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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", | |
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| "sha256:d3bc210757dacfbe3b2bf90a1938d68df319841d9eef59fa44da3bb64f1bbb26" | |
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| }, | |
| "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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