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Singularity
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Bootstrap: docker
From: python:3
%labels
Topic VariantEffect
%post
#This is based on debian buster...
apt-get update --fix-missing && apt-get install -y python3-pip git openjdk-11-jdk
cd /
git clone --depth=50 --branch=master https://github.com/afonsoguerra/SnpEffWrapper.git sanger-pathogens/SnpEffWrapper
cd sanger-pathogens/SnpEffWrapper
bash install_dependencies.sh
rm -rf /sanger-pathogens/SnpEffWrapper/build/clinEff/
rm -rf /sanger-pathogens/SnpEffWrapper/build/*.zip
python3 -m pip install setuptools==58
python3 -m pip install pyvcf3
python3 -m pip install /sanger-pathogens/SnpEffWrapper
%runscript
#export SNPEFF_EXEC=/sanger-pathogens/SnpEffWrapper/build/snpEff_v4_1l_core/snpEff.jar
#exec snpEffBuildAndRun --snpeff-exec /sanger-pathogens/SnpEffWrapper/build/snpEff_v4_1l_core/snpEff.jar --java-exec /usr/bin/java "$@"
export SNPEFF_EXEC=/sanger-pathogens/SnpEffWrapper/build/snpEff_v4_3t_core/snpEff.jar
exec snpEffBuildAndRun --snpeff-exec /sanger-pathogens/SnpEffWrapper/build/snpEff_v4_3t_core/snpEff.jar --java-exec /usr/bin/java "$@"