From ce3c9c6fb44841418e8069b2e2590e7eb921287c Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 22 Jul 2010 12:20:46 +0000
Subject: [PATCH] initial checkin: Bioconductor: ShortRead qa

SVN: 17156
---
 deep_sequencing_unit/source/R/createQaReport.R     |  7 +++++++
 deep_sequencing_unit/source/bash/createQaReport.sh | 10 ++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 deep_sequencing_unit/source/R/createQaReport.R
 create mode 100644 deep_sequencing_unit/source/bash/createQaReport.sh

diff --git a/deep_sequencing_unit/source/R/createQaReport.R b/deep_sequencing_unit/source/R/createQaReport.R
new file mode 100644
index 00000000000..3463d50a994
--- /dev/null
+++ b/deep_sequencing_unit/source/R/createQaReport.R
@@ -0,0 +1,7 @@
+require(multicore)
+require (ShortRead)
+args <- commandArgs(TRUE)
+fastq_file <- args[1]
+qa <- qa(getwd(),args[1], type="fastq")
+report_dest <- paste(fastq_file, "ShortRead_qa", sep="_")
+qa_report <- report (qa, dest=report_dest , type="html")
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/bash/createQaReport.sh b/deep_sequencing_unit/source/bash/createQaReport.sh
new file mode 100644
index 00000000000..1da680cf906
--- /dev/null
+++ b/deep_sequencing_unit/source/bash/createQaReport.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+R_SCRIP_PATH=/usr/local/dsu/R-scripts
+
+for i in `ls -1 *.fastq`
+do
+        Rscript --vanilla $R_SCRIP_PATH/createQaReport.R $i &
+done
+wait $!
+echo * DONE *
-- 
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