The Dockerfile plus scripts in terra-rstudio-anvil builds rstudio #518
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,45 @@ | ||
| FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0 | ||
|
|
||
| USER root | ||
|
|
||
| ENV R_VERSION="4.5.2" | ||
| ENV R_HOME="/usr/local/lib/R" | ||
| ENV TZ="Etc/UTC" | ||
|
|
||
| COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh | ||
| RUN /rocker_scripts/install_R_source.sh | ||
|
|
||
| ENV CRAN="https://cloud.r-project.org" | ||
| ENV LANG=en_US.UTF-8 | ||
|
|
||
| COPY scripts/bin/ /rocker_scripts/bin/ | ||
| COPY scripts/setup_R.sh /rocker_scripts/setup_R.sh | ||
| RUN <<EOF | ||
|
vjcitn marked this conversation as resolved.
|
||
| if grep -q "1000" /etc/passwd; then | ||
| userdel --remove "$(id -un 1000)"; | ||
| fi | ||
| /rocker_scripts/setup_R.sh | ||
| EOF | ||
|
|
||
| ENV S6_VERSION="v2.1.0.2" | ||
| ENV RSTUDIO_VERSION="2026.01.1+403" | ||
| ENV DEFAULT_USER="rstudio" | ||
|
Collaborator
There was a problem hiding this comment. ENV DEFAULT_USER="rstudio" sets DEFAULT_USER, not USER. So ENV USER=jupyter from terra-base is still in the container's environment at runtime. In init_userconf.sh, USER=${DEFAULT_USER} overrides it locally within that script, but that change doesn't |
||
|
|
||
| COPY scripts/install_rstudio.sh /rocker_scripts/install_rstudio.sh | ||
| COPY scripts/install_s6init.sh /rocker_scripts/install_s6init.sh | ||
| COPY scripts/default_user.sh /rocker_scripts/default_user.sh | ||
| COPY scripts/init_set_env.sh /rocker_scripts/init_set_env.sh | ||
| COPY scripts/init_userconf.sh /rocker_scripts/init_userconf.sh | ||
| COPY scripts/pam-helper.sh /rocker_scripts/pam-helper.sh | ||
| RUN /rocker_scripts/install_rstudio.sh | ||
|
|
||
| EXPOSE 8787 | ||
| CMD ["/init"] | ||
|
Collaborator
There was a problem hiding this comment. This needs to be /etc/jupyter/bin/jupyter notebook /init Which is the main reason why Rstudio did not start on Terra |
||
|
|
||
| COPY scripts/install_pandoc.sh /rocker_scripts/install_pandoc.sh | ||
| RUN /rocker_scripts/install_pandoc.sh | ||
|
|
||
| COPY scripts/install_quarto.sh /rocker_scripts/install_quarto.sh | ||
| RUN /rocker_scripts/install_quarto.sh | ||
|
|
||
| COPY scripts /rocker_scripts | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| docker pull us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.17.0 | ||
| docker inspect us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.17.0 | \ | ||
| python3 -m json.tool | grep -A 50 '"Labels"' |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| docker inspect us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.17.0 | \ | ||
| python3 -m json.tool | grep -A 300 '"Env"' |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| docker pull us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.21.0 | ||
| #docker inspect us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.17.0 | \ | ||
| # python3 -m json.tool | grep -A 50 '"Labels"' |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| docker inspect us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.21.0 | \ | ||
| python3 -m json.tool | grep -A 300 '"Env"' |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,165 @@ | ||
| "Env": [ | ||
| "PATH=/opt/venv/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/bin", | ||
| "NVARCH=x86_64", | ||
| "NVIDIA_REQUIRE_CUDA=cuda>=12.6 brand=unknown,driver>=470,driver<471 brand=grid,driver>=470,driver<471 brand=tesla,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=vapps,driver>=470,driver<471 brand=vpc,driver>=470,driver<471 brand=vcs,driver>=470,driver<471 brand=vws,driver>=470,driver<471 brand=cloudgaming,driver>=470,driver<471 brand=unknown,driver>=535,driver<536 brand=grid,driver>=535,driver<536 brand=tesla,driver>=535,driver<536 brand=nvidia,driver>=535,driver<536 brand=quadro,driver>=535,driver<536 brand=quadrortx,driver>=535,driver<536 brand=nvidiartx,driver>=535,driver<536 brand=vapps,driver>=535,driver<536 brand=vpc,driver>=535,driver<536 brand=vcs,driver>=535,driver<536 brand=vws,driver>=535,driver<536 brand=cloudgaming,driver>=535,driver<536 brand=unknown,driver>=550,driver<551 brand=grid,driver>=550,driver<551 brand=tesla,driver>=550,driver<551 brand=nvidia,driver>=550,driver<551 brand=quadro,driver>=550,driver<551 brand=quadrortx,driver>=550,driver<551 brand=nvidiartx,driver>=550,driver<551 brand=vapps,driver>=550,driver<551 brand=vpc,driver>=550,driver<551 brand=vcs,driver>=550,driver<551 brand=vws,driver>=550,driver<551 brand=cloudgaming,driver>=550,driver<551", | ||
| "NV_CUDA_CUDART_VERSION=12.6.77-1", | ||
| "CUDA_VERSION=12.6.2", | ||
| "LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64", | ||
| "NVIDIA_VISIBLE_DEVICES=all", | ||
| "NVIDIA_DRIVER_CAPABILITIES=compute,utility", | ||
| "NV_CUDA_LIB_VERSION=12.6.2-1", | ||
| "NV_NVTX_VERSION=12.6.77-1", | ||
| "NV_LIBNPP_VERSION=12.3.1.54-1", | ||
| "NV_LIBNPP_PACKAGE=libnpp-12-6=12.3.1.54-1", | ||
| "NV_LIBCUSPARSE_VERSION=12.5.4.2-1", | ||
| "NV_LIBCUBLAS_PACKAGE_NAME=libcublas-12-6", | ||
| "NV_LIBCUBLAS_VERSION=12.6.3.3-1", | ||
| "NV_LIBCUBLAS_PACKAGE=libcublas-12-6=12.6.3.3-1", | ||
| "NV_LIBNCCL_PACKAGE_NAME=libnccl2", | ||
| "NV_LIBNCCL_PACKAGE_VERSION=2.23.4-1", | ||
| "NCCL_VERSION=2.23.4-1", | ||
| "NV_LIBNCCL_PACKAGE=libnccl2=2.23.4-1+cuda12.6", | ||
| "NVIDIA_PRODUCT_NAME=CUDA", | ||
| "NV_CUDA_CUDART_DEV_VERSION=12.6.77-1", | ||
| "NV_NVML_DEV_VERSION=12.6.77-1", | ||
| "NV_LIBCUSPARSE_DEV_VERSION=12.5.4.2-1", | ||
| "NV_LIBNPP_DEV_VERSION=12.3.1.54-1", | ||
| "NV_LIBNPP_DEV_PACKAGE=libnpp-dev-12-6=12.3.1.54-1", | ||
| "NV_LIBCUBLAS_DEV_VERSION=12.6.3.3-1", | ||
| "NV_LIBCUBLAS_DEV_PACKAGE_NAME=libcublas-dev-12-6", | ||
| "NV_LIBCUBLAS_DEV_PACKAGE=libcublas-dev-12-6=12.6.3.3-1", | ||
| "NV_CUDA_NSIGHT_COMPUTE_VERSION=12.6.2-1", | ||
| "NV_CUDA_NSIGHT_COMPUTE_DEV_PACKAGE=cuda-nsight-compute-12-6=12.6.2-1", | ||
| "NV_NVPROF_VERSION=12.6.80-1", | ||
| "NV_NVPROF_DEV_PACKAGE=cuda-nvprof-12-6=12.6.80-1", | ||
| "NV_LIBNCCL_DEV_PACKAGE_NAME=libnccl-dev", | ||
| "NV_LIBNCCL_DEV_PACKAGE_VERSION=2.23.4-1", | ||
| "NV_LIBNCCL_DEV_PACKAGE=libnccl-dev=2.23.4-1+cuda12.6", | ||
| "LIBRARY_PATH=/usr/local/cuda/lib64/stubs", | ||
| "NV_CUDNN_VERSION=9.5.0.50-1", | ||
| "NV_CUDNN_PACKAGE_NAME=libcudnn9-cuda-12", | ||
| "NV_CUDNN_PACKAGE=libcudnn9-cuda-12=9.5.0.50-1", | ||
| "NV_CUDNN_PACKAGE_DEV=libcudnn9-dev-cuda-12=9.5.0.50-1", | ||
| "R_VERSION=4.4.2", | ||
| "R_HOME=/usr/local/lib/R", | ||
| "TZ=Etc/UTC", | ||
| "CRAN=https://p3m.dev/cran/__linux__/noble/latest", | ||
| "LANG=en_US.UTF-8", | ||
| "NVBLAS_CONFIG_FILE=/etc/nvblas.conf", | ||
| "PYTHON_CONFIGURE_OPTS=--enable-shared", | ||
| "RETICULATE_AUTOCONFIGURE=0", | ||
| "PURGE_BUILDDEPS=false", | ||
| "VIRTUAL_ENV=/opt/venv", | ||
| "S6_VERSION=v2.1.0.2", | ||
| "RSTUDIO_VERSION=2024.09.0+375", | ||
| "DEFAULT_USER=rstudio", | ||
| "BIOCONDUCTOR_USE_CONTAINER_REPOSITORY=TRUE", | ||
| "TARGETARCH=amd64", | ||
| "TARGETPLATFORM=linux/amd64", | ||
| "PLATFORM=linux/amd64", | ||
| "LIBSBML_CFLAGS=-I/usr/include", | ||
| "LIBSBML_LIBS=-lsbml", | ||
| "BIOCONDUCTOR_DOCKER_VERSION=3.20.30", | ||
| "BIOCONDUCTOR_VERSION=3.20", | ||
| "BIOCONDUCTOR_NAME=bioconductor_docker", | ||
| "RSTUDIO_PORT=8001", | ||
| "RSTUDIO_HOME=/etc/rstudio", | ||
| "RSTUDIO_USERSETTING=/home/rstudio/.config/rstudio/rstudio-prefs.json" | ||
| ], | ||
| "Cmd": [ | ||
| "/init" | ||
| ], | ||
| "ArgsEscaped": true, | ||
| "Image": "", | ||
| "Volumes": null, | ||
| "WorkingDir": "", | ||
| "Entrypoint": [ | ||
| "/opt/nvidia/nvidia_entrypoint.sh" | ||
| ], | ||
| "OnBuild": null, | ||
| "Labels": { | ||
| "com.nvidia.cudnn.version": "9.5.0.50-1", | ||
| "description": "Bioconductor docker image with system dependencies to install all packages.", | ||
| "license": "Artistic-2.0", | ||
| "maintainer": "maintainer@bioconductor.org", | ||
| "name": "bioconductor/bioconductor_docker", | ||
| "org.opencontainers.image.created": "2025-08-04T22:15:40.642Z", | ||
| "org.opencontainers.image.description": "Docker containers for Anvil Project", | ||
| "org.opencontainers.image.licenses": "MIT", | ||
| "org.opencontainers.image.ref.name": "ubuntu", | ||
| "org.opencontainers.image.revision": "476f3b706dd40d0916e72a09a94af39c318fbdcc", | ||
| "org.opencontainers.image.source": "https://github.com/anvilproject/anvil-docker", | ||
| "org.opencontainers.image.title": "anvil-docker", | ||
| "org.opencontainers.image.url": "https://github.com/anvilproject/anvil-docker", | ||
| "org.opencontainers.image.version": "3.21.0", | ||
| "url": "https://github.com/Bioconductor/bioconductor_docker", | ||
| "vendor": "Bioconductor Project", | ||
| "version": "" | ||
| } | ||
| }, | ||
| "Architecture": "amd64", | ||
| "Os": "linux", | ||
| "Size": 22552048216, | ||
| "GraphDriver": { | ||
| "Data": { | ||
| "LowerDir": "/var/lib/docker/overlay2/cf7fa246b27127fbc7faf946613c6c510c94f63c31f23c8acdd48946a1376db0/diff:/var/lib/docker/overlay2/e43fcff0cf93fead086d7c7d637b7ea27419335a97e9a47c6789a34cbbc5067f/diff:/var/lib/docker/overlay2/7dca531e0be25a39c10c7b350ceff4bc52bdd991cedb979371a4944de729a75c/diff:/var/lib/docker/overlay2/901f19ba09c04ae37cc370307f0a49258164673154e46789ad9458fd283eb474/diff:/var/lib/docker/overlay2/db305e49910017986896288b0bc122b455da538e89c7b8fbb248ee239d341cb9/diff:/var/lib/docker/overlay2/ad958a6dce5ca6d872dbf0f78702ebe6125d048a8156ed1da4dff31000743273/diff:/var/lib/docker/overlay2/cc2745ca8d60a5ddd4c5e7288ce26e28ce518735b5be9af561f0c969970b57ac/diff:/var/lib/docker/overlay2/c915fe2c6bb9f41425c3c8c5cc24479ff7077f792f66f22171bf1fccc091052a/diff:/var/lib/docker/overlay2/a744b802620cf50e33d06fc1b516ff1ac180630f8978827c82499dd7afc4f59b/diff:/var/lib/docker/overlay2/e9aae12bc74af242baca3f61dd13be7ed18d6d3b99a1b83fcff4d324365d6cc5/diff:/var/lib/docker/overlay2/9e13e642345089611749d662fafb31633906a352385e2a6c2f820e0102124178/diff:/var/lib/docker/overlay2/99521c756b309b32f1c98db856d2f397cfe0e2eefd5e564f4bd60b4c42551507/diff:/var/lib/docker/overlay2/238606af66d8e73e0a639e5a97a4d0a2c3fd26a6f8f5b7cc2f9861b0da8b23d8/diff:/var/lib/docker/overlay2/31b160971f8683ec58b0bcb851b9064fb90819b217023a4709e17ff7c540fc0c/diff:/var/lib/docker/overlay2/deb8b144ebe8c277b95f5aa1a0cdc71c7c2f6eeeb04cf7ab29415e002010dc48/diff:/var/lib/docker/overlay2/4b390a09102afdb4a397a6784638c2fef38b91894a5398bf6692b52b09483d5b/diff:/var/lib/docker/overlay2/9b84a1431b6058083ea0ab25dc960d102a4feef1fb73aa6db537d7f106ca7ea9/diff:/var/lib/docker/overlay2/35206508ab924b12ea1880910e619a4529dae96047ac069d9c854d71a379f55e/diff:/var/lib/docker/overlay2/255b955b5ec20d0478944975107c6469b81b0cb7c3c2529c3ca48d7ec8a1ed24/diff:/var/lib/docker/overlay2/f6231f5352bc7cd9f5c177ccb529adc645779bf439f984a43f2f369b48e8599b/diff:/var/lib/docker/overlay2/f9dab2de85797e45fa22b24093eda1a4523fc03b1318573837a507ec934bcce6/diff:/var/lib/docker/overlay2/5a040c1712359815ac7808157ec1139d6c1fb62841a4cc5d3fdc4dd4edc4c809/diff:/var/lib/docker/overlay2/4a7cf1c929a2e3fce703623eea51f142f89e0b8417aa2f2a5d01ed054948cf80/diff:/var/lib/docker/overlay2/f5dd1e6e11f8c46e749f3c67c582091ed82cf7936e3cfbbb94c8bff76f06a992/diff:/var/lib/docker/overlay2/2affb8ca06066d579b99d69e293936b5e16e784517ff3f3ce9974c7cc59f33f5/diff:/var/lib/docker/overlay2/d7f41261a0ac48a6c3d7d7a6a5e590816c85af825ffe665c4738ecb0b880a8d3/diff:/var/lib/docker/overlay2/e98f0b85645c860710f6de1ff4a2263bbe156265903bfa335a719570d3da32fc/diff:/var/lib/docker/overlay2/aa055c547f73243358117ab47ca7d6972a87ed8d079674bd424bc11e30beaa67/diff:/var/lib/docker/overlay2/5cfa1717ac7ee656f80216fb1431f1865a5933d1e92577f0107875e3be5a279e/diff:/var/lib/docker/overlay2/97cfbfcbe716845bed6434fd316bdc41af144b70eef6b4c1038d6263ce141b03/diff:/var/lib/docker/overlay2/b253011f1e3a3f0f5b6e978756eb1580b3291c7455cdd92a0e71b2a1fda83d91/diff:/var/lib/docker/overlay2/36ef20d3f44e09e48abd323a5bf0bbe462094aef623db033b5768154f5057db7/diff:/var/lib/docker/overlay2/d7ac05737772209a1f77f52ed7a03f05b2412ffb1aaa02f72ab0f8b2798e76bc/diff:/var/lib/docker/overlay2/ecc4ef6a3893ccc48d4c55548c3e0bb743e131f05b4dab7b822910550c983800/diff:/var/lib/docker/overlay2/fd771b2d601447470b31cebcec6d08f721a48fcf9e4c73a0ffb631fddbc5c51e/diff:/var/lib/docker/overlay2/57da82d6ada11df566149b1caf325c8bc4cff18700c67c2069e8cbc099332596/diff:/var/lib/docker/overlay2/9448d956fc82fcc0a7ef8466120916cf1158d2ec4a6c3eeca394be2ab1c38d98/diff:/var/lib/docker/overlay2/316ff691b6dbb1a108701e293659d0e0d5f881e7cc90160b32e6a9eacedd33ff/diff:/var/lib/docker/overlay2/a6f3d1664d8db7d8dce31209b4b96b69dab0528e0f65b0db68ed0ff19d428c09/diff:/var/lib/docker/overlay2/d57b876a47ab6ae165c5a03aee85f8f7ef4cfd35d3f4cf9399c8132878370c9c/diff:/var/lib/docker/overlay2/6e1018bb32f0f828578e5c53a3ca0a4c06c40cbb7f0191f9fe430f5c74364221/diff:/var/lib/docker/overlay2/1a772f5c0c2d2b0bc5a293925b48e8b2be1e672190f53f3b7a59edf6bd9e7789/diff:/var/lib/docker/overlay2/7fab9fe8fa157ee9ec06098dbb64dc08dc72b8c8f22c0b3ba3247a47e4c22501/diff", | ||
| "MergedDir": "/var/lib/docker/overlay2/8d4dbf8bcab4a54c33ca3cd44a6854dc887dddefbefbb4c0ab42188cafb66830/merged", | ||
| "UpperDir": "/var/lib/docker/overlay2/8d4dbf8bcab4a54c33ca3cd44a6854dc887dddefbefbb4c0ab42188cafb66830/diff", | ||
| "WorkDir": "/var/lib/docker/overlay2/8d4dbf8bcab4a54c33ca3cd44a6854dc887dddefbefbb4c0ab42188cafb66830/work" | ||
| }, | ||
| "Name": "overlay2" | ||
| }, | ||
| "RootFS": { | ||
| "Type": "layers", | ||
| "Layers": [ | ||
| "sha256:fa0f10cc481ea09f029a04c379029a205cd975840c811f16286b28ae103c66ea", | ||
| "sha256:5225ca3cb880c4f82c5f98a59eb2e95d5a6d21996662f5e75119db17d78acdaa", | ||
| "sha256:46acf2e7015e00c4d84fc11aec061fb226c38ef3604e1fe6c1af43925cdf6f76", | ||
| "sha256:822218c66829845d1985100a6422bbfbd92f9d483d7406b4f93a522391946f09", | ||
| "sha256:d76ec6899bbc1dec0ffd051cc1a673e65de5791812875d4c409d2be9e3b04d79", | ||
| "sha256:2fec42eddb5075bb4028faf0862e37952ce6591db431c39599a94c29a1d3e879", | ||
| "sha256:45928fda1f9dac6e5196403f1c668e2b632ea44c963f952ae92d22a273c2bff1", | ||
| "sha256:ee42cf5b162e166f478f50d30477ad3bd88a0525ad5388497df5ebf084904b0a", | ||
| "sha256:04ad012990cc55cc6c125ae91a205db550ca5c56eb758ed0742be03a0ddea091", | ||
| "sha256:39941670d27ae7d9153b3829a5f47d5acba056b423c22145c796f3aa294baf95", | ||
| "sha256:3c74a83640964a860398a4c7d28d617efb16b9943674345ece655032d95b3400", | ||
| "sha256:64d84285af57bcccce61916d6f3835d935e14dadd144663237207f161dbfd140", | ||
| "sha256:2690b20baf7991d2704712eb8855cdeff86d93f3a218bd863e2df701fb0c8663", | ||
| "sha256:df7479a6fee187801acd8fc787605594846fa42d41c77c3c1d25e0d463bdb77a", | ||
| "sha256:1a057aa5ce6b12de968d59a0ed4f1e127a83af697d149efdda347cca6abadfdc", | ||
| "sha256:71fe6e08b936f31e87a0f8fc962c0d70c440f01cf8f7a6c465ac1bea0733db25", | ||
| "sha256:c37bc2b16106d3c060397e5e49b78f8d00a75cc7954fa2d499e510a7b177433c", | ||
| "sha256:8462eb4005c228cf2fc565ef358eeeb08b315f84b34915ee7975f7b830c40e4e", | ||
| "sha256:1ca9fc8199eae8739e92b17eb1169f00eb0650a5e5653a8811a3e6ecbdda2b01", | ||
| "sha256:212cbed791e51d261b8f30f4541f90f2e003a75b015d03a179cdbe7270e506e6", | ||
| "sha256:03f1a063b3958b4f0d22e29fff52be903a92aa9d13287636f1fcdb0304110ddf", | ||
| "sha256:5a74226d9d75178d4be6f039b489185364da1bb1a4c50b9a2f13e1b8356d45f4", | ||
| "sha256:465fca3f6af1de841e6fd1a86e41d4d24601ec32b940d00f9cd7efc26ee34115", | ||
| "sha256:f1858cd63ba282168086483248c29c0c89c36950babc49c10a872243cd4eaa02", | ||
| "sha256:3e6f3bb2dc5f1e46f726b92779ce6125e31d11fb5100372f6e105891d6ec5af6", | ||
| "sha256:06e6290035ad64329229b7c87d66b0e286ebacefb23093f0209725c30cf2c0ac", | ||
| "sha256:44a7ddc18326fbd23c14a046e9e029cf682cbf8a4464c74c6957462e8128fb3f", | ||
| "sha256:3041769de4052bb736cbf2c37b03ac2111f69ce8869a6b00b31029c0ca0ed93c", | ||
| "sha256:aac4e71a76b3b4c87b01743f92cb8c0a32ce50f6c59b678d3c6fb26db4617918", | ||
| "sha256:391a73ccea8ec27ffe9eae01c1d2c45d6bfbe92aa37029dec59ea2169e769dc6", | ||
| "sha256:06d0484895bd4df25a3cfd585fc9873f8908b30217c0d666172433173142c71f", | ||
| "sha256:4fa8d28a68af62218990ef8fc2092039a12fad306d4b603823e0d9b23bf6cb0d", | ||
| "sha256:79c253d3a564479c1664e2530b3a77affbc428421d3347391e6cb47fcf2fc5b7", | ||
| "sha256:8b1a49a44de9ac97e74168307580a48a503be6cbc29559eecd8eb78fd6eff461", | ||
| "sha256:5031d2154709f869770ba96b1cce22d7d7ded9848176c52e64868d19cf9a9bf8", | ||
| "sha256:3d4f67349bc3ce7b82f4e0da335969a2a869230d92fab23c535dab1cf9193455", | ||
| "sha256:8b4ad3f4121516840c23cab248b5ab00c9ebdcbd1cd0772f443bdae0bd390aba", | ||
| "sha256:a6b66718f88ca8892e079cd4be90c62f44c2beff3265de854cbe16102a5e1b98", | ||
| "sha256:25be4b61ee67b1b7bbe46091e5adbfd5295a29723070b4942b761b6621986223", | ||
| "sha256:ee2557e7ed0d79fc83ed737610cf7dd1c0d681e16df377bf0ff48beb0500ea44", | ||
| "sha256:d1b52e7af32a726c1c56c961d9e64058efb2a662bd04abfac892418038d76f71", | ||
| "sha256:92ca48456b537f8d60e8808a36e1b706b5c3d2972c03822e0cffc19b41a9398a", | ||
| "sha256:a50f7a20e9d62e37c400a04193e1b0b24e59012e09c4448fffc3feb9858908f7", | ||
| "sha256:ff7de508166034bd4a1f7c16c0d3d69b8d6eb24622106fa56b30dd42d9ad46e6" | ||
| ] | ||
| }, | ||
| "Metadata": { | ||
| "LastTagTime": "0001-01-01T00:00:00Z" | ||
| } | ||
| } | ||
| ] |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change | ||
|---|---|---|---|---|
| @@ -0,0 +1,45 @@ | ||||
| # check=skip=SecretsUsedInArgOrEnv | ||||
| FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0 | ||||
|
|
||||
| USER root | ||||
|
|
||||
| ENV R_VERSION="4.5.2" | ||||
| ENV R_HOME="/usr/local/lib/R" | ||||
| ENV TZ="Etc/UTC" | ||||
|
|
||||
| COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh | ||||
| RUN /rocker_scripts/install_R_source.sh | ||||
|
|
||||
| ENV CRAN="https://cloud.r-project.org" | ||||
| ENV LANG=en_US.UTF-8 | ||||
|
|
||||
| COPY scripts/bin/ /rocker_scripts/bin/ | ||||
| COPY scripts/setup_R.sh /rocker_scripts/setup_R.sh | ||||
| RUN <<EOF | ||||
| if grep -q "1000" /etc/passwd; then | ||||
| userdel --remove "$(id -un 1000)"; | ||||
| fi | ||||
| /rocker_scripts/setup_R.sh | ||||
| EOF | ||||
|
|
||||
| ENV S6_VERSION="v2.1.0.2" | ||||
| ENV RSTUDIO_VERSION="2026.01.1+403" | ||||
| ENV DEFAULT_USER="rstudio" | ||||
| ENV RSTUDIO_PORT=8001 | ||||
| ENV RSTUDIO_HOME=/etc/rstudio | ||||
| ENV RSTUDIO_USERSETTING=/home/rstudio/.config/rstudio/rstudio-prefs.json | ||||
|
|
||||
| COPY scripts/install_rstudio.sh /rocker_scripts/install_rstudio.sh | ||||
| COPY scripts/install_s6init.sh /rocker_scripts/install_s6init.sh | ||||
| COPY scripts/default_user.sh /rocker_scripts/default_user.sh | ||||
| COPY scripts/init_set_env.sh /rocker_scripts/init_set_env.sh | ||||
| COPY scripts/init_userconf.sh /rocker_scripts/init_userconf.sh | ||||
|
|
||||
| RUN /rocker_scripts/install_rstudio.sh | ||||
|
|
||||
| ENV PASSWORD="bioc" | ||||
|
|
||||
|
Comment on lines
+40
to
+41
There was a problem hiding this comment. Setting a fixed default
Suggested change
|
||||
| ENV RSTUDIO_HOME=/home/rstudio | ||||
| EXPOSE 8001 | ||||
| ENTRYPOINT ["/init"] | ||||
|
|
||||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
This Dockerfile no longer extends
terra-jupyter-ror installs any Jupyter components, which conflicts with the image name (terra-jupyter-bioconductor) and the existing README that describes it as a Jupyter-compatible Leonardo image. If this image is still intended for notebook service, it likely needs the Jupyter stack (and/or should remainFROM .../terra-jupyter-r).