diff --git a/bash/bioinfo_utils.sh b/bash/bioinfo_utils.sh index 64ba9c3c0e6f32f964b8a3315268e99b17dabacc..bb35305f0ff50df356405f48d3b3aab8cdd1fba6 100644 --- a/bash/bioinfo_utils.sh +++ b/bash/bioinfo_utils.sh @@ -102,7 +102,7 @@ createCuffDbTrickyDisk <- function(dbDir, gtfFile, genome, ...){ system(paste("cp -r", dbDir, tmpdir)) oldWD <- getwd() setwd(tmpdir) - cuff <- readCufflinks(rebuild=T, gtf=gtfFile, genome, ...) + cuff <- readCufflinks(rebuild=T, gtf=gtfFile, genome=genome, ...) system(paste("cp cuffData.db", dbDir)) system(paste("rm -r", tmpdir)) @@ -111,6 +111,7 @@ createCuffDbTrickyDisk <- function(dbDir, gtfFile, genome, ...){ return(cuff) } +#gtfFile="mm10_ensGene_pc.gtf"; genomeBuild="mm10" gtfFile=commandArgs(TRUE)[1] genomeBuild=commandArgs(TRUE)[2]