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diff ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline_RUN.sh @ 0:e2b290eeb07b draft default tip

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author daumsoft
date Sun, 09 Sep 2018 21:33:01 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline_RUN.sh	Sun Sep 09 21:33:01 2018 -0400
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+if [ "$#" -ne 1 ]; then
+ echo "[usage:] ICGC_pipeline_RUN.sh  tar.gz(fastq in file)"
+ exit 1;
+fi
+
+INPUT_TAR_GZ=$1
+
+ln -s $INPUT_TAR_GZ  ${INPUT_TAR_GZ}.tar.gz
+INPUT_TAR_GZ=${INPUT_TAR_GZ}.tar.gz
+
+$GALAXY_HOME/package/DAUMSOFT/RNA-seq/ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline.sh $INPUT_TAR_GZ > log.out 2>&1   
+