Bactsnp
This recipe installs BactSNP dependencies via BioConda, then downloade the package from GitHub.
To be used with the fill_template tool.
Bootstrap: docker
From: centos:centos7.6.1810
%environment
source /opt/software/conda/bin/activate /opt/software/conda_env
%post
yum -y install epel-release wget which nano curl zlib-devel
yum -y groupinstall "Development Tools"
mkdir -p /opt/software
cd /opt/software
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
/opt/software/conda/bin/conda config --add channels defaults
/opt/software/conda/bin/conda config --add channels conda-forge
/opt/software/conda/bin/conda config --add channels bioconda
/opt/software/conda/bin/conda create -p /opt/software/conda_env -y samtools picard art mummer
source /opt/software/conda/bin/activate /opt/software/conda_env
wget https://github.com/IEkAdN/BactSNP/releases/download/v1.1.0/bactsnp-1.1.0.linux64.tgz
tar xf bactsnp-1.1.0.linux64.tgz
rm bactsnp-1.1.0.linux64.tgz
cd bactsnp-1.1.0.linux64
make
mv bactsnp /opt/software/conda_env/bin/
cd /opt/software
%runscript
exec bactsnp "$@"
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