afonsoguerra/SnpEffWrapper:latest

$ singularity pull shub://afonsoguerra/SnpEffWrapper:latest

Singularity Recipe

Bootstrap: docker

From: python:3

%labels
    Topic VariantEffect

%post
    #This is based on debian buster...
    apt-get update --fix-missing && apt-get install -y python-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    
    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 "$@"
    export SNPEFF_EXEC=/sanger-pathogens/SnpEffWrapper/build/snpEff_v4_3t_core/snpEff.jar
    exec snpEffBuildAndRun --snpeff-exec /sanger-pathogens/SnpEffWrapper/build/snpEff_v4_3t_core/snpEff.jar --java-exec /usr/bin/java "$@"

Collection


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Metrics

key value
id /containers/afonsoguerra-SnpEffWrapper-latest
collection name afonsoguerra/SnpEffWrapper
branch master
tag latest
commit ca963d6d971b898d884634e531360e23295aced3
version (container hash) d1dd8a6fe47194a7e8629374974eba2b829e1c965b1c7df2b422a6b09287d46e
build date 2020-11-18T10:40:11.460Z
size (MB) 745.62890625
size (bytes) 781848576
SIF Download URL (please use pull with shub://)
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