📦 Make symlinks real in FSL 5.0.9-5 installation

⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣀⣀⣀⣀⣀⢀⣀⣀⣀⣀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⣠⠶⠚⠉⠉⠉⠉⠉⠉⠙⠛⠿⣍⣉⠛⢶⣤⣀⣀⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⢀⡴⠋⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠉⠳⢦⣍⠻⣌⠉⠛⠲⢤⣄⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⣠⡟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠈⠳⣬⡑⢤⡀⠀⠀⠙⠳⢶⣤⣄⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⢰⡏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠈⠙⢦⡙⠀⠀⠀⠀⠀⠙⠺⡙⢶⣶⠤⣄⣀⣀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⢸⡿⠶⠤⣤⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠙⢦⠀⠀⠀⠀⠀⠀⠙⢦⡈⢳⡄⠀⠉⠉⠓⣤⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠈⢳⢦⣀⡀⠀⠀⠀⠀⠀⠀⠀⢀⣀⣀⣀⣀⣀⣀⣀⣀⠀⠈⠻⣄⠀⠀⠀⠀⠀⠈⢳⡀⠙⣆⠀⠀⠀⠀⢳⡄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⢠⡟⠰⠋⠉⠙⠓⠒⠒⠒⠛⠉⠉⠉⢉⣀⣀⣀⠀⠈⠉⠉⠲⢤⣙⣦⡀⢀⠀⠀⠀⠀⢳⡀⠘⢧⠀⠀⠀⠀⢻⡄⠀⠀⠀⠀⢀⣀⣤⡶⣶⣖⣿⣿⠖
⠀⠀⠀⠀⠀⠀⠀⢸⠃⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠈⠁⠀⠉⢳⡀⠀⠀⠀⠀⢻⠘⢧⡈⣇⠀⠀⠀⠀⢳⠀⠘⣧⠀⠀⠀⠸⡇⣀⡤⢶⡟⣹⣯⠗⠊⢉⡴⠋⠁⠀
⠀⠀⠀⠀⠀⠀⢀⣞⠀⣠⣤⡄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠳⠀⠀⠀⠀⣼⠀⠘⣷⠘⡄⠀⠀⠀⠀⣇⠀⢸⡆⠀⣀⡼⠛⠁⣠⡾⠛⠿⢿⣿⡟⠃⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠈⣿⣰⠋⠀⢻⠀⠀⠀⠀⠀⠀⢀⡴⠶⠶⢦⡀⠀⠀⠀⠀⠀⠀⢀⡟⠀⠀⠈⣧⢹⡄⠀⠀⠀⢻⡀⠀⣿⠶⠁⣀⠴⠋⠁⠀⠀⣠⠾⠋⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⣠⣤⣤⣇⣇⣴⣶⣾⠀⠀⠀⠀⠀⣴⠋⠀⠀⠀⠀⣷⡀⠀⠀⠀⠀⠀⣸⠁⠀⠀⠀⠹⣆⣻⡄⠀⠀⢸⡇⠀⢿⠖⠚⠁⠀⠀⣀⡴⠊⠁⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⣸⡏⠀⠀⠛⢿⣷⣷⠋⠀⠀⠀⠀⣶⠇⢀⣤⣤⣄⠀⢼⠟⠀⠀⠀⠀⠀⡟⠀⠀⠀⠀⠀⢻⡀⢻⣶⣖⣺⡇⠀⢸⣦⣤⣴⠖⠛⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⢠⡞⠻⣧⠀⠀⠀⠀⠙⠳⣄⡀⠀⠀⠀⣿⠀⣞⣿⣯⣽⣇⡞⠀⠀⠀⠀⠀⢸⠃⠀⠀⠀⠀⠀⠸⡇⠈⢳⠉⢸⡇⠀⢸⠀⢸⠇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⡿⠀⢠⠙⣧⡀⠀⠀⠀⠀⠈⢳⠀⠀⠀⠻⡖⣿⣿⣿⣿⡟⠀⠀⠀⠀⠀⠀⣿⠀⠀⠀⠀⠀⠀⠀⢷⠀⠈⢷⣸⡇⠀⣿⢀⡿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⢸⣇⠀⠻⡇⠈⠳⣄⠀⠀⠀⢀⣼⠀⠀⠀⠀⠉⠀⠀⠁⠀⠀⠀⠀⠀⠀⠀⠀⣿⠀⠀⠀⠀⠀⠀⠀⢸⡀⠀⠈⣿⠀⠀⡟⡾⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠈⣿⡀⠀⠹⡄⠀⠈⠓⠶⠶⠚⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠹⣆⠀⠀⠀⠀⠀⠀⢸⡇⠀⠀⢹⡄⢸⡿⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠸⣇⠀⠀⠹⣦⡀⠀⠀⠀⠀⠀⠀⠀⠀⢰⡄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⠿⠖⠲⢶⣄⠀⠀⢸⠇⠀⠀⠘⣷⠟⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠹⡆⠀⠀⢻⠙⠲⢤⣄⣀⣀⣀⣀⣠⣤⣿⣄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣠⣤⣄⡀⠘⡇⠀⣼⠀⠀⠀⠀⣧⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠹⣄⠀⠘⡗⠚⠻⠷⠒⠒⢲⣶⠞⠋⠀⠘⠆⠀⠀⠀⠀⠀⠀⠀⠀⠀⠉⠀⠀⠈⠃⢠⡇⢠⡇⠀⠀⠀⠀⣸⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠻⣴⡄⠘⢦⣀⣀⣠⠶⠋⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣄⡀⠀⠀⠀⠀⢀⣴⠟⠀⣼⠁⠀⠀⠀⠀⣿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠙⣎⠢⢤⣀⣀⣀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣠⡼⠛⠒⠶⠶⠚⠋⠁⢀⡴⠃⠀⠀⠀⠀⣸⡏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠈⠳⢤⣀⣀⣀⣀⣀⣀⣀⣀⣀⣀⣀⡤⠤⠶⠚⢋⡟⠛⠓⠒⠶⣶⣒⠚⠛⠉⠀⠀⠀⠀⠀⣰⡟⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢉⣩⢭⡉⢉⣩⢿⡏⠀⠀⠀⠀⠀⠀⣼⠛⢦⡀⠀⠀⠀⠉⠉⠓⠒⠶⠶⠖⠒⠋⠉⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⡞⠁⠀⠙⣯⠁⢸⡇⠀⠀⠀⠀⣀⡴⣏⡀⠀⠙⣦⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⢠⣾⠀⠀⠀⠀⢹⡄⠈⠛⠓⠒⢚⣻⡵⠞⠋⠙⣆⠀⠈⠻⣤⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⣀⡤⢾⡏⠀⠀⠀⠀⣠⠟⠛⠛⠶⣤⠾⠋⠀⠀⠀⠀⢹⡆⠀⠀⠀⠙⠶⢤⣀⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⣾⠋⠀⣸⠇⠀⠀⠀⢰⡟⠀⠀⠀⣰⠏⠀⠀⠀⠀⠀⠀⢸⡇⠀⠀⠀⠀⠀⠀⠈⠙⣦⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⣿⠀⣸⡿⠀⠀⠀⣠⢿⡇⠀⠀⢠⡏⠀⠀⠀⠀⠀⠀⠀⣾⠃⠀⠀⠀⠀⠀⠀⠀⠀⣿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠙⢶⡇⠀⠀⠤⠚⠁⣨⣧⠀⠀⡟⢧⠀⠀⠀⠀⠀⠀⡄⣿⠀⠀⠀⠀⠀⠀⠀⠀⢰⡟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⡿⠀⠀⠀⢀⡠⢚⡽⠛⠦⣼⡇⠘⣧⠀⠀⠀⠀⠀⣧⠇⠀⠀⠀⠀⠀⠀⠀⣠⡿⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⢸⡇⠀⣠⠞⠋⣰⠞⠁⠀⠀⠈⣷⡀⠈⠀⠀⠀⠀⠐⣿⠀⠀⠀⠀⠀⠀⣠⡾⠋⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠸⣗⣿⣥⡴⠛⠁⠀⠀⠀⠀⠀⢸⡇⠀⠀⠀⠀⠀⠀⡟⠒⠶⠶⠖⠒⠋⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠉⠉⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⢻⡄⠀⠀⠀⠀⠀⣷⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠈⢷⡀⠀⠀⠀⢰⡇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠙⢦⣄⣠⣟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀

[rebuild FSL.5.0.9-5.neurodebian-xenial]

.dockerignore

@@ -1,8 +1,8 @@
-!.github/scripts
 bids-examples
 .circleci
 cpac_runs
 .env*
 .git
 .github
+!.github/scripts
 *.tar.gz

.github/Dockerfiles/FSL.5.0.9-5.neurodebian-xenial.Dockerfile

@@ -20,12 +20,15 @@ USER root
 
 ARG DEBIAN_FRONTEND=noninteractive
 
+COPY .github/scripts/make_real.sh /
+
 # install FSL
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
       fsl-core=5.0.9-5~nd16.04+1 \
       fsl-atlases \
-      fsl-mni152-templates=5.0.7-2
+      fsl-mni152-templates=5.0.7-2 && \
+    /make_real.sh "/usr/share/fsl/5.0/data"
 
 # setup FSL environment
 ENV FSLDIR=/usr/share/fsl/5.0 \
@@ -62,8 +65,8 @@ COPY --from=FSL /usr/lib/libznz.so.2 /usr/lib/libznz.so.2
 COPY --from=FSL /usr/share/doc/fsl-core /usr/share/doc/fsl-core
 COPY --from=FSL /usr/share/man/man1/fsl-5.0-core.1.gz /usr/share/man/man1/
 COPY --from=FSL /usr/share/man/man1/fsl.1.gz /usr/share/man/man1/
-COPY --from=FSL /usr/share/data/fsl-mni152-templates /usr/share/data/fsl-mni152-templates
-COPY --from=FSL /usr/share/doc/fsl-mni152-templates /usr/share/doc/fsl-mni152-templates
+COPY --from=FSL /usr/share/data/fsl-* /usr/share/data/
+COPY --from=FSL /usr/share/doc/fsl-* /usr/share/doc/
 COPY --from=FSL /usr/share/fsl /usr/share/fsl
 # install C-PAC resources into FSL
 COPY --from=data /fsl_data/standard /usr/share/fsl/5.0/data/standard

.github/scripts/make_real.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# Function to convert symlinked subpaths to real paths
+convert_symlinks() {
+  # Iterate over all items (files and directories) in the current directory
+  for ITEM in "$1"/*; do
+    echo $ITEM
+    if [[ -L "$ITEM" ]]; then
+      # If the item is a symlink, convert it to a real path
+      TARGET=$(readlink -f "$ITEM")
+      rm "$ITEM"
+      cp -r "$TARGET" "$ITEM"
+      echo "Converted symlink to real path: $ITEM"
+    elif [[ -d "$ITEM" ]]; then
+      # If the item is a directory, recursively call the function on it
+      convert_symlinks "$ITEM"
+    fi
+  done
+}
+
+convert_symlinks $1