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The deep variant (complete) manifest (deep-variant.manifest) and the Singularity recipe generated from it to build a deepvariant Singularity image
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[ | |
{ | |
"Id": "sha256:c0acf3d54dce5eabf6ae422593a3d266e1d5d61129d53f32ec943d133b395a6c", | |
"RepoTags": [ | |
"gcr.io/deepvariant-docker/deepvariant:0.5.0" | |
], | |
"RepoDigests": [ | |
"gcr.io/deepvariant-docker/deepvariant@sha256:c95f3eba028ad8e3fe3fb4fd6fcc6ba0cd27ff14139c79bba2a9d4acc5a2591c" | |
], | |
"Parent": "", | |
"Comment": "", | |
"Created": "2018-01-29T20:37:52.869007338Z", | |
"Container": "c0ddcb49aa663b7042497275d25c39221db72cffea017c21d45942feadaf052e", | |
"ContainerConfig": { | |
"Hostname": "", | |
"Domainname": "", | |
"User": "", | |
"AttachStdin": false, | |
"AttachStdout": false, | |
"AttachStderr": false, | |
"Tty": false, | |
"OpenStdin": false, | |
"StdinOnce": false, | |
"Env": [ | |
"PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", | |
"DV_GPU_BUILD=0" | |
], | |
"Cmd": [ | |
"/bin/sh", | |
"-c", | |
"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" | |
], | |
"ArgsEscaped": true, | |
"Image": "sha256:9d30e8ce67321c61be656426c99dc22c6a8be8f1f03a3adcf8e0dd7d08281ed3", | |
"Volumes": null, | |
"WorkingDir": "", | |
"Entrypoint": null, | |
"OnBuild": [], | |
"Labels": null | |
}, | |
"DockerVersion": "17.06.1-ce", | |
"Author": "", | |
"Config": { | |
"Hostname": "", | |
"Domainname": "", | |
"User": "", | |
"AttachStdin": false, | |
"AttachStdout": false, | |
"AttachStderr": false, | |
"Tty": false, | |
"OpenStdin": false, | |
"StdinOnce": false, | |
"Env": [ | |
"PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", | |
"DV_GPU_BUILD=0" | |
], | |
"Cmd": [ | |
"/bin/bash" | |
], | |
"ArgsEscaped": true, | |
"Image": "sha256:9d30e8ce67321c61be656426c99dc22c6a8be8f1f03a3adcf8e0dd7d08281ed3", | |
"Volumes": null, | |
"WorkingDir": "", | |
"Entrypoint": null, | |
"OnBuild": [], | |
"Labels": null | |
}, | |
"Architecture": "amd64", | |
"Os": "linux", | |
"Size": 1293568614, | |
"VirtualSize": 1293568614, | |
"GraphDriver": { | |
"Data": null, | |
"Name": "aufs" | |
}, | |
"RootFS": { | |
"Type": "layers", | |
"Layers": [ | |
"sha256:ff986b10a018b48074e6d3a68b39aad8ccc002cdad912d4148c0f92b3729323e", | |
"sha256:9c7183e0ea88b265d83708dfe5b9189c4e12f9a1d8c3e5bce7f286417653f9b7", | |
"sha256:c98ef191df4b42c3fd5155d23385e75ee59707c6a448dfc6c8e4e9c005a3df11", | |
"sha256:92914665e7f61f8f19b56bf7983a2b3758cb617bef498b37adb80899e8b86e32", | |
"sha256:6f4ce6b888495c7c9bd4a0ac124b039d986a3b18250fa873d11d13b42f6a79f4", | |
"sha256:d981835cfeee9f8e1b8e68fde5e29ca342e554f41065429ff993c77c99262121", | |
"sha256:959f030108b71cedde109ac857d1bb4d760c1e18caa3cdbe89c714e968e759bf", | |
"sha256:9edfd6bd057d9c5da040a314efd9a7c257ef8158629c5990ea74fc3b745ac051", | |
"sha256:051edfa0dcb187fa742d00482e05f0c7e32e1b6665fa492a031054abb88e655e", | |
"sha256:51c8d662a1b2d33f15b969bd7bdd70e5a12130ca7a7793d63c944ed31dd5e169", | |
"sha256:d3bc210757dacfbe3b2bf90a1938d68df319841d9eef59fa44da3bb64f1bbb26" | |
] | |
}, | |
"Metadata": { | |
"LastTagTime": "0001-01-01T00:00:00Z" | |
} | |
} | |
] |
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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 |
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