--tries=5 --mirror --no-parent --no-directories --no-host-directories --cut-dirs=2 --accept=gi_taxid_prot.dmp.gz,taxdump.tar.gz gunzip @downloadDir@/taxonomy/gi_taxid_prot.dmp.gz gunzip @downloadDir@/taxonomy/taxdump.tar.gz tar -xf @downloadDir@/taxonomy/taxdump.tar -C @downloadDir@/taxonomy/ rm -f @downloadDir@/taxonomy/taxdump.tar --names @downloadDir@/taxonomy/names.dmp --nodes @downloadDir@/taxonomy/nodes.dmp --gencode @downloadDir@/taxonomy/gencode.dmp --merged @downloadDir@/taxonomy/merged.dmp --restart @taxonomy.restart@ --verbose @commit@ --tries=5 --mirror --no-parent --no-directories --no-host-directories --cut-dirs=3 --accept=chromosome.nt --comment "load predicted %EXT_DB_NAME%" --externalDatabaseName %EXT_DB_NAME% --externalDatabaseVersion %EXT_DB_RLS_VER% --sequenceTypeName "chromosome" --nucleotideType "DNA" --ncbiTaxId @ncbiTaxId@ --sequenceFile @downloadDir@/ToxoChroms/chromosome.nt --regexSourceId ">(\S+)\s" --regexChromosome ">(\S+)\s" --regexDesc ">\S+\s+(.+)\b" --tableName DoTS::VirtualSequence @commit@ --tries=5 --mirror --no-parent --no-directories --no-host-directories --cut-dirs=3 --accept=3prime.raw awk -F:::: 'x++; x==1{print "tag\n" $1}' 3prime.raw > 3prime --cfg_file @pipelineDir@/@ToxoSageTags.3PrimeConfigFile@ --data_file @downloadDir@/3primeToxoSageTags/3prime --manufacturer @ToxoSageTags.Contact@ --technology_type @ToxoSageTags.OntologyEntryValue@ @commit@ --tries=5 --mirror --no-parent --no-directories --no-host-directories --cut-dirs=3 --accept=5prime.raw awk -F:::: 'x++; x==1{print "tag\n" $1}' 5prime.raw > 5prime --cfg_file @pipelineDir@/@ToxoSageTags.5PrimeConfigFile@ --data_file @downloadDir@/5primeToxoSageTags/5prime --manufacturer @ToxoSageTags.Contact@ --technology_type @ToxoSageTags.OntologyEntryValue@ @commit@ --tries=5 --mirror --no-parent --no-directories --no-host-directories --cut-dirs=3 --accept=freqs.tsv --contact @ToxoSageTags.Contact@ --arrayDesignName @ToxoSageTagResults.arrayDesignName@ --arrayDesignVersion @ToxoSageTagResults.arrayDesignVersion@ --studyName @ToxoSageTagResults.studyName@ --studyDescription @ToxoSageTagResults.studyDescription@ --freqFile @downloadDir@/ToxoSageTagFreqs/freqs.tsv @commit@