--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas_wrapper.sh	Wed Apr 22 05:34:06 2015 -0400
@@ -0,0 +1,90 @@
+#!/bin/sh -e
+#
+# Wrapper script to run CEAS as a Galaxy tool
+#
+# This runs the Cistrome versions of CEAS, which provides two executables:
+# - ceas (same as the "official" version)
+# - ceasBW (modified version that accepts a bigwig file as input)
+#
+# Usage: ceas_wrapper.sh $BED_IN $GDB_IN $EXTRA_BED_IN $LOG_OUT $PDF_OUT $XLS_OUT $DBKEY
+#
+# Process command line
+echo $*
+BED_IN=$1
+GDB_IN=$2
+EXTRA_BED_IN=$3
+LOG_OUT=$4
+PDF_OUT=$5
+XLS_OUT=$6
+#
+# Collect remaining args
+CEAS=ceas
+OPTIONS=
+while [ ! -z "$7" ] ; do
+    if [ "$7" == "--bigwig" ] ; then
+	CEAS=ceasBW
+    fi
+    if [ "$7" == "--length" ] ; then
+	chrom_sizes=$8
+	if [ ! -f "$chrom_sizes" ] ; then
+	    echo "ERROR no file $chrom_sizes" >&2
+	    echo "Please update your Galaxy instance to include this file"
+	    exit 1
+	fi
+    fi
+    OPTIONS="$OPTIONS $7"
+    shift
+done
+#
+# Convenience variables for local files
+base_name="ceas"
+log_file=${base_name}.log
+r_script=${base_name}.R
+pdf_report=${base_name}.pdf
+xls_file=${base_name}.xls
+#
+# Get CEAS version
+echo Running $CEAS
+$CEAS --version >$log_file 2>/dev/null
+#
+# Construct and run CEAS command line
+ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
+if [ "$EXTRA_BED_IN" != "None" ] ; then
+    ceas_cmd="$ceas_cmd -e $EXTRA_BED_IN"
+fi
+echo "Running $ceas_cmd"
+$ceas_cmd >>$log_file 2>&1
+#
+# Move outputs to final destination
+if [ -e $log_file ] ; then
+    echo "Moving $log_file to $LOG_OUT"
+    /bin/mv $log_file $LOG_OUT
+else
+    echo ERROR failed to make log file >&2
+    exit 1
+fi
+if [ -e $xls_file ] ; then
+    echo "Moving $xls_file to $XLS_OUT"
+    /bin/mv $xls_file $XLS_OUT
+else
+    echo ERROR failed to generate XLS file >&2
+    exit 1
+fi
+#
+# Run the R script to generate the PDF report
+if [ -e $r_script ] ; then
+    echo "Running $r_script to generate $pdf_report"
+    R --vanilla < $r_script
+    if [ -e $pdf_report ] ; then
+	echo "Moving $xls_file to $XLS_OUT"
+	/bin/mv $pdf_report $PDF_OUT
+    else
+	echo ERROR failed to generate PDF report >&2
+	exit 1
+    fi
+else
+    echo ERROR no R script to generate PDF report >&2
+    exit 1
+fi
+#
+# Done