Created
March 25, 2014 03:03
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Example to download an SRA study wholly within R on wolfpack (our internal cluster)
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| # wolfpack modules required: hugfre/R/3.0.2 fabbus/aspera/3.1.1.70290 | |
| ascpCMD <- "ascp -QT -l1000M -i /share/ClusterShare/software/contrib/fabbus/aspera/3.1.1.70290/asperaweb_id_dsa.putty" | |
| library(SRAdb) | |
| if (!file.exists("../SRAmetadb.sqlite")) db <- getSRAdbFile("../") else db <- "../SRAmetadb.sqlite" | |
| con <- dbConnect(dbDriver("SQLite"), db) # load the SRA database | |
| accession <- "SRP026604" | |
| ascpSRA(accession, con, ascpCMD, "sra") |
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This example downloads 'sra' files, but if available can directly download 'sralite' or 'fastq' files by changing the parameter to ascpSRA()