From 54013ebe288ff5c45e81ff949e888a23ca2efb66 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 14 Jul 2015 09:51:43 +0200
Subject: [PATCH] use short queue for star
---
dge_workflow/star_align.sh | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/dge_workflow/star_align.sh b/dge_workflow/star_align.sh
index e5ddf3f..f7d4f0d 100755
--- a/dge_workflow/star_align.sh
+++ b/dge_workflow/star_align.sh
@@ -52,6 +52,7 @@ fi
## build index if not present
if [ ! -f "${star_index}/SA" ]; then
+chmod -R +w ${star_index}
mailme "${project}: creating STAR index for $igenome"
mkdir ${star_index}
@@ -87,7 +88,7 @@ for fastqFile in $fastqFiles ; do
STAR --genomeDir $star_index --readFilesIn $fastqFile --runThreadN 6 --readFilesCommand zcat --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile $gtfFile
mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
samtools index ${fastqBaseName}.bam
- " -n 5 -R span[hosts=1] -q medium | joblist .tophatjobs
+ " -n 5 -R span[hosts=1] -q short | joblist .tophatjobs
done
wait4jobs .tophatjobs
--
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