diff summarize_unique_barcodes.sh @ 19:ceb96c265bd1 draft

Trying to set environment r lib path dependencies.

--- a/summarize_unique_barcodes.sh	Wed Feb 11 07:32:32 2015 -0500
+++ b/summarize_unique_barcodes.sh	Wed Feb 11 08:05:10 2015 -0500
@@ -25,9 +25,10 @@
 -t: Trim untemplated nucleotides.
 -k: Produce k2n file. Warning: Can be sloooow!
 -r: Rscript path
+-l: R lib path
 -o: Output folder (default: "output_dir")
 -------------------------------------
-Usage : summarize_unique_barcodes.sh -f <BAM_file> -b <BARCODES> -p <PRIMING_POSITION> -t -k -r <R_SCRIPT_PATH>
+Usage : summarize_unique_barcodes.sh -f <BAM_file> -b <BARCODES> -p <PRIMING_POSITION> -t -k -r <R_SCRIPT_PATH> -l <R_LIB_PATH>
 End-of-message
 exit
 }
@@ -37,7 +38,7 @@
 trim_flag="False"
 
 #parse input
-while getopts hf:b::p:o:ktr: myarg
+while getopts hf:b::p:o:ktr:l: myarg
 do  case "$myarg" in
     h)  print_help
         exit ;;
@@ -48,6 +49,7 @@
     p)  priming_pos="$OPTARG" ;;
     o)  output_dir="$OPTARG" ;;
     r)  R_SCRIPT_PATH="$OPTARG" ;; #required
+    l)  R_LIB_PATH="$OPTARG" ;; #required
     [?])  echo "ERROR: Unknown parameter"
         print_help
         exit 1 ;;
@@ -220,7 +222,7 @@
 
 #Produce k2n file
 if [ "$k2n" == "True" ]; then
-    Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt
+    Rscript $R_SCRIPT_PATH/k2n.R $R_LIB_PATH merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt
 fi
 
 #Remove temp files