From 0171a89170fe6f572f6ef0b203f5e75dbd4ea4cc Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 12 Aug 2014 14:43:08 +0200
Subject: [PATCH] started migration of cluster tools to github
---
bash/lsf_bioinfo_utils.sh | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
create mode 100644 bash/lsf_bioinfo_utils.sh
diff --git a/bash/lsf_bioinfo_utils.sh b/bash/lsf_bioinfo_utils.sh
new file mode 100644
index 0000000..31e518a
--- /dev/null
+++ b/bash/lsf_bioinfo_utils.sh
@@ -0,0 +1,19 @@
+
+mmFastqc(){
+ outputDir="fastqc_reports"
+# filePattern="fastq.gz"
+# outputDir=$1
+# filePattern=$2
+ mkdir $outputDir
+ for fastqFile in *fastq *fastq.gz ; do
+ if [ ! -f $fastqFile ]; then
+ continue;
+ fi
+ echo processing $fastqFile
+# bsub -q medium --J fastqc_$(basename $fastqFile) "fastqc -j /sw/bin/java -o $outputDir -f fastq $fastqFile" | joblist .fastqc_jobs
+ mysub "fastqc__$(basename $fastqFile)" "fastqc -j /sw/bin/java -o $outputDir -f fastq $fastqFile" -q medium | joblist .fastqc_jobs
+ done
+ wait4jobs .fastqc_jobs
+}
+export -f mmFastqc
+
--
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