Bioc323

terra-jupyter-bioconductor/Dockerfile

@@ -1 +1,45 @@
-FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.7
+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"
+
+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"]
+
+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

terra-rstudio-anvil/CHECK/chk1

@@ -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"'

terra-rstudio-anvil/CHECK/chk2

@@ -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"'

terra-rstudio-anvil/CHECK/chk3

@@ -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"'

terra-rstudio-anvil/CHECK/chk4

@@ -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"'

terra-rstudio-anvil/CHECK/o4

@@ -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"
+        }
+    }
+]

terra-rstudio-anvil/Dockerfile

@@ -0,0 +1,49 @@
+# check=skip=SecretsUsedInArgOrEnv
+FROM us.gcr.io/broad-dsp-gcr-public/terra-base:1.0.0
+
+USER root
+
+# should be one of patched, devel
+ENV R_VERSION="patched"  
+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 mkdir /rstudio
+RUN chmod 777 /rstudio
+
+RUN /rocker_scripts/install_rstudio.sh
+
+ENV PASSWORD="bioc"
+
+ENV RSTUDIO_HOME=/home/rstudio
+EXPOSE 8001
+ENTRYPOINT ["/init"]
+