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improved herediclass download&install
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MarvinDo committed Feb 14, 2024
1 parent 47767f9 commit 49c6db1
Showing 1 changed file with 5 additions and 1 deletion.
6 changes: 5 additions & 1 deletion tools/script/install_herediclass.sh
Original file line number Diff line number Diff line change
Expand Up @@ -89,10 +89,14 @@ python $variant_classification_path/install_dependencies/data_filter_clinvar.py
cd $variant_classification_path
cp config.yaml config_production.yaml
sed -r -i "s:/home/katzkean/:$variant_classification_path/:g" config_production.yaml
sed -r -i "s:gene_specific:gene_specific_production:g" config_production.yaml
sed -r -i "s:variant_classification/::g" config_production.yaml

gene_specific_config_path=$variant_classification_path/gene_specific
for filename in $gene_specific_config_path/*.yaml; do
extension=_production
gene_sepcific_config_path_production=$gene_specific_config_path$extension
cp -r $gene_specific_config_path $gene_sepcific_config_path_production
for filename in $gene_sepcific_config_path_production/*.yaml; do
sed -r -i "s:/home/katzkean/:$variant_classification_path/:g" $filename
sed -r -i "s:variant_classification/::g" $filename
done
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