From 284879abf92c11bd448202a894628ea98a717a01 Mon Sep 17 00:00:00 2001
From: Jon Clucas <jon.clucas@childmind.org>
Date: Mon, 7 Aug 2023 18:49:05 -0400
Subject: [PATCH] :bug: Restore `bc` in Jammy w/ FreeSurfer installation

& double up on  until FCP-INDI/C-PAC#1974 is resolved
---
 .github/Dockerfiles/base-ABCD-HCP.Dockerfile     |  2 +-
 .github/Dockerfiles/base-fMRIPrep-LTS.Dockerfile |  2 +-
 .github/Dockerfiles/base-lite.Dockerfile         |  2 +-
 .github/Dockerfiles/base-standard.Dockerfile     | 14 +++++++++-----
 4 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/.github/Dockerfiles/base-ABCD-HCP.Dockerfile b/.github/Dockerfiles/base-ABCD-HCP.Dockerfile
index a3c0d244f2..81726e9128 100644
--- a/.github/Dockerfiles/base-ABCD-HCP.Dockerfile
+++ b/.github/Dockerfiles/base-ABCD-HCP.Dockerfile
@@ -89,7 +89,7 @@ RUN locale-gen --purge en_US.UTF-8 \
   && echo -e 'LANG="en_US.UTF-8"\nLANGUAGE="en_US:en"\n' > /etc/default/locale \
   && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
   && ldconfig \
-  && chmod 777 / \
+  && chmod 777 / /home/c-pac_user \
   && chmod 777 $(ls / | grep -v sys | grep -v proc) \
   && apt-get clean \
   && apt-get autoremove -y \
diff --git a/.github/Dockerfiles/base-fMRIPrep-LTS.Dockerfile b/.github/Dockerfiles/base-fMRIPrep-LTS.Dockerfile
index 3180125783..ac069ce62c 100644
--- a/.github/Dockerfiles/base-fMRIPrep-LTS.Dockerfile
+++ b/.github/Dockerfiles/base-fMRIPrep-LTS.Dockerfile
@@ -121,7 +121,7 @@ RUN sed -i 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \
     apt-get autoremove -y && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
     ldconfig && \
-    chmod 777 / && \
+    chmod 777 / /home/c-pac_user && \
     chmod 777 $(ls / | grep -v sys | grep -v proc)
 
 # set user
diff --git a/.github/Dockerfiles/base-lite.Dockerfile b/.github/Dockerfiles/base-lite.Dockerfile
index 27d8c75268..f38be261dc 100644
--- a/.github/Dockerfiles/base-lite.Dockerfile
+++ b/.github/Dockerfiles/base-lite.Dockerfile
@@ -88,7 +88,7 @@ RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && find / -type f -print0 | sort -t/ -k2 | xargs -0 rdfind -makehardlinks true \
     && rm -rf results.txt \
     && ldconfig \
-    && chmod 777 / \
+    && chmod 777 / /home/c-pac_user \
     && chmod 777 $(ls / | grep -v sys | grep -v proc)
 
 # set user
diff --git a/.github/Dockerfiles/base-standard.Dockerfile b/.github/Dockerfiles/base-standard.Dockerfile
index d9d835fdba..1abba7948d 100644
--- a/.github/Dockerfiles/base-standard.Dockerfile
+++ b/.github/Dockerfiles/base-standard.Dockerfile
@@ -23,9 +23,11 @@ LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 USER root
 
 # Installing FreeSurfer
-RUN yes | mamba install tcsh \
-  && yes | mamba clean --all \
-  && cp -l `which tcsh` /bin/tcsh
+RUN apt-get update \
+    && apt-get install --no-install-recommends -y bc \
+    && yes | mamba install tcsh \
+    && yes | mamba clean --all \
+    && cp -l `which tcsh` /bin/tcsh
 ENV FREESURFER_HOME="/usr/lib/freesurfer" \
     NO_FSFAST=1
 ENV PATH="$FREESURFER_HOME/bin:$PATH" \
@@ -40,11 +42,13 @@ COPY --from=FreeSurfer /usr/lib/freesurfer/ /usr/lib/freesurfer/
 COPY dev/docker_data/license.txt $FREESURFER_HOME/license.txt
 
 # link libraries & clean up
-RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
+RUN apt-get autoremove -y \
+    && apt-get autoclean -y \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
     && find / -type f -print0 | sort -t/ -k2 | xargs -0 rdfind -makehardlinks true \
     && rm -rf results.txt \
     && ldconfig \
-    && chmod 777 / \
+    && chmod 777 / /home/c-pac_user \
     && chmod 777 $(ls / | grep -v sys | grep -v proc)
 
 # set user