#!/usr/bin/bash set -x set -euo pipefail # Interpreted environment variables. # # PATH_DB_BASE -- base directory for database defaults # default: /data/annonars # HTTP_HOST -- host to listen on # default: 0.0.0.0 # HTTP_PORT -- port # default: 8080 # # PATH_DB_CLINVAR_37 -- path to ClinVar database for GRCh37, defaults to $PATH_DB_BASE/grch37/clinvar/rocksdb # PATH_DB_CLINVAR_38 -- path to ClinVar database for GRCh37, defaults to $PATH_DB_BASE/grch38/clinvar/rocksdb # PATH_DB_CLINVAR_SV_37 -- path to ClinVar database for GRCh37, defaults to $PATH_DB_BASE/grch37/clinvar-sv/rocksdb # PATH_DB_CLINVAR_SV_38 -- path to ClinVar database for GRCh37, defaults to $PATH_DB_BASE/grch38/clinvar-sv/rocksdb # PATH_DB_CADD_37 -- path to CADD database for GRCh37, defaults to $PATH_DB_BASE/grch37/cadd/rocksdb # PATH_DB_CADD_38 -- path to CADD database for GRCh38, defaults to $PATH_DB_BASE/grch38/cadd/rocksdb # PATH_DB_DBSNP_37 -- path to dbSNP database for GRCh37, defaults to $PATH_DB_BASE/grch37/dbsnp/rocksdb # PATH_DB_DBSNP_38 -- path to dbSNP database for GRCh38, defaults to $PATH_DB_BASE/grch38/dbsnp/rocksdb # PATH_DB_DBNSFP_37 -- path to dbNSFP database for GRCh37, defaults to $PATH_DB_BASE/grch37/dbnsfp/rocksdb # PATH_DB_DBNSFP_38 -- path to dbNSFP database for GRCh38, defaults to $PATH_DB_BASE/grch38/dbnsfp/rocksdb # PATH_DB_DBSCSNV_37 -- path to dbscSNV database for GRCh37, defaults to $PATH_DB_BASE/grch37/dbscsnv/rocksdb # PATH_DB_DBSCSNV_38 -- path to dbscSNV database for GRCh38, defaults to $PATH_DB_BASE/grch38/dbscsnv/rocksdb # PATH_DB_GNOMAD_MTDNA_37 -- path to gnomAD mtDNA database for GRCh37, defaults to $PATH_DB_BASE/grch37/gnomad-mtdna/rocksdb # PATH_DB_GNOMAD_MTDNA_38 -- path to gnomAD mtDNA database for GRCh38, defaults to $PATH_DB_BASE/grch38/gnomad-mtdna/rocksdb # PATH_DB_GNOMAD_EXOMES_37 -- path to gnomAD exomes database for GRCh37, defaults to $PATH_DB_BASE/grch37/gnomad-exomes/rocksdb # PATH_DB_GNOMAD_EXOMES_38 -- path to gnomAD exomes database for GRCh38, defaults to $PATH_DB_BASE/grch38/gnomad-exomes/rocksdb # PATH_DB_GNOMAD_GENOMES_37 -- path to gnomAD genomes database for GRCh37, defaults to $PATH_DB_BASE/grch37/gnomad-genomes/rocksdb # PATH_DB_GNOMAD_GENOMES_38 -- path to gnomAD genomes database for GRCh38, defaults to $PATH_DB_BASE/grch38/gnomad-genomes/rocksdb # PATH_DB_HELIXMTDB_37 -- path to HelixMTdb database for GRCh37, defaults to $PATH_DB_BASE/grch37/helixmtdb/rocksdb # PATH_DB_HELIXMTDB_38 -- path to HelixMTdb database for GRCh38, defaults to $PATH_DB_BASE/grch38/helixmtdb/rocksdb # PATH_DB_CONS_37 -- path to UCSC conservation database for GRCh37, defaults to $PATH_DB_BASE/grch37/cons/rocksdb # PATH_DB_CONS_38 -- path to UCSC conservation database for GRCh38, defaults to $PATH_DB_BASE/grch38/cons/rocksdb # # PATH_GENES -- path to the genes RocksDB, defaults to $PATH_DB_BASE/genes/rocksdb PATH_DB_BASE=${PATH_HPO_DIR-/data/annonars} HTTP_HOST=${HTTP_HOST-0.0.0.0} HTTP_PORT=${HTTP_PORT-8080} PATH_DB_CLINVAR_37=${PATH_DB_CLINVAR_37-$PATH_DB_BASE/grch37/clinvar/rocksdb} PATH_DB_CLINVAR_38=${PATH_DB_CLINVAR_38-$PATH_DB_BASE/grch38/clinvar/rocksdb} PATH_DB_CLINVAR_SV_37=${PATH_DB_CLINVAR_SV_37-$PATH_DB_BASE/grch37/clinvar-sv/rocksdb} PATH_DB_CLINVAR_SV_38=${PATH_DB_CLINVAR_SV_38-$PATH_DB_BASE/grch38/clinvar-sv/rocksdb} PATH_DB_CADD_37=${PATH_DB_CADD_37-$PATH_DB_BASE/grch37/cadd/rocksdb} PATH_DB_CADD_38=${PATH_DB_CADD_38-$PATH_DB_BASE/grch38/cadd/rocksdb} PATH_DB_DBSNP_37=${PATH_DB_DBSNP_37-$PATH_DB_BASE/grch37/dbsnp/rocksdb} PATH_DB_DBSNP_38=${PATH_DB_DBSNP_38-$PATH_DB_BASE/grch38/dbsnp/rocksdb} PATH_DB_DBNSFP_37=${PATH_DB_DBNSFP_37-$PATH_DB_BASE/grch37/dbnsfp/rocksdb} PATH_DB_DBNSFP_38=${PATH_DB_DBNSFP_38-$PATH_DB_BASE/grch38/dbnsfp/rocksdb} PATH_DB_DBSCSNV_37=${PATH_DB_DBSCSNV_37-$PATH_DB_BASE/grch37/dbscsnv/rocksdb} PATH_DB_DBSCSNV_38=${PATH_DB_DBSCSNV_38-$PATH_DB_BASE/grch38/dbscsnv/rocksdb} PATH_DB_GNOMAD_MTDNA_37=${PATH_DB_GNOMAD_MTDNA_37-$PATH_DB_BASE/grch37/gnomad-mtdna/rocksdb} PATH_DB_GNOMAD_MTDNA_38=${PATH_DB_GNOMAD_MTDNA_38-$PATH_DB_BASE/grch38/gnomad-mtdna/rocksdb} PATH_DB_GNOMAD_EXOMES_37=${PATH_DB_GNOMAD_EXOMES_37-$PATH_DB_BASE/grch37/gnomad-exomes/rocksdb} PATH_DB_GNOMAD_EXOMES_38=${PATH_DB_GNOMAD_EXOMES_38-$PATH_DB_BASE/grch38/gnomad-exomes/rocksdb} PATH_DB_GNOMAD_GENOMES_37=${PATH_DB_GNOMAD_GENOMES_37-$PATH_DB_BASE/grch37/gnomad-genomes/rocksdb} PATH_DB_GNOMAD_GENOMES_38=${PATH_DB_GNOMAD_GENOMES_38-$PATH_DB_BASE/grch38/gnomad-genomes/rocksdb} PATH_DB_HELIXMTDB_37=${PATH_DB_HELIXMTDB_37-$PATH_DB_BASE/grch37/helixmtdb/rocksdb} PATH_DB_HELIXMTDB_38=${PATH_DB_HELIXMTDB_38-$PATH_DB_BASE/grch38/helixmtdb/rocksdb} PATH_DB_CONS_37=${PATH_DB_CONS_37-$PATH_DB_BASE/grch37/cons/rocksdb} PATH_DB_CONS_38=${PATH_DB_CONS_38-$PATH_DB_BASE/grch38/cons/rocksdb} PATH_GENES=${PATH_GENES-$PATH_DB_BASE/genes/rocksdb} PATH_GENES_CLINVAR=${PATH_GENES_CLINVAR-$PATH_DB_BASE/clinvar-genes/rocksdb} first=${1-} if [ "$first" == exec ]; then shift exec "$@" else exec \ annonars \ server run \ $(test -e $PATH_DB_CLINVAR_37 && echo --path-clinvar $PATH_DB_CLINVAR_37) \ $(test -e $PATH_DB_CLINVAR_38 && echo --path-clinvar $PATH_DB_CLINVAR_38) \ $(test -e $PATH_DB_CLINVAR_SV_37 && echo --path-clinvar-sv $PATH_DB_CLINVAR_SV_37) \ $(test -e $PATH_DB_CLINVAR_SV_38 && echo --path-clinvar-sv $PATH_DB_CLINVAR_SV_38) \ $(test -e $PATH_DB_CADD_37 && echo --path-cadd $PATH_DB_CADD_37) \ $(test -e $PATH_DB_CADD_38 && echo --path-cadd $PATH_DB_CADD_38) \ $(test -e $PATH_DB_DBSNP_37 && echo --path-dbsnp $PATH_DB_DBSNP_37) \ $(test -e $PATH_DB_DBSNP_38 && echo --path-dbsnp $PATH_DB_DBSNP_38) \ $(test -e $PATH_DB_DBNSFP_37 && echo --path-dbnsfp $PATH_DB_DBNSFP_37) \ $(test -e $PATH_DB_DBNSFP_38 && echo --path-dbnsfp $PATH_DB_DBNSFP_38) \ $(test -e $PATH_DB_DBSCSNV_37 && echo --path-dbscsnv $PATH_DB_DBSCSNV_37) \ $(test -e $PATH_DB_DBSCSNV_38 && echo --path-dbscsnv $PATH_DB_DBSCSNV_38) \ $(test -e $PATH_DB_GNOMAD_MTDNA_37 && echo --path-gnomad-mtdna $PATH_DB_GNOMAD_MTDNA_37) \ $(test -e $PATH_DB_GNOMAD_MTDNA_38 && echo --path-gnomad-mtdna $PATH_DB_GNOMAD_MTDNA_38) \ $(test -e $PATH_DB_GNOMAD_EXOMES_37 && echo --path-gnomad-exomes $PATH_DB_GNOMAD_EXOMES_37) \ $(test -e $PATH_DB_GNOMAD_EXOMES_38 && echo --path-gnomad-exomes $PATH_DB_GNOMAD_EXOMES_38) \ $(test -e $PATH_DB_GNOMAD_GENOMES_37 && echo --path-gnomad-genomes $PATH_DB_GNOMAD_GENOMES_37) \ $(test -e $PATH_DB_GNOMAD_GENOMES_38 && echo --path-gnomad-genomes $PATH_DB_GNOMAD_GENOMES_38) \ $(test -e $PATH_DB_HELIXMTDB_37 && echo --path-helixmtdb $PATH_DB_HELIXMTDB_37) \ $(test -e $PATH_DB_HELIXMTDB_38 && echo --path-helixmtdb $PATH_DB_HELIXMTDB_38) \ $(test -e $PATH_DB_CONS_37 && echo --path-ucsc-conservation $PATH_DB_CONS_37) \ $(test -e $PATH_DB_CONS_38 && echo --path-ucsc-conservation $PATH_DB_CONS_38) \ $(test -e $PATH_GENES && echo --path-genes $PATH_GENES) \ $(test -e $PATH_GENES_CLINVAR && echo --path-clinvar-genes $PATH_GENES_CLINVAR) \ \ --listen-host "$HTTP_HOST" \ --listen-port "$HTTP_PORT" fi exit $?