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BootStrap: library
From: ubuntu:20.04
%environment
export PATH=/bioinf-tools/SPAdes/bin/:$PATH
export LANG=C.UTF-8
export ARIBA_BOWTIE2=/bioinf-tools/bowtie2/bowtie2
export ARIBA_CDHIT=cdhit-est
export MPLBACKEND="agg"
%setup
mkdir $SINGULARITY_ROOTFS/ariba
rsync -a install_dependencies.sh MANIFEST.in LICENSE scripts ariba requirements.txt setup.py third_party $SINGULARITY_ROOTFS/ariba/
%post
export PATH=/bioinf-tools/SPAdes/bin/:$PATH
export ARIBA_BOWTIE2=/bioinf-tools/bowtie2/bowtie2
export ARIBA_CDHIT=cdhit-est
/ariba/install_dependencies.sh /bioinf-tools
cd /ariba
python3 -m pip install -r requirements.txt
python3 setup.py clean --all
python3 setup.py test
python3 setup.py install
%runscript
ariba "$@"
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