From eff72edd5663f79503541b5ab89cae168c9183be Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 11 Nov 2014 11:12:36 +0100
Subject: [PATCH] fixed for new cummerbund version
---
bash/bioinfo_utils.sh | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/bash/bioinfo_utils.sh b/bash/bioinfo_utils.sh
index 64ba9c3..bb35305 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]
--
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