add path to pipeline

Extract_PharmGKB_Variants.sh

@@ -24,7 +24,7 @@ if [ ${PRINT_HELP} -eq 1 ]
 then
 	echo "Usage:"
 	echo ""
-	echo "bash -p <path/to/PharmGKB/file> -b <path/to/bam/file> -s <path/to/hlascan/files> -v <path/to/vcf/file>  -o <path/to/output/dir> -h [print/this/help] Extract_PharmGKB_Variants.sh"
+	echo "bash Extract_PharmGKB_Variants.sh -p <path/to/PharmGKB/file> -b <path/to/bam/file> -s <path/to/hlascan/files> -v <path/to/vcf/file>  -o <path/to/output/dir> -h [print/this/help]"
 	echo ""
 	echo "<Mandatory>: "
 	echo "-p <PharmGKB file>: Path to PharmGKB tsv file download at PharmGKB site."
@@ -111,8 +111,12 @@ then
 	exit 13
 fi
 
+# find pipeline directory
+PIPELINEPATH=$(dirname $0)
+
 echo "Input pharmgkb file: $PHARMGKB"
 echo "Path to HLAscan: $HLASCAN"
+echo "Path to create_html.py: $PIPELINEPATH/create_html.py"
 echo "HLAscan executable: $HLASCAN/hla-paper/haplo_scan_v4.0-hla.py"
 echo "Gene list for HLAscan: $HLASCAN/hla-ref-5gene/gene_list"
 echo "Input bam file: $BAM"
@@ -125,4 +129,4 @@ echo "Output HTML file: $OUTPUTDIR/Report.html"
 python2.7 $HLASCAN/hla-paper/haplo_scan_v4.0-hla.py $BAM $HLASCAN/hla-ref-5gene/gene_list $OUTPUTDIR/HLAscan_result/ 1>> $OUTPUTDIR/HLAscan_log.txt 2>> $OUTPUTDIR/HLAscan_log.txt
 
 #create HTML
-python2.7 create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
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+python2.7 $PIPELINEPATH/create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
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Readme.md

@@ -51,16 +51,17 @@ https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Nebraska_NA12878_HG001_
 
 ### Execution
 
-    bash -p <PharmGKB file> -b <bam file> -s <path to HLAscan files> -v <vcf file>  -o <output dir> Extract_PharmGKB_Variants.sh
+    bash Extract_PharmGKB_Variants.sh
 
-    Options:
+    <Mandatory>
 	-p <path to PharmGKB file> : Path to PharmGKB tsv file download at PharmGKB site.
 	-b <path to bam file> : Path to bam file provided by alignement.
 	-s <path to hlascan files> : Path to HLAscan tools download and unzipped.
 	-v <path to vcf file> : Path to vcf file provided by variant calling
 	-o <output_path>: Output path.
-    -h print help
+
+    -h print help and exit
 
 #### Data test
 
-    bash -p data_test/PharmGKB_Epilepsy.tsv -b data_test/NA12878.5gene.bam -s <path to HLAscan files> -v data_test/NIST-hg001-7001-b-gatk.vcf  -o data_test/ Extract_PharmGKB_Variants.sh
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+    bash Extract_PharmGKB_Variants.sh -p data_test/PharmGKB_Epilepsy.tsv -b data_test/NA12878.5gene.bam -s <path to HLAscan files> -v data_test/NIST-hg001-7001-b-gatk.vcf  -o data_test/
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