singularity.def

Bootstrap: docker
From: ubuntu:20.04
Stage: spython-base

%files
dependencies/ /GenomeVariator/
src/ /GenomeVariator/
utils/ /GenomeVariator/
%labels
author="Rodrigo Martin <rodrigo.martin@bsc.es>"
%post

# Install dependencies
apt-get update && apt-get upgrade -y && DEBIAN_FRONTEND=noninteractive apt-get install -y \
python3 \
python3-pip \
git \
wget \
build-essential \
libz-dev \
libglib2.0-dev \
libbz2-dev \
liblzma-dev \
default-jre \
autoconf \
samtools \
biobambam2 \
bwa


mkdir $HOME/bin

# Python dependencies
pip install pysam variant-extractor

# Velvet
wget https://github.com/dzerbino/velvet/archive/refs/tags/v1.2.10.tar.gz && tar -xvzf v1.2.10.tar.gz
make -C velvet-1.2.10
cp velvet-1.2.10/velvetg $HOME/bin && cp velvet-1.2.10/velveth $HOME/bin

# Exonerate
git clone https://github.com/adamewing/exonerate.git
cd exonerate && autoreconf -fi  && ./configure && make && make install

export PATH=$PATH:$HOME/bin

# Copy the content of the repository to the folder GenomeVariator
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"