--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build-and-run-job-scripts.sh	Tue May 01 10:45:22 2018 -0400
@@ -0,0 +1,49 @@
+# run SHELL_SCRIPT within tool outputs directory
+cd ${REPORT_FILES_PATH}
+
+#--------- job 1: index genome --------
+# create genome directory for genome indexes
+mkdir -p ${X_d}/genomeDir
+
+cat >temp.sh <<EOF
+STAR \\
+  --runMode genomeGenerate \\
+  --genomeDir ${X_d}/genomeDir \\
+  --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
+  --sjdbGTFfile ${X_B} \\
+  --sjdbOverhang ${X_C} \\
+  > genome-indexing.log.txt 2>&1
+EOF
+
+grep -v None temp.sh > index-genome.sh
+
+# run star
+sh index-genome.sh
+
+#--------- job 2: mapping ---------
+cat >temp.sh <<EOF
+STAR \\
+  --genomeDir ${X_d}/genomeDir \\
+  --readFilesIn \\
+  ${X_F} \\
+  ${X_R} \\
+  > mapping.log.txt 2>&1
+EOF
+
+grep -v None temp.sh > mapping.sh
+
+# remove temp.sh
+rm temp.sh
+
+# run mapping
+sh mapping.sh
+
+
+
+#--------- job 3: SAM to sorted BAM ------
+echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
+sh sam2bam.sh
+
+#--------- job 4: evaluate mapping -------
+echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
+sh flagstat.sh
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