Commit ad81a1c9 authored by simon verdez's avatar simon verdez

add path to pipeline

parent fd649755
...@@ -24,7 +24,7 @@ if [ ${PRINT_HELP} -eq 1 ] ...@@ -24,7 +24,7 @@ if [ ${PRINT_HELP} -eq 1 ]
then then
echo "Usage:" echo "Usage:"
echo "" echo ""
echo "bash -p <path/to/PharmGKB/file> -b <path/to/bam/file> -s <path/to/hlascan/files> -v <path/to/vcf/file> -o <path/to/output/dir> -h [print/this/help] Extract_PharmGKB_Variants.sh" echo "bash Extract_PharmGKB_Variants.sh -p <path/to/PharmGKB/file> -b <path/to/bam/file> -s <path/to/hlascan/files> -v <path/to/vcf/file> -o <path/to/output/dir> -h [print/this/help]"
echo "" echo ""
echo "<Mandatory>: " echo "<Mandatory>: "
echo "-p <PharmGKB file>: Path to PharmGKB tsv file download at PharmGKB site." echo "-p <PharmGKB file>: Path to PharmGKB tsv file download at PharmGKB site."
...@@ -111,8 +111,12 @@ then ...@@ -111,8 +111,12 @@ then
exit 13 exit 13
fi fi
# find pipeline directory
PIPELINEPATH=$(dirname $0)
echo "Input pharmgkb file: $PHARMGKB" echo "Input pharmgkb file: $PHARMGKB"
echo "Path to HLAscan: $HLASCAN" 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 "HLAscan executable: $HLASCAN/hla-paper/haplo_scan_v4.0-hla.py"
echo "Gene list for HLAscan: $HLASCAN/hla-ref-5gene/gene_list" echo "Gene list for HLAscan: $HLASCAN/hla-ref-5gene/gene_list"
echo "Input bam file: $BAM" echo "Input bam file: $BAM"
...@@ -125,4 +129,4 @@ echo "Output HTML file: $OUTPUTDIR/Report.html" ...@@ -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 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 #create HTML
python2.7 create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html python2.7 $PIPELINEPATH/create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
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...@@ -51,16 +51,17 @@ https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Nebraska_NA12878_HG001_ ...@@ -51,16 +51,17 @@ https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Nebraska_NA12878_HG001_
### Execution ### 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. -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. -b <path to bam file> : Path to bam file provided by alignement.
-s <path to hlascan files> : Path to HLAscan tools download and unzipped. -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 -v <path to vcf file> : Path to vcf file provided by variant calling
-o <output_path>: Output path. -o <output_path>: Output path.
-h print help
-h print help and exit
#### Data test #### 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 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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