added herediclassify bedtools install

src/frontend_celery/start_herediclass.sh

@@ -57,6 +57,12 @@ autoclass_path=$ROOT/tools/herediclass
 cd $autoclass_path
 
 source .venv/bin/activate
+export PATH="$autoclass_path/tools/bedtools2/bin:$PATH"
+export PATH="$ROOT/tools/samtools:$PATH"
+export PATH="$ROOT/tools/htslib:$PATH"
+
+#which sortBed
+#which samtools
 
 if [ "${WEBAPP_ENV}" == "dev" ]
 then

tools/script/install_herediclass.sh

@@ -77,14 +77,22 @@ bash $variant_classification_path/install_dependencies/install_pyensembl.sh -v 1
 
 sed -r -i "s:/variant_classification::g" $variant_classification_path/install_dependencies/download_data.sh
 
-bash $variant_classification_path/install_dependencies/download_data.sh -p $variant_classification_path
 
+# download data
+bash $variant_classification_path/install_dependencies/download_data.sh -p $variant_classification_path
 
 cd databases/Clinvar
 wget --no-check-certificate https://download.imgag.de/ahdoebm1/extern/clinvar_spliceai_all_sorted.vcf.gz
 in_path_spliceai_clinvar=$variant_classification_path/databases/Clinvar/clinvar_spliceai_all_sorted.vcf.gz
 python $variant_classification_path/install_dependencies/data_filter_clinvar.py -i $in_path_spliceai_clinvar
 
+# install bedtools
+cd $variant_classification_path
+mkdir -p tools
+cd tools
+chmod 755 $variant_classification_path/install_dependencies/install_bedtools.sh
+$variant_classification_path/install_dependencies/install_bedtools.sh -p $variant_classification_path/tools -v 2.29.1
+
 
 # adjust configuration
 cd $variant_classification_path