diff --git a/tools/script/install_herediclass.sh b/tools/script/install_herediclass.sh index 8227a4c9..0e14a96f 100755 --- a/tools/script/install_herediclass.sh +++ b/tools/script/install_herediclass.sh @@ -39,45 +39,45 @@ cd $path variant_classification_path=$path/$foldername cd $variant_classification_path -#wget https://www.python.org/ftp/python/3.10.13/Python-3.10.13.tgz -#tar -zxvf Python-3.10.13.tgz -#cd Python-3.10.13 -#mkdir -p .localpython -#./configure --prefix=$variant_classification_path/.localpython -#make -#make install - -#cd .. -#cd .localpython/bin -#./pip3 install virtualenv - - -#cd ../.. -#.localpython/bin/python3.10 -m venv .venv -#source .venv/bin/activate -#pip install --upgrade pip -#pip install wheel -#pip install setuptools -#python3 -m pip install --upgrade setuptools wheel -#pip install -r requirements.txt -##pip install pyyaml -##pip install cyvcf2 -##pip install biopython -##pip install pyensembl==2.2.9 -##pip install hgvs -##pip install pybedtools -##pip install openpyxl -##pip install jsonschema -##pip install pandas -##pip install fastapi -##pip install uvicorn - -#cd $variant_classification_path -#bash $variant_classification_path/install_dependencies/install_pyensembl.sh -v 110 - -#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 $variant_classification_path +wget https://www.python.org/ftp/python/3.10.13/Python-3.10.13.tgz +tar -zxvf Python-3.10.13.tgz +cd Python-3.10.13 +mkdir -p .localpython +./configure --prefix=$variant_classification_path/.localpython +make +make install + +cd .. +cd .localpython/bin +./pip3 install virtualenv + + +cd ../.. +.localpython/bin/python3.10 -m venv .venv +source .venv/bin/activate +pip install --upgrade pip +pip install wheel +pip install setuptools +python3 -m pip install --upgrade setuptools wheel +pip install -r requirements.txt +#pip install pyyaml +#pip install cyvcf2 +#pip install biopython +#pip install pyensembl==2.2.9 +#pip install hgvs +#pip install pybedtools +#pip install openpyxl +#pip install jsonschema +#pip install pandas +#pip install fastapi +#pip install uvicorn + +cd $variant_classification_path +bash $variant_classification_path/install_dependencies/install_pyensembl.sh -v 110 + +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 cd databases/Clinvar