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PeterSu92PeterSu92
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Merge branch 'master' into BENCH-8893_yp
2 parents 9b93851 + fb83386 commit 025ceb2

21 files changed

Lines changed: 39 additions & 36 deletions

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‎feature-versions/state.json‎

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},
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"ghcr.io/devcontainers/features/common-utils": {
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"tag": "2",
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"installed": "sha256:dbf431d6b42d55cde50fa1df75c7f7c3999a90cde6d73f7a7071174b3c3d0cc4",
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"installed": "sha256:cb0c4d3c276f157eed17935747e364178d75fee17f55c4e129966f64633deb3a",
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"filter": "src\\/.*\\/\\.devcontainer\\.json"
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},
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"ghcr.io/devcontainers/features/node": {
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},
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"us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-wondershaper": {
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"tag": "latest",
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"installed": "sha256:ff6cb0ed80e949a67394b2015267e375c55e1fc577ffacb6fc6f76b5c82acb5c",
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"installed": "sha256:f0b22ef4dc3553a32b2703a2f37ce2108147d036356fdbfc4fa0b5b24e51f456",
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"filter": "src\\/.*\\/docker-compose.yaml"
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},
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"us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-jupyter-extension-builder": {
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"tag": "latest",
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"installed": "sha256:8e29733a48c7f1d8fc0995c9be47f99244eb57307bcc1a4dbf432efdaaffcb69",
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"installed": "sha256:e24c13fdc8f5c746fb3833c15b5913ed090603f23efbf8004ce0bae5b0d7e896",
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"filter": "src\\/.*\\/Dockerfile"
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},
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"us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-aou-jupyter": {
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"tag": "latest",
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"installed": "sha256:e2043ab778c20cd3480502f075ec7ac89d7876207612a2ea54aaef40a72ea429",
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"installed": "sha256:7a5aad9e719b301f7c2d7e2b18399595e2618c9617ac31e2c728a647f225d704",
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"filter": "src\\/.*\\/Dockerfile"
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},
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"us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-workbench-jupyter": {
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"tag": "latest",
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"installed": "sha256:62089d6cef2015e08361928c6bb6ae003afd0800a3e682a536171b3bcb0765b1",
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"installed": "sha256:1dc9709007faf7b17810b01bd5c1dd439609e19e63a2fc34fb3afff9618d43bc",
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"filter": "src\\/.*\\/Dockerfile"
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},
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"ghcr.io/rocker-org/devcontainer/tidyverse": {
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},
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"lscr.io/linuxserver/code-server": {
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"tag": "latest",
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"installed": "sha256:7bd334657f13505abc1e20afeeee5670ad8f818e68853c810889184e597f3051",
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"installed": "sha256:7e9523734c003b6336781942df7b48aa6936a9df6931c12a19a1f7ad7858eeba",
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"filter": "src\\/.*\\/(docker-compose\\.yaml|Dockerfile)"
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},
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"golang": {
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"tag": "1.26-alpine",
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"installed": "sha256:91eda9776261207ea25fd06b5b7fed8d397dd2c0a283e77f2ab6e91bfa71079d",
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"installed": "sha256:3ad57304ad93bbec8548a0437ad9e06a455660655d9af011d58b993f6f615648",
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"filter": "src\\/.*\\/Dockerfile"
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},
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"nvcr.io/nvidia/nemo": {
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},
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"mikefarah/yq": {
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"tag": "4",
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"installed": "sha256:0cb4a78491b6e62ee8a9bf4fbeacbd15b5013d19bc420591b05383a696315e60",
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"installed": "sha256:11a1f0b604b13dbbdc662260d8db6f644b22d8553122a25c1b5b2e8713ca6977",
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"filter": "startupscript\\/butane\\/050-parse-devcontainer\\.sh"
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},
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"gcr.io/go-containerregistry/crane": {
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"tag": "latest",
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"installed": "sha256:d3a706262093746258f20107ab4e95536f9d6d45c8c3f3acf6b02b1801b440d6",
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"installed": "sha256:6f95e0e453f09944a625fa219d6879aa2dfaf3f4c7fe3ac9bf41a0a41d45ec46",
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"filter": "startupscript\\/butane\\/prefetch-oci-features\\.sh"
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}
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}

‎features/src/workbench-tools/install.sh‎

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"conda-forge::bgenix"
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"conda-forge::cromwell"
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"bioconda::ensembl-vep>=115"
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"bioconda::nextflow"
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"bioconda::nextflow=25.10.2"
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"bioconda::plink"
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"bioconda::plink2"
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"bioconda::regenie"

‎src/aou-common/extension-builder/Dockerfile‎

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FROM us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-jupyter-extension-builder@sha256:8e29733a48c7f1d8fc0995c9be47f99244eb57307bcc1a4dbf432efdaaffcb69
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FROM us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-jupyter-extension-builder@sha256:e24c13fdc8f5c746fb3833c15b5913ed090603f23efbf8004ce0bae5b0d7e896
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COPY extension /extension
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‎src/aou-common/load-envs/Dockerfile‎

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FROM golang@sha256:91eda9776261207ea25fd06b5b7fed8d397dd2c0a283e77f2ab6e91bfa71079d
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FROM golang@sha256:3ad57304ad93bbec8548a0437ad9e06a455660655d9af011d58b993f6f615648
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WORKDIR /source
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RUN --mount=type=bind,source=.,target=/source,rw \
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mkdir -p /dist && \

‎src/aou-sas/sas-pre-deploy.sh‎

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# Data directories (on the sas-data volume)
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###############################################################################
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mkdir -p /data/saswork /data/utilloc
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chown -R aou:aougroup /data
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###############################################################################
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# AoU environment loader (staged in Dockerfile at /opt/sas/aou/)
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###############################################################################
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if [ -d /opt/sas/aou ]; then
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cp -n /opt/sas/aou/load-env /opt/sas/aou/load-env.sh /data/ 2>/dev/null || true
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chown aou:aougroup /data/load-env /data/load-env.sh 2>/dev/null || true
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fi
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# Chown only the directories we manage, not /data/workspace (contains gcsfuse mounts)
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chown aou:aougroup /data
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chown -R aou:aougroup /data/saswork /data/utilloc

‎src/aou-sas/setup-sas-env.sh‎

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readonly USER_NAME="${1}"
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readonly DATA_DIR="${2}"
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if [ -f "${DATA_DIR}/load-env.sh" ]; then
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sudo -u "${USER_NAME}" bash -c "source '${DATA_DIR}/load-env.sh'" || true
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if [ -f "/opt/sas/aou/load-env.sh" ]; then
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sudo -u "${USER_NAME}" bash -c "source '/opt/sas/aou/load-env.sh'" || true
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fi
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# Extract export statements from .bashrc to get workbench environment variables

‎src/common/secret-receiver/Dockerfile‎

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FROM golang@sha256:91eda9776261207ea25fd06b5b7fed8d397dd2c0a283e77f2ab6e91bfa71079d
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FROM golang@sha256:3ad57304ad93bbec8548a0437ad9e06a455660655d9af011d58b993f6f615648
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WORKDIR /source
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RUN --mount=type=bind,source=.,target=/source,rw \
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mkdir -p /dist && \

‎src/custom-workbench-jupyter-template/Dockerfile‎

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FROM us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-workbench-jupyter@sha256:62089d6cef2015e08361928c6bb6ae003afd0800a3e682a536171b3bcb0765b1
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FROM us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-workbench-jupyter@sha256:1dc9709007faf7b17810b01bd5c1dd439609e19e63a2fc34fb3afff9618d43bc
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# Install jupyter extensions
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RUN --mount=type=bind,from=jupyter-extension-builder,source=/dist,target=/tmp/extensions \

‎src/jupyter-aou/Dockerfile‎

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FROM us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-aou-jupyter@sha256:e2043ab778c20cd3480502f075ec7ac89d7876207612a2ea54aaef40a72ea429
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FROM us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-aou-jupyter@sha256:7a5aad9e719b301f7c2d7e2b18399595e2618c9617ac31e2c728a647f225d704
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# Install jupyter extensions
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RUN --mount=type=bind,from=jupyter-extension-builder,source=/dist,target=/tmp/extensions \

‎src/jupyter-aou/docker-compose.yaml‎

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# TODO(PHP-87353): Add remotefuse back. See https://github.com/verily-src/workbench-app-devcontainers/pull/227
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wondershaper:
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container_name: "wondershaper"
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image: "us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-wondershaper@sha256:ff6cb0ed80e949a67394b2015267e375c55e1fc577ffacb6fc6f76b5c82acb5c"
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image: "us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-wondershaper@sha256:f0b22ef4dc3553a32b2703a2f37ce2108147d036356fdbfc4fa0b5b24e51f456"
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restart: always
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network_mode: "host"
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cap_add:

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