freesurfer: update image using TRE guidance

SMI · Jun 20, 2024 · 4f656b1 · 4f656b1
1 parent 66b718e
commit 4f656b1
Showing 1 changed file with 61 additions and 11 deletions.
diff --git a/software/Freesurfer/Dockerfile b/software/Freesurfer/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM docker.io/ubuntu@sha256:e9569c25505f33ff72e88b2990887c9dcf230f23259da296eb814fc2b41af999
 
 ARG FREESURFER_VERSION="7.4.1"
 ARG FREESURFER_DEB_MD5="bfe85dd76677cfb7ca2b247b9ac6148e"
@@ -7,26 +7,76 @@ ENV \
     LANG="en_GB.UTF-8" \
     LC_ALL="en_GB.UTF-8"
 
+SHELL ["/bin/bash", "-euo", "pipefail", "-c"]
+
 RUN : \
     && apt-get update -qq \
+    && apt-get upgrade -qq \
     && DEBIAN_FRONTEND=noninteractive apt-get install \
-           -qq -y --no-install-recommends \
-           ca-certificates \
-           curl \
+         -qq -y --no-install-recommends \
+         bash \
+         bc \
+         binutils \
+         ca-certificates \
+         csh \
+         curl \
+         file \
+         gettext \
+         gzip \
+         language-pack-en \
+         libbsd0 \
+         libegl1 \
+         libgl1 \
+         libglu1-mesa \
+         libglvnd0 \
+         libglx0 \
+         libjpeg62 \
+         libncurses5 \
+         libopengl0 \
+         libpcre3 \
+         libquadmath0 \
+         libsm6 \
+         libwayland-cursor0 \
+         libx11-dev \
+         libxcb-icccm4 \
+         libxcb-image0 \
+         libxcb-keysyms1 \
+         libxcb-render-util0 \
+         libxcb-render0 \
+         libxcb-shape0 \
+         libxcb-sync1 \
+         libxcb-xfixes0 \
+         libxcb-xinerama0 \
+         libxcb-xinput0 \
+         libxcb-xkb1 \
+         libxdmcp6 \
+         libxext6 \
+         libxi6 \
+         libxkbcommon-x11-0 \
+         libxkbcommon0 \
+         libxrender1 \
+         libxss1 \
+         libxt6 \
+         make \
+         perl \
+         tar \
+         tcsh \
+         x11-apps \
+         xorg \
+         xorg-dev \
+         xserver-xorg-video-intel \
+         xterm \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
     && :
 
 RUN : \
-    && set -eu \
     && deb="freesurfer_ubuntu22-${FREESURFER_VERSION}_amd64.deb" \
     && curl -sfLo "${deb}" "https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}/${deb}" \
     && echo "${FREESURFER_DEB_MD5} ${deb}" | md5sum -c \
-    && apt-get update -qq \
-    && DEBIAN_FRONTEND=noninteractive apt-get install \
-           -y --no-install-recommends \
-           "./${deb}" \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
+    && dpkg -i "${deb}" \
     && rm "${deb}" \
     && :
+
+RUN groupadd --system nonroot && useradd --no-log-init --system --gid nonroot nonroot
+USER nonroot