From af60666f5d82bb479b84b56e370ab4828b9887b2 Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 19 Jan 2011 20:28:59 +0000
Subject: [PATCH] An example template for the shell script used to run the full
 calling pipeline on the broad system

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5022 348d0f76-0448-11de-a6fe-93d51630548a
---
 shell/queue.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100755 shell/queue.sh

diff --git a/shell/queue.sh b/shell/queue.sh
new file mode 100755
index 000000000..278137387
--- /dev/null
+++ b/shell/queue.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+
+SAMPLE_SET=$1
+STING_HOME=/humgen/gsa-firehose2/pipeline/repositories/StingProduction
+REFSEQ_TABLE=/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg19.txt
+JOB_QUEUE=gsa
+SHORT_QUEUE=gsa
+BIG_QUEUE=gsa
+TMP_DIR=$PWD/tmp
+
+mkdir $PWD/tmp
+source /broad/software/scripts/useuse
+use LSF
+use R-2.10
+use Oracle-full-client
+use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
+
+java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -bigMemQueue "$BIG_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript ~/Sting/R/DataProcessingReport/GetTearsheetStats.R -S ~/Sting/scala/qscript/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2