diff rDiff/galaxy/rdiff_run.sh @ 0:0f80a5141704

version 0.3 uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/galaxy/rdiff_run.sh	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,90 @@
+#/bin/bash
+# Galaxy wrapper script for rDiff version 0.3
+# Copyright (C) 2013 cBio Department Memorial Sloan-Kettering Cancer Center
+
+#Licence Information: GPL
+#This program is free software; you can redistribute it and/or modify 
+#it under the terms of the GNU General Public License as published by 
+#the Free Software Foundation; either version 3 of the License, or 
+#(at your option) any later version
+
+set -e 
+
+PROG=`basename $0`
+DIR=`dirname $0`
+. ${DIR}/../bin/rdiff_config.sh
+
+echo
+echo ${PROG}: This program is part of the rDiff version $RDIFF_VERSION.
+echo
+echo rDiff performs differential expression testing from RNA-Seq measurements.
+echo 
+
+if [ -z "$1" -o "$1" == '--help' ];
+then
+  echo Usage: $0 poisson\|param\|nonparam in.gff readLength out.resultfile out_result_dir S1_in.bam?:S2_in.bam?:   
+  echo "     :" $0 poisson\|param\|nonparam in.gff readLength out.resultfile out_result_dir S1_R1_in.bam?S1_R2_in.bam?:S2_R1_in.bam?S2_R2_in.bam?:   
+  echo "   or:" $0 --help
+  echo 
+  false
+fi
+
+if [ "$1" != 'poisson' -a "$1" != 'param' -a "$1" != 'nonparam' ];
+then
+  echo invalid parameter: $1
+  echo 
+  echo "For usage:" $0 --help
+  false
+fi
+
+TEST_METH=$1 ## Test method 
+shift
+GFF_INPUT=$1 ## Genome annotation in GFF format 
+shift
+readlength=$1 ## Sequencing read length 
+shift 
+RDIFF_OUT=$1 ## rDiff result file
+shift
+RDIFF_OUT_PATH=$1 ## temp session working directory 
+shift
+
+if [ -d $RDIFF_OUT_PATH ]
+then       
+	echo "Using the extra file path as : $RDIFF_OUT_PATH"
+else
+	mkdir -p ${RDIFF_OUT_PATH} ## create the temp working directory
+fi 
+
+## changing tool working directory to the session path
+cd ${RDIFF_OUT_PATH}
+
+## Seperating the files according to the sample and correspondinf replicates. 
+SAMPLE_LIST=()
+for SAMPLES in $@
+do
+    IFS='?' 
+    for BAM_FILE in ${SAMPLES}
+    do
+        if [ $BAM_FILE = ":" ]; ## samples are seperated with ':'
+        then
+            SAMPLE_LIST+=(${SAMPLE_FNAME%?}) ## samples are separating 
+            SAMPLE_FNAME=""
+            continue
+        fi
+        if [ ! -f ${BAM_FILE}.bai ]
+        then
+            echo "Indexing $BAM_FILE"
+            ${RDIFF_SAMTOOLS_INCLUDE_DIR}/samtools index $BAM_FILE
+        else
+            echo "$BAM_FILE already indexed"
+        fi
+        La_fn=$BAM_FILE
+        SAMPLE_FNAME="$SAMPLE_FNAME$BAM_FILE," ## adding a ',' between each BAM files.
+    done
+done
+
+## rDiff execution call 
+${DIR}/../bin/rdiff -o ${RDIFF_OUT_PATH} -d / -g ${GFF_INPUT} -a ${SAMPLE_LIST[0]} -b ${SAMPLE_LIST[1]} -m ${TEST_METH} -L ${readlength}
+
+## rdiff out file
+ln -fs ${RDIFF_OUT_PATH}/P_values_rDiff_"${TEST_METH/param/parametric}".tab ${RDIFF_OUT}