singularity.def

Bootstrap: docker
From: continuumio/miniconda3:23.5.2-0
Stage: build

%files
environment.yml .
%labels
authors="andrea.talenti@ed.ac.uk"
description="Docker image containing base requirements for nf-LO pipelines"

%post
# Add anaconda to path, if not already present
export PATH=/opt/conda/bin:${PATH}

# Add missing mamba dependency then clean cache
apt-get update -qq && apt-get install -y -qq \
        libarchive-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# Install mamba
conda install -c conda-forge -y mamba

# Install the package as normal:
mamba env create -f environment.yml

# Install conda-pack:
mamba install -c conda-forge conda-pack

# Use conda-pack to create a standalone enviornment
# in /venv:
conda-pack -n nf-LO -o /tmp/env.tar && \
mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
rm /tmp/env.tar

# We've put venv in same path it'll be in final image,
# so now fix up paths:
/venv/bin/conda-unpack


# The runtime-stage image; we can use Debian as the
# base image since the Conda env also includes Python
# for us.


Bootstrap: docker
From: debian:buster
Stage: runtime

%files from build
/venv /venv
%post

# Install procps in debian to make it compatible with reporting
apt-get update && \
apt install -y procps gcc g++ curl make pkg-config zlib1g-dev git python2.7 file && \
apt-get clean

# Install NCBI datasets
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets' && \
mv datasets /usr/local/bin && \
chmod a+x /usr/local/bin/datasets

# Define working directory
mkdir /app && cd /app

# Add minimal dependencies
apt-get update -y -qq && \
apt-get upgrade -y -qq && \
apt-get install -y -qq make pkg-config zlib1g-dev git python2.7 && \
apt-get clean

# Link python2.7 to python
ln /usr/bin/python2.7 /usr/bin/python

# Install mafTools
git clone https://github.com/ComparativeGenomicsToolkit/sonLib.git && \
cd sonLib && \
make && \
cd ../

git clone https://github.com/ComparativeGenomicsToolkit/pinchesAndCacti.git && \
cd pinchesAndCacti && \
make && \
cd ../

git clone https://github.com/dentearl/mafTools.git && \
cd mafTools && \
sed -i 's/\${cxx}/\${cxx}\ \-lm/g' */Makefile && \
sed -i 's/char\ fmtName\[10\]/char\ fmtName\[30\]/g' lib/sharedMaf.c && \
sed -i 's/char\ fmtName\[10\]/char\ fmtName\[30\]/g' mafToFastaStitcher/src/mafToFastaStitcherAPI.c && \
make && \
cp ./bin/* /usr/local/bin && \
chmod a+x /usr/local/bin/*

# Clean-up post installation
cd / && rm -rf /app/*
apt-get remove -y -qq python2.7 make pkg-config git && \
apt-get clean -y -qq && \
apt-get autoremove -y -qq

%environment
export PATH=/venv/bin/:$PATH