From 3c31df51c2e300e46732026d63954d728b7825f1 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Fri, 1 Jul 2016 12:56:18 +0200
Subject: [PATCH] fixed partition name
---
dge_workflow/dge_utils.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 0da173b..9ea82af 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -186,7 +186,7 @@ for bamFile in $bamFiles; do
sample=$(basename $bamFile .bam)
echo "converting $bamFile to bigwig format"
- jl submit -j .bigwig -q short -n "${project}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile -g ${genomeFai} | wigToBigWig -clip stdin ${genomeFai} ${sample}.bw"
+ jl submit -j .bigwig -w 10:00 -n "${project}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile -g ${genomeFai} | wigToBigWig -clip stdin ${genomeFai} ${sample}.bw"
done
jl wait --report .bigwig
@@ -270,7 +270,7 @@ dge_create_star_index(){
cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 10"
#eval $cmd
#STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
- jl submit --wait -t 5 -q medium -n "${project}_star_index" "$cmd"
+ jl submit --wait -t 5 -w 10:00 -m 30g -n "${project}_star_index" "$cmd"
## prevent further modification
# chmod -w $(dirname ${star_index})
--
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