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# Build image
BootStrap: library
From: ubuntu:22.04
Stage: build
%post
apt-get -y update
apt-get install -y autoconf build-essential cmake g++ gfortran git libcurl4-gnutls-dev hdf5-tools libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev libbz2-dev libhdf5-dev libncurses-dev liblzma-dev zlib1g-dev libdeflate-dev
apt-get clean
rm -rf /var/lib/apt/lists/*
cd /opt
git clone --recursive https://github.com/dellytools/delly.git
cd /opt/delly/
make STATIC=1 all
make install
# Final image
BootStrap: library
From: alpine:latest
Stage: final
%files from build
/opt/delly/bin/delly /bin/delly
%post
DELLYVERSION=`./bin/delly --version`
echo "export DELLYVERSION=\"${DELLYVERSION}\"" >> $SINGULARITY_ENVIRONMENT
CREATEDATE=`date`
echo "export CREATEDATE=\"${CREATEDATE}\"" >> $SINGULARITY_ENVIRONMENT
%environment
export PATH=/bin:$PATH
%runscript
delly
%labels
Singularity definition file version v0.0.1
%help
This is a container running delly.
You can run delly on files inside the directory where you start
the container, i.e.: singularity exec delly.sif delly call -g ref.fa input.bam
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