changeset 4:5b5460b79488 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_ucsc_track.sh	Tue Jul 15 07:19:14 2014 -0400
@@ -0,0 +1,59 @@
+#!/bin/bash
+
+# This tool creates a UCSC track line given a bigWig or bedGraph input file, a track name and genome assembly.
+
+## Define URL prefix
+
+URL="http://data.bric.dk/galaxy/UCSC"
+
+#parse input
+while getopts hi:t:n:o: myarg
+do      case "$myarg" in
+        h)      echo "Usage: create UCSC track line -i <INPUT_FILE> -t <FILE_TYPE> -n <TRACK_NAME> -o <ASSEMBLY>"
+                exit ;;
+        i)      input_file="$OPTARG" ;;
+	t)	file_type="$OPTARG" ;;
+        n)      track_name="$OPTARG" ;; 
+        o)      org_assembly="$OPTARG" ;;
+        [?])    echo "Usage: create UCSC track line -i <INPUT_FILE> -t <FILE_TYPE> -n <TRACK_NAME> -o <ASSEMBLY>"
+
+                exit 1 ;;
+        esac
+done
+
+####################################################################
+# Check if a link to that file exists in the UCSC webfolder
+flag=0 
+
+for link in `ls -1 $UCSCPATH` 
+do 
+    if [ `readlink -f $input_file` == `readlink -f $UCSCPATH/$link` ] ; then
+        link_path=/$link # use already existing link
+	flag=1 
+    fi
+done
+
+# If link to input file doesn't exist, create anonymous soft-link for input file in a folder accessible from the web.
+
+if [ $flag == 0 ]; then
+    
+    link_path=`mktemp -u --tmpdir=/`
+    ln -s $input_file $UCSCPATH$link_path
+fi
+
+####################################################################
+##Convert 4th character of file_type to uppercase (e.g. bigwig -> bigWig). UCSC browser doesn't recognize the file type otherwise.
+
+##Split file_type string to prefix (big) and suffix (wig, bed) and uppercase the first character of the latter.
+prefix=`echo ${file_type:0:3}`
+suffix=`echo ${file_type:3} | sed -e "s/\b\(.\)/\u\1/g"`
+
+file_type=`echo ${prefix}${suffix}`
+
+####################################################################
+#Contruct URL
+bigURL=`echo ${URL}${link_path}`
+
+####################################################################
+## Print track line
+echo "track name='$track_name' db=$org_assembly type=$file_type visibility=full alwaysZero=ON bigDataUrl=$bigURL"