Create a wrapper launcher for ExpansionHunter

.gitignore

 *~
 *.bam
-*.bai
+*.bai
\ No newline at end of file
+*.sh.o*
+*.sh.po*
+*.failed
+#*#
\ No newline at end of file

launch_expansionhunter.sh

@@ -13,3 +13,13 @@
 ## Creation Date : 20191102
 ## last revision date : 20191102
 ## Known bugs : None
+
+INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
+OUTPUTPREFIX=test
+LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
+
+qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
+
+
+
+

wrapper_expansionhunter.sh

@@ -5,7 +5,7 @@
 ## Version : 0.0.1
 ## Licence : FIXME
 ## Description : a wrapper for qsubing ExpansionHunter script for STR detection
-## Usage : qsub -pe smp 1 -v INPUTFILE=/path/to/the/matrix/file>,OUTPUTDIR=</path/to/the/output/dir>,[BASENAME=analysis_basename],[TESTTYPE=et|qlf|lrt],[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_expansionhunter.sh
+## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_expansionhunter.sh
 ## Output : FIXME
 ## Requirements : FIXME
 
@@ -29,7 +29,7 @@ echo "$(date +"%F_%H-%M-%S"): START"
 # Check if input file exists
 if [ ! -f "$INPUTFILE" ]
 then
-    echo "Input file does not exist"
+    echo "Input file '$INPUTFILE' does not exist"
     echo "$(date +"%F_%H-%M-%S"): END"
     touch expansionhunter.failed
     exit 1
@@ -46,21 +46,17 @@ fi
 
 # Create .bam and .bai symbolic links
 TMPDIR="$(mktemp -d)"
-ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFLE")"
+ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFILE")"
 ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
 
-#FIXME TODO create a pipeline to launch the qsub script
-#ln -s /archive/gad/shared/bam_new_genome_temp/dijen017.bam ./dijen017.bam
-#ln -s /archive/gad/shared/bam_new_genome_temp/dijen017.bai ./dijen017.bam.bai
-
 # Launch script command and check exit code
 echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
-    --reads "$TMPDIR/$(basename "$INPUTFLE")" \
+    --reads "$TMPDIR/$(basename "$INPUTFILE")" \
     --reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
     --variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
-    --output-prefix "$OUTPUTPREFIX""
+    --output-prefix $OUTPUTPREFIX"
 /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
-    --reads "$TMPDIR/$(basename "$INPUTFLE")" \
+    --reads "$TMPDIR/$(basename "$INPUTFILE")" \
     --reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
     --variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
     --output-prefix "$OUTPUTPREFIX"
@@ -81,8 +77,3 @@ then
 fi
 
 echo "$(date +"%F_%H-%M-%S"): END"
-
-
-
-
-