nullarbor Dockerfile

README.md

Assuming the Docker image has been built and pushed to Dockerhub, and you've downloaded the raw reads and reference genome into /mnt/nullarbor_test/input, you can run it under Singularity like:

singularity run --bind /mnt/nullarbor_test/input:/input \
                --bind /mnt/nullarbor_test/output:/output \
                docker://pansapiens/nullarbor:latest \
                --name PRJEB13012 --mlst efaecium \
                --ref /input/Enterococcus_faecium_505.ASM29533v2.dna_sm.toplevel.fa \
                --input /input/samples.tsv --force --outdir /output/

Dockerfile

FROM continuumio/miniconda3
LABEL   maintainer="Andrew Perry <andrew.perry@monash.edu>"

ARG     KRAKEN_DB_URL=https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_4GB.tgz
ARG     CENTRIFUGE_DB_URL=ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
ENV     KRAKEN_DB_PATH=/databases/minikraken
ENV     CENTRIFUGE_DB_PATH=/databases/centrifuge-db

ENV     KRAKEN_DEFAULT_DB=$KRAKEN_DB_PATH/minikraken_20171013_4GB
ENV     CENTRIFUGE_DEFAULT_DB=$CENTRIFUGE_DB_PATH/p_compressed+h+v

ENV PATH="/opt/conda/bin:${PATH}"
RUN echo 'PATH="/opt/conda/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games"' >/etc/environment

# RUN      useradd --system -s /sbin/nologin nullarbor

RUN apt-get -y update && \
    apt-get -y install curl procps build-essential && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN mkdir -p $KRAKEN_DB_PATH && \
    curl -fsSL $KRAKEN_DB_URL | tar -C $KRAKEN_DB_PATH -xzvf -

RUN mkdir -p $CENTRIFUGE_DB_PATH && \
    curl $CENTRIFUGE_DB_URL | tar -C $CENTRIFUGE_DB_PATH -xvzf -

RUN conda install -y -c bioconda -c conda-forge nullarbor

# samtools openssl fix - this step can be removed once this problem is properly fixed in future package versions
RUN conda install -y -c bioconda samtools=1.9 bcftools --force-reinstall
RUN conda install -y openssl=1.1
RUN conda install -y perl --force-reinstall
# ensure samtools and bcftools run without libcrypto error
RUN samtools --version
RUN bcftools --version

# kraken2 seems to clobber the /opt/conda/libexec/classify binary from kraken,
# so we force install kraken again to ensure classify is the correct version
RUN conda install -y -c bioconda kraken --force-reinstall

# sanity check
RUN nullarbor.pl --check

ENTRYPOINT ["nullarbor.pl"]