you can contact lee_jianfeng@sjtu.edu.cn
source_url = [
             "https://data.omim.org/downloads/{{license}}/{{version}}.txt",
             "http://bioinfo.rjh.com.cn/download/bioinstaller/omim/{{license}}/{{version}}.txt",
             "https://omim.org/static/omim/data/{{version}}.txt"
             ]
url_all_download = false
version_available = ["mim2gene", "genemap2", "genemap", "mimTitles", "morbidmap"]

[db_biosystems]
source_url = ["ftp://ftp.ncbi.nih.gov/pub/biosystems/biosystems.{{version}}/"]
source_is_dir = true
version_available = ["20170414", "20170421"]

[db_denovo_db]
source_url = "http://denovo-db.gs.washington.edu/denovo-db.variants.v.{{version}}.tsv.gz"
version_available = "1.5"

[db_hpo]
source_url = "http://compbio.charite.de/jenkins/job/hpo.annotations.monthly/{{version}}/artifact/annotation/*zip*/annotation.zip"
version_available = "lastStableBuild"

[db_tumorfusions]
source_url = "http://www.tumorfusions.org/downloads/{{version}}.txt.gz"
version_available = "pancanfus"

[db_gtex]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/gtex/v7/{{version}}"
version_available = [
                     "GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_exon_reads.txt.gz", "GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.gct.gz", "GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_reads.gct.gz", "GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_tpm.gct.gz", "GTEx_Analysis_2016-01-15_v7_RSEMv1.2.22_transcript_expected_count.txt.gz", "GTEx_Analysis_2016-01-15_v7_RSEMv1.2.22_transcript_tpm.txt.gz", "GTEx_Analysis_2016-01-15_v7_STARv2.4.2a_junctions.gct.gz", "GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_635Ind_PASS_AB02_GQ20_HETX_MISS15_PLINKQC.lookup_table.txt.gz", "GTEx_Analysis_v7_Annotations_SampleAttributesDD.xlsx.gz", "GTEx_Analysis_v7_Annotations_SubjectPhenotypesDD.xlsx.gz", "GTEx_Analysis_v7_eQTL_covariates.tar.gz", "GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz", "GTEx_Analysis_v7_eQTL.tar.gz", "GTEx_Analysis_v7.metasoft.txt.gz", "GTEx_droncseq_hip_pcf.tar.gz", "GTEx_v7_Annotations_SampleAttributesDS.txt", "GTEx_v7_Annotations_SubjectPhenotypesDS.txt", "Homo_sapiens_assembly19.fasta.gz", "biobank_collection_20171126_031201.txt.gz", "gencode.v19.genes.patched_contigs_exons.txt.gz", "gencode.v19.genes.v7.patched_contigs.gtf.gz", "gencode.v19.transcripts.patched_contigs.gtf.gz"
                     ]

[db_hgnc]
source_url = ["ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/locus_groups/{{version}}.txt",
              "ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/{{version}}.txt",
              "http://bioinfo.rjh.com.cn/download/bioinstaller/hgnc/{{version}}.txt"]
version_available = ["protein-coding_gene", "non-coding_RNA", "phenotype",
                     "pseudogene", "other", "withdrawn", "protein-coding_gene_alt_loci",
                     "non-coding_RNA_alt_loci", "pseudogene_alt_loci",
                     "other_alt_loci", "genefamilies"]
url_all_download = false

[db_atcircdb]
source_url = "http://genome.sdau.edu.cn/circRNAdata/{{version}}"
version_available = ["sw_final_circ_web_final.xlsx", "enrich_circ.csv", "SRRList_622samples_website.csv",
                     "SRRList_150samples_CIRI2_validation.xlsx", "psTarget.csv",
                     "TAPIR.csv", "Sun.xls", "Ye.csv"]

[db_circnet]
source_url = "http://140.120.203.41/{{version}}.zip"
version_available = "CircNetData"

[db_circbase]
source_url = "http://circrna.org/download/{{version}}"
version_available = ["hsa_hg19_circRNA.txt", "hsa_hg19_circRNA.xlsx",
                     "hsa_hg19_circRNA.bed", "hsa_graph.png",
                     "ce6_circID_to_name.txt", "mm9_circID_to_name.txt",
                     "hg19_circID_to_name.txt", "find_circ.tar.gz",
                     "mouse_mm9_circRNAs_putative_spliced_sequence.fa.gz",
                     "human_hg19_circRNAs_putative_spliced_sequence.fa.gz"]

[db_circrnadb]
source_url = "http://202.195.183.4:8000/circrnadb/doc/{{version}}.zip"
version_available = ["circRNADb", "genes.gtf", "Protein_features",
                     "Protein_expression_evidence", "circRNA_parentalgene-diseases"]

[db_exorbase]
source_url = "http://www.exorbase.org/exoRBase/download/download?file={{version}}.txt"
version_available = ["Normal_circRNA_RPM", "CHD_circRNA_RPM", "CRC_circRNA_RPM", "HCC_circRNA_RPM", "PAAD_circRNA_RPM", "WhB_circRNA_RPM", "Samples_combined_circRNA_RPM", "Normal_lncRNA_TPM", "CHD_lncRNA_TPM", "CRC_lncRNA_TPM", "HCC_lncRNA_TPM", "PAAD_lncRNA_TPM", "WhB_lncRNA_TPM", "Samples_combined_lncRNA_TPM", "Normal_mRNA_TPM", "CHD_mRNA_TPM", "CRC_mRNA_TPM", "HCC_mRNA_TPM", "PAAD_mRNA_TPM", "WhB_mRNA_TPM", "Samples_combined_mRNA_TPM", "circRNA_ann", "lncRNA_ann", "mRNA_ann",
"Experimental_revised"]

[db_exsnp]
source_url = "http://www.exsnp.org/data/{{version}}.txt"
version_available = ["raw_eQTL", "GSexSNP_allc_allp_ld8", "GSexSNP_allc_allp_ld5",
            "GSexSNP_allc_allp_ld3", "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_BD",
            "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_CAD", "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_CD",
            "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_HT", "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_RA",
            "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_T1D", "WTCCC_DZ_allc_allp_GSeQTL_0.05cM_list_T2D"]
tag = ["eqtl"]

[db_rvarbase]
source_url = "ftp://rv.psych.ac.cn/pub/rv/{{version}}.txt.gz"
version_available = ["dbsnp_info1", "dbvar_info"]
tag = ["eqtl"]

[db_seeqtl]
source_url = ["http://www.bios.unc.edu/research/genomic_software/seeQTL/data/{{version}}.tar.gz",
              "http://www.bios.unc.edu/research/genomic_software/seeQTL/data/{{version}}.txt"]
url_all_download = false
version_available = [
                     "pca_genotype", "genotype_expression_data",
                     "eQTL_Qvalue_cutoff_hapmap3_cis_hg19", "eQTL_Qvalue_cutoff_hapmap3_trans_hg19",
                     "eQTL_Qvalue_cutoff_Myers_cis_hg19", "eQTL_Qvalue_cutoff_Myers_trans_hg19",
                     "data.montgomery", "data.argonne", "data.yale"
                     ]
tag = ["eqtl"]

[db_fantom_cage_peaks]
source_url = "http://fantom.gsc.riken.jp/5/datafiles/latest/extra/{{version}}/"
source_is_dir = true
version_available = "CAGE_peaks"

[db_fantom_co_expression_clusters]
source_url = "http://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/{{version}}/"
source_is_dir = true
version_available = "Co-expression_clusters"

[db_fantom_enhancers]
source_url = "http://fantom.gsc.riken.jp/5/datafiles/latest/extra/{{version}}/"
source_is_dir = true
version_available = "Enhancers"

[db_fantom_motifs]
source_url = "http://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/Motifs/{{version}}/"
source_is_dir = true
version_available = ["/", "TFBS", "jaspar_Significance_of_the_correlation_with_CAGE_expression",
                      "novel_GREAT_analysis_results", "novel_Significance_of_the_correlation_with_CAGE_expression"]

[db_fantom_ontology]
source_url = "http://fantom.gsc.riken.jp/5/datafiles/latest/extra/{{version}}/"
source_is_dir = true
version_available = ["Ontology"]

[db_fantom_tss_classifier]
source_url = "http://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/{{version}}/"
source_is_dir = true
version_available = ["TSS_classifier"]

[db_snipa3]
source_url = [
              "http://snipa.helmholtz-muenchen.de/snipa3/data/annotation/grch37/ensembl87/{{version}}.tabix.gz",
              "http://snipa.helmholtz-muenchen.de/snipa3/data/annotation/grch37/ensembl87/{{version}}.tabix.gz.tbi"
              ]
version_available = ["!!glue {sprintf('chr%s', 1:22)}", "chrX"]


[db_rddpred]
source_url = "http://epigenomics.snu.ac.kr/RDDpred/prior_data/{{version}}.MES.txt.gz"
version_available = ["Human", "Mouse", "Drosophila", "Arabidopsis"]

[db_lncediting]
source_url = "http://bioinfo.life.hust.edu.cn/LNCediting/static/human/download/{{version}}"

version_available = ["table1_lncrna_info", "table2_edit_sequence", "table3_edit_site_info",
                     "table4_mirna_info", "table5_mirna_profile", "table7_function_gain",
                     "table8_function_loss"]

[db_eggnog]
source_url = ["http://eggnogdb.embl.de/download/eggnog_4.5/data/{{version}}/{{version}}.members.tsv.gz",
              "http://eggnogdb.embl.de/download/eggnog_4.5/data/{{version}}/{{version}}.annotations.tsv.gz",
              "http://eggnogdb.embl.de/download/eggnog_4.5/data/{{version}}/{{version}}.trees.tsv.gz",
              "http://eggnogdb.embl.de/download/eggnog_4.5/data/{{version}}/{{version}}.raw_algs.tsv.gz",
              "http://eggnogdb.embl.de/download/eggnog_4.5/data/{{version}}/{{version}}.trimmed_algs.tsv.gz",
              "http://eggnogdb.embl.de/download/eggnog_4.5/data/{{version}}/{{version}}.hmm.tsv.gz"]
version_available = ["NOG", "aciNOG", "acidNOG", "acoNOG", "actNOG", "agaNOG", "agarNOG", "apiNOG", "aproNOG", "aquNOG", "arNOG", "arcNOG", "artNOG", "arthNOG", "ascNOG", "aveNOG", "bacNOG", "bactNOG", "bacteNOG", "basNOG", "bctoNOG", "biNOG", "bproNOG", "braNOG", "carNOG", "chaNOG", "chlNOG", "chlaNOG", "chloNOG", "chlorNOG", "chloroNOG", "chorNOG", "chrNOG", "cloNOG", "cocNOG", "creNOG", "cryNOG", "cyaNOG", "cytNOG", "debNOG", "defNOG", "dehNOG", "deiNOG", "delNOG", "dipNOG", "dotNOG", "dproNOG", "droNOG", "eproNOG", "eryNOG", "euNOG", "eurNOG", "euroNOG", "eurotNOG", "fiNOG", "firmNOG", "flaNOG", "fuNOG", "fusoNOG", "gproNOG", "haeNOG", "halNOG", "homNOG", "hymNOG", "hypNOG", "inNOG", "kinNOG", "lepNOG", "lilNOG", "maNOG", "magNOG", "meNOG", "metNOG", "methNOG", "methaNOG", "necNOG", "negNOG", "nemNOG", "onyNOG", "opiNOG", "perNOG", "plaNOG", "pleNOG", "poaNOG", "prNOG", "proNOG", "rhaNOG", "roNOG", "sacNOG", "saccNOG", "sorNOG", "sordNOG", "sphNOG", "spiNOG", "spriNOG", "strNOG", "synNOG", "tenNOG", "thaNOG", "theNOG", "therNOG", "thermNOG", "treNOG", "veNOG", "verNOG", "verrNOG", "virNOG"]

[db_rbp_var]
source_url = "http://159.226.67.237/sun/RBP-Var/res/{{version}}.RBP-Var.score.p.txt.gz"
version_available = ["RNAedit", "dbSNP"]

[db_docm]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/docm/docm_{{version}}.txt.gz"
version_available = ["3.2", "3_clinvar_export"]

[db_cancer_hotspots]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/cancer_hotspots/cancer_hotspots_{{version}}.txt.gz"
version_available = ["v1_sheet1", "v1_sheet2", "v2_sheet1", "v2_sheet2"]

[db_intogen]
source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/intogen/intogen_cancer_{{version}}.zip",
              "http://bioinfo.rjh.com.cn/download/bioinstaller/intogen/intogen_{{version}}.zip"]
url_all_download = false
version_available = ["drivers-2014.12", "drivers_actionability-2014.12", "driver_mutations_catalog-2016.5"]

[db_disgenet]
source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/disgenet/{{version}}.tsv.gz",
              "http://bioinfo.rjh.com.cn/download/bioinstaller/disgenet/{{version}}.tar.gz"]
url_all_download = false
version_available = ["all_gene_disease_associations", "all_gene_disease_pmid_associations", "all_variant_disease_associations", "all_variant_disease_pmid_associations", "befree_gene_disease_associations", "befree_variant_disease_associations", "curated_gene_disease_associations", "curated_variant_disease_associations", "pubannotator", "pubannotator_variant_disease"]

[db_cgi]
source_url = ["http://bioinfo.rjh.com.cn/download/bioinstaller/cgi/{{version}}_latest.zip"]
version_available = ["cancer_bioactivities", "catalog_of_cancer_genes", "catalog_of_validated_oncogenic_mutations", "cgi_biomarkers"]

[db_oncokb]
source_url = "http://oncokb.org/api/v1/utils/{{version}}.txt"
version_available = ["allAnnotatedVariants", "allActionableVariants"]

[db_mirdb]
source_url = "http://mirdb.org/download/miRDB_v{{version}}_prediction_result.txt.gz"
version_available = ["5.0", "4.0", "3.0", "2.0", "1.0"]

[db_mirtarbase]
source_url = "http://mirtarbase.mbc.nctu.edu.tw/cache/download/{{version}}/miRTarBase_MTI.xlsx"
version_available = ["7.0"]

[db_mirnest]
source_url = "http://rhesus.amu.edu.pl/mirnest/copy/downloads/{{version}}.gz"
version_available = ["mirnest_EST_predictions", "mirnest_targets", "mirnest_deep_predictions",
                                  "mirnest_degradomes", "mirnest_mirtrons", "mirnest_mirna_gene_structure"]

[db_rbpdb]
source_url = "http://rbpdb.ccbr.utoronto.ca/downloads/{{version}}"
version_available = ["RBPDB_v1.3.1_2012-11-21.sql", "RBPDB_v1.3.1_2012-11-21_TDT.zip",
                                  "RBPDB_v1.3.1_2012-11-21_CSV.zip"]

[db_appris]
source_url = "http://apprisws.bioinfo.cnio.es/pub/current_release/datafiles/homo_sapiens/{{version}}/appris_data.principal.txt"
version_available = ["GRCh38", "rs108v26", "up201703v26", "a1v26", "GRCh37", "rs105v24", "g12v24"]

[db_lncipedia]
source_url = "https://lncipedia.org/downloads/lncipedia_{{version}}"
version_available = "!!glue {strsplit('@>@str <- c('%s_hg19.bed', '%s_hg38.bed', '%s_hc_hg19.bed', '%s_hc_hg38.bed', '%s.fasta', '%s_hc.fasta', '%s_hg19.gff', '%s_hg38.gff', '%s_hc_hg19.gff', '%s_hc_hg38.gff', '%s_hg19.gtf', '%s_hg38.gtf', '%s_hc_hg19.gtf', '%s_hc_hg38.gtf'); c(sprintf(str, '5_1'), sprintf(str, '5_2'))@<@', ' ')[[1]]}"

[db_msigdb]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/msigdb/{{version}}"
version_available = ["c1.all.v6.2.entrez.gmt", "c1.all.v6.2.symbols.gmt", "c2.all.v6.2.entrez.gmt", "c2.all.v6.2.symbols.gmt", "c2.cgp.v6.2.entrez.gmt", "c2.cgp.v6.2.symbols.gmt", "c2.cp.biocarta.v6.2.entrez.gmt", "c2.cp.biocarta.v6.2.symbols.gmt", "c2.cp.kegg.v6.2.entrez.gmt", "c2.cp.kegg.v6.2.symbols.gmt", "c2.cp.reactome.v6.2.entrez.gmt", "c2.cp.reactome.v6.2.symbols.gmt", "c2.cp.v6.2.entrez.gmt", "c2.cp.v6.2.symbols.gmt", "c3.all.v6.2.entrez.gmt", "c3.all.v6.2.symbols.gmt", "c3.mir.v6.2.entrez.gmt", "c3.mir.v6.2.symbols.gmt", "c3.tft.v6.2.entrez.gmt", "c3.tft.v6.2.symbols.gmt", "c4.all.v6.2.entrez.gmt", "c4.all.v6.2.symbols.gmt", "c4.cgn.v6.2.entrez.gmt", "c4.cgn.v6.2.symbols.gmt", "c4.cm.v6.2.entrez.gmt", "c4.cm.v6.2.symbols.gmt", "c5.all.v6.2.entrez.gmt", "c5.all.v6.2.symbols.gmt", "c5.bp.v6.2.entrez.gmt", "c5.bp.v6.2.symbols.gmt", "c5.cc.v6.2.entrez.gmt", "c5.cc.v6.2.symbols.gmt", "c5.mf.v6.2.entrez.gmt", "c5.mf.v6.2.symbols.gmt", "c6.all.v6.2.entrez.gmt", "c6.all.v6.2.symbols.gmt", "c7.all.v6.2.entrez.gmt", "c7.all.v6.2.symbols.gmt", "msigdb.v6.2.entrez.gmt", "msigdb.v6.2.symbols.gmt", "msigdb_v3.0.zip", "msigdb_v3.1.zip", "msigdb_v4.0.zip", "msigdb_v5.0.zip", "msigdb_v5.1.zip", "msigdb_v5.1_chip.zip", "msigdb_v5.2.zip", "msigdb_v5.2_chip.zip", "msigdb_v6.0.zip", "msigdb_v6.0_chip.zip", "msigdb_v6.1.zip", "msigdb_v6.1_chip.zip", "msigdb_v6.2.xml", "msigdb_v6.2.zip"]

[db_mircancer]
source_url = "http://mircancer.ecu.edu/downloads/{{version}}.txt"
version_available = ["miRCancerOctober2017", "miRCancerMarch2017", "miRCancerDecember2016", "miRCancerSeptember2016", "miRCancerJune2016", "miRCancerMarch2016", "miRCancerDecember2015", "miRCancerSeptember2015", "miRCancerJune2015", "miRCancerMarch2015", "miRCancerDecember2014", "miRCancerSeptember2014", "miRCancerJune2014", "miRCancerMarch2014", "miRCancerDecember2013", "miRCancerSeptember2013", "miRCancerJune2013", "miRCancerMarch2013", "miRCancerNovember2012"]

[db_dcdb]
source_url = "http://www.cls.zju.edu.cn/dcdb/downloadfile/{{version}}.zip"
version_available = ["DCDB2_plaintxt", "DCDB2.sql", "targets", "Drug_combinations",
                                  "components_identifier"]

[db_oncomirdb]
source_url = "http://lifeome.net/database/oncomirdb/oncomirdb.v-{{version}}_download.txt"
version_available = "1.1-20131217"

[db_islandviewer]
source_url = "http://www.pathogenomics.sfu.ca/islandviewer/download/datasets/all_gis_{{version}}.txt.tar.gz"
version_available = ["islandviewer_iv4", "islandpick_iv4", "islandpath_dimob_iv4",
                                  "sigi_hmm_iv4", "islander_iv4"]

[db_hpdi]
source_url = "http://bioinfo.wilmer.jhu.edu/PDI/{{version}}"
version_available = ["protein_chip_full_seq.csv", "protein_annotation.txt",
                                  "pro2motif.txt", "DNA_motifs.txt", "motif2protein.txt",
                                  "all_pwm.zip", "all_gpr_files.zip", "supplemental.pdf"]

[db_dbsno]
source_url = "http://140.138.144.145/~dbSNO/download/dbSNO{{version}}_all_data.txt.gz"
version_available = "v2"

[db_phosphonetworks]
soource_url = "http://www.phosphonetworks.org/download/{{version}}"
version_available = ["rawKSI.csv", "refKSI.csv", "comKSI.csv", "motifSite.csv",
                                  "motifMatrix.csv",  "motifLogo.tar", "highResolutionNetwork.csv",
                                  "supplemental.pdf"]

[db_consensuspathdb]
source_url = "http://cpdb.molgen.mpg.de/download/ConsensusPathDB_{{version}}.gz"
version_available = ["human_PPI", "human_PPI.psi25"]

[db_instruct]
source_url = "http://instruct.yulab.org/download/{{version}}.sin"
version_available = ["sapiens", "thaliana", "elegans", "melanogaster", "musculus", "cerevisiae", "pombe"]

[db_redoxdb]
source_url = "https://biocomputer.bio.cuhk.edu.hk/RedoxDB/download/{{version}}"
version_available = ["redoxdb.A.txt", "redoxdb.B.txt", "redoxdb.A.fa", "redoxdb.B.fa"]

[db_sm2mir]
source_url = "http://210.46.85.180:8080/sm2mir/files/{{versin}}.xls"
version_available = ["SM2miR3", "SM2miR2n", "SM2miR"]

[db_hmdb]
source_url = "http://www.hmdb.ca/system/downloads/current/{{version}}.zip"
avaliable_version = ["hmdb_proteins", "hmdb_metabolites", "structures"]

[db_awesome]
source_url = "http://www.awesome-hust.com/downloads/{{version}}.zip"
version_available = ["awesomeAll"]

[db_cellmarker]
source_url = "http://biocc.hrbmu.edu.cn/CellMarker/download/{{version}}_cell_markers.txt"
version_available = ["all", "Human", "Mouse", "Single"]

[db_lncrnadisease]
source_url = "http://www.rnanut.net/lncrnadisease/download/{{version}}.xlsx"
version_available = ["experimental%20circRNA-disease%20information", "experimental%20lncRNA-disease%20information", "predicted%20lncRNA-disease%20information", "all%20ncRNA-disease%20information"]

[db_ewasdb]
source_url = "http://www.bioapp.org/ewasdb/Public/file/{{version}}.rar"
version_available = ["ewas_singlemarker", "GO_Category", "KEGG_Pathway"]

[db_cancersplicingqtl]
source_url = "http://www.cancersplicingqtl-hust.com/downloads/{{version}}.xlsx"
version_available = ["ACC_sQTLs", "BLCA_sQTLs", "BRCA_sQTLs", "CESC_sQTLs", "CHOL_sQTLs", "COAD_sQTLs", "DLBC_sQTLs", "ESCA_sQTLs", "GBM_sQTLs", "HNSC_sQTLs", "KICH_sQTLs", "KIRC_sQTLs", "KIRP_sQTLs", "LAML_sQTLs", "LGG_sQTLs", "LIHC_sQTLs", "LUAD_sQTLs", "LUSC_sQTLs", "MESO_sQTLs", "OV_sQTLs", "PAAD_sQTLs", "PCPG_sQTLs", "PRAD_sQTLs", "READ_sQTLs", "SARC_sQTLs", "SKCM_sQTLs", "STAD_sQTLs", "TGCT_sQTLs", "THCA_sQTLs", "THYM_sQTLs", "UCEC_sQTLs", "UCS_sQTLs", "UVM_sQTLs", "ACC_Survival_sQTLs", "BLCA_Survival_sQTLs", "BRCA_Survival_sQTLs", "CESC_Survival_sQTLs", "CHOL_Survival_sQTLs", "COAD_Survival_sQTLs", "DLBC_Survival_sQTLs", "ESCA_Survival_sQTLs", "GBM_Survival_sQTLs", "HNSC_Survival_sQTLs", "KICH_Survival_sQTLs", "KIRC_Survival_sQTLs", "KIRP_Survival_sQTLs", "LAML_Survival_sQTLs", "LGG_Survival_sQTLs", "LIHC_Survival_sQTLs", "LUAD_Survival_sQTLs", "LUSC_Survival_sQTLs", "MESO_Survival_sQTLs", "OV_Survival_sQTLs", "PAAD_Survival_sQTLs", "PCPG_Survival_sQTLs", "PRAD_Survival_sQTLs", "READ_Survival_sQTLs", "SARC_Survival_sQTLs", "SKCM_Survival_sQTLs", "STAD_Survival_sQTLs", "TGCT_Survival_sQTLs", "THCA_Survival_sQTLs", "THYM_Survival_sQTLs", "UCEC_Survival_sQTLs", "UCS_Survival_sQTLs", "UVM_Survival_sQTLs", "ACC_GWAS_sQTLs", "BLCA_GWAS_sQTLs", "BRCA_GWAS_sQTLs", "CESC_GWAS_sQTLs", "CHOL_GWAS_sQTLs", "COAD_GWAS_sQTLs", "DLBC_GWAS_sQTLs", "ESCA_GWAS_sQTLs", "GBM_GWAS_sQTLs", "HNSC_GWAS_sQTLs", "KICH_GWAS_sQTLs", "KIRC_GWAS_sQTLs", "KIRP_GWAS_sQTLs", "LAML_GWAS_sQTLs", "LGG_GWAS_sQTLs", "LIHC_GWAS_sQTLs", "LUAD_GWAS_sQTLs", "LUSC_GWAS_sQTLs", "MESO_GWAS_sQTLs", "OV_GWAS_sQTLs", "PAAD_GWAS_sQTLs", "PCPG_GWAS_sQTLs", "PRAD_GWAS_sQTLs", "READ_GWAS_sQTLs", "SARC_GWAS_sQTLs", "SKCM_GWAS_sQTLs", "STAD_GWAS_sQTLs", "TGCT_GWAS_sQTLs", "THCA_GWAS_sQTLs", "THYM_GWAS_sQTLs", "UCEC_GWAS_sQTLs", "UCS_GWAS_sQTLs", "UVM_GWAS_sQTLs"]

[db_pmkb]
source_url = "https://pmkb.weill.cornell.edu/therapies/download.xlsx"
version_available = "latest"

[db_sedb]
source_url = "http://www.licpathway.net/sedb/download/{{version}}"
version_available = "latest"

[db_lnc2cancer]
source_url = "http://www.bio-bigdata.net/lnc2cancer/download/{{version}}.txt"
version_available = ["all_lnc_cancer_associations", "Circulating_lnc_cancer_associations", "Prognostic_lnc_cancer_associations",
                     "Drug-resistant_lnc_cancer_associations", "LncRNAs%20regulated%20by%20TF%20in%20cancers",
                     "LncRNAs%20regulated%20by%20miRNA%20in%20cancers", "LncRNAs%20regulated%20by%20variant%20in%20cancers",
                     "LncRNAs%20regulated%20by%20methylation%20in%20cancers"]

[db_fusiongdb]
source_url = "https://ccsm.uth.edu/FusionGDB/tables/{{version}}.txt"
version_available = ["TCGA_ChiTaRS_combined_fusion_information_on_hg19", "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_fgID",
                     "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19", "TCGA_ChiTaRS_combined_fusion_Prot_feature_retention_search_UniProt_for_Hgene",
                     "TCGA_ChiTaRS_combined_fusion_Prot_feature_retention_search_UniProt_for_Tgene", 
                     "fusion_ppi", "fusion_uniprot_related_drugs", "fgene_disease_associations", 
                     "uniprot_gsymbol", "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_In-frame_100k_check_aminoacid_seq",
                     "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_In-frame_100k_check_cds_seq",
                     "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_In-frame_100k_check_transcript_seq",
                     "In-frame_fgene_num_samples"]
