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added tracy singularity definition file
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tobiasrausch committed Jul 11, 2019
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7 changes: 7 additions & 0 deletions singularity/README.md
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You can build a [tracy](https://github.com/gear-genomics/tracy) singularity container (SIF file) using

`sudo singularity build tracy.sif tracy.def`

Once you have built the container you can run analysis using

`singularity exec tracy.sif tracy basecall input.ab1`
44 changes: 44 additions & 0 deletions singularity/tracy.def
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# Build image
BootStrap: library
From: ubuntu:16.04
Stage: build

%post
apt-get -y update
apt-get install -y build-essential cmake g++ gfortran git 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
apt-get clean
rm -rf /var/lib/apt/lists/*
cd /opt
git clone --recursive https://github.com/gear-genomics/tracy.git
cd /opt/tracy/
make STATIC=1 all
make install


# Final image
BootStrap: library
From: alpine:3.9
Stage: final

%files from build
/opt/tracy/bin/tracy /bin/tracy

%post
TRACYVERSION=`./bin/tracy --version`
echo "export TRACYVERSION=\"${TRACYVERSION}\"" >> $SINGULARITY_ENVIRONMENT
CREATEDATE=`date`
echo "export CREATEDATE=\"${CREATEDATE}\"" >> $SINGULARITY_ENVIRONMENT

%environment
export PATH=/bin:$PATH

%runscript
tracy

%labels
Singularity definition file version v0.0.1

%help
This is a container running tracy.
You can run tracy on files inside the directory where you start
the container, i.e.: singularity exec tracy.sif tracy basecall input.ab1

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