A DeepVariant image for Singularity, reliant on a localimage pull of layers first

Singularity.spec

Bootstrap: localimage
From: /home/vanessa/.singularity/shub/deepvariant-docker-deepvariant:0.5.0.simg

# sregistry get gcr.io/deepvariant-docker/deepvariant:0.5.0
# sudo singularity build deepvariant Singularity

%environment
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    DV_GPU_BUILD=0
    export PATH DV_GPU_BUILD

%apprun download_testdata
    mkdir input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam.bai -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/test_nist.b37_chr20_100kbp_at_10mb.bed -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/test_nist.b37_chr20_100kbp_at_10mb.vcf.gz -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/test_nist.b37_chr20_100kbp_at_10mb.vcf.gz.tbi -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/ucsc.hg19.chr20.unittest.fasta -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/ucsc.hg19.chr20.unittest.fasta.fai -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/ucsc.hg19.chr20.unittest.fasta.gz -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/ucsc.hg19.chr20.unittest.fasta.gz.fai -P input
    wget https://storage.googleapis.com/deepvariant/quickstart-testdata/ucsc.hg19.chr20.unittest.fasta.gz.gzi -P input

%apprun download_models
    mkdir models
    wget https://storage.googleapis.com/deepvariant/models/DeepVariant/0.5.0/DeepVariant-inception_v3-0.5.0%2Bcl-182548131.data-wgs_standard/model.ckpt.data-00000-of-00001 -P models
    wget https://storage.googleapis.com/deepvariant/models/DeepVariant/0.5.0/DeepVariant-inception_v3-0.5.0%2Bcl-182548131.data-wgs_standard/model.ckpt.index -P models
    wget https://storage.googleapis.com/deepvariant/models/DeepVariant/0.5.0/DeepVariant-inception_v3-0.5.0%2Bcl-182548131.data-wgs_standard/model.ckpt.meta -P models

%apprun make_examples
    exec /opt/deepvariant/bin/make_examples \
    --mode calling \
    --ref /dv2/input/ucsc.hg19.chr20.unittest.fasta.gz \
    --reads /dv2/input/NA12878_S1.chr20.10_10p1mb.bam \
    --examples output.examples.tfrecord \
    --regions "chr20:10,000,000-10,010,000"

%apprun call_variants
    exec /opt/deepvariant/bin/call_variants \
    --outfile call_variants_output.tfrecord \
    --examples output.examples.tfrecord \
    --checkpoint /dv2/models/model.ckpt

%apprun postprocess_variants
 exec /opt/deepvariant/bin/postprocess_variants \
    --ref /dv2/input/ucsc.hg19.chr20.unittest.fasta.gz \
    --infile call_variants_output.tfrecord \
    --outfile output.vcf


%runscript
if [ $# -eq 0 ]; then
    echo '''Example Usage:

    # download data to input and models
    singularity run --app download_testdata deepvariant
    singularity run --app download_models deepvariant

    # make the examples, mapping inputs
    singularity run --bind input:/dv2/input/ --app make_examples deepvariant

    # call variants, mapping models
    singularity run --bind models:/dv2/models/ --app call_variants deepvariant

    # postprocess variants
    singularity run --bind input:/dv2/input/ --app postprocess_variants deepvariant

    # https://github.com/google/deepvariant/blob/master/docs/deepvariant-docker.md
'''
else
    exec "$@"
fi
    

%post
    apt-get install -y wget

    # https://github.com/google/deepvariant/blob/r0.5/deepvariant/docker/Dockerfile
    BASH_HEADER='#!/bin/bash' && \
    printf "%s\n%s\n" \
        "${BASH_HEADER}" \
        'python /opt/deepvariant/bin/make_examples.zip "$@"' > \
        /opt/deepvariant/bin/make_examples && \
    printf "%s\n%s\n" \
        "${BASH_HEADER}" \
        'python /opt/deepvariant/bin/call_variants.zip "$@"' > \
        /opt/deepvariant/bin/call_variants && \
    printf "%s\n%s\n" \
        "${BASH_HEADER}" \
        'python /opt/deepvariant/bin/postprocess_variants.zip "$@"' > \
        /opt/deepvariant/bin/postprocess_variants && \
    printf "%s\n%s\n" \
        "${BASH_HEADER}" \
        'python /opt/deepvariant/bin/model_train.zip "$@"' > \
        /opt/deepvariant/bin/model_train && \
    printf "%s\n%s\n" \
        "${BASH_HEADER}" \
        'python /opt/deepvariant/bin/model_eval.zip "$@"' > \
        /opt/deepvariant/bin/model_eval && \
    chmod +x /opt/deepvariant/bin/make_examples \
             /opt/deepvariant/bin/call_variants \
             /opt/deepvariant/bin/postprocess_variants \
             /opt/deepvariant/bin/model_train \
             /opt/deepvariant/bin/model_eval