nSPECTRa/singularity.def at main · evotools/nSPECTRa · GitHub

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Bootstrap: docker
From: condaforge/miniforge3:26.1.1-3
Stage: build

%labels
MyLabel nspectra
authors="andrea.talenti@ed.ac.uk"
description="Docker image containing base requirements for nf-LO pipelines"
%post


# Install the package as normal:
mamba create -n nspectra -c conda-forge -c bioconda -y python=3.10 \
    pip matplotlib numpy>=1.22.4 pandas polars==1.9.0 \
    pyarrow pysam scipy bioconda::java-jdk
mamba install -n nspectra -y \
    bioconda::samtools bioconda::bcftools bioconda::vcftools \
    bioconda::bedtools bioconda::plink=1.90
mamba install -n nspectra -y bioconda::ucsc-twobitinfo bioconda::ucsc-fatotwobit \
    bioconda::ucsc-wigtobigwig bioconda::ucsc-bigwigtobedgraph
mamba install -n nspectra -y bioconda::vcflib==1.0.3
mamba install -n nspectra -y bioconda::shapeit4
mamba install -n nspectra -y bioconda::shapeit5
mamba install -n nspectra -y \
    bioconda::perl-bioperl \
    bioconda::phast=1.5 bioconda::mutyper bioconda::perl-bio-db-hts \
    bioconda::tabix bioconda::tabixpp=1.1.0
mamba install -n nspectra -y \
    conda-forge::r-base>=4.1.0 \
    conda-forge::r-cowplot \
    conda-forge::r-tidyverse \
    conda-forge::r-reshape2 \
    conda-forge::r-ggfortify \
    conda-forge::r-ggforce \
    conda-forge::r-lazyeval \
    conda-forge::r-plyr

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

# Use conda-pack to create a standalone enviornment
# in /venv:
conda-pack -n nspectra -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: ubuntu:24.04
Stage: runtime

%files from build
/venv /venv
%post

# Install procps in debian to make it compatible with reporting
apt-get update && apt install -y file jellyfish procps g++ curl git wget parallel && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

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

# Copy /venv from the previous stage:

# When image is run, run the code with the environment
# activated:
PATH=/venv/bin/:$PATH
SHELL ["/bin/bash", "-c"]
%environment
export PATH=/venv/bin/:$PATH
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"