build seurattools successfully on saban docker

Dockerfile.shinyapp

@@ -54,7 +54,6 @@ RUN R -e 'BiocManager::install("wiggleplotr")'
 RUN R -e 'BiocManager::install("ensembldb")'
 ARG GITHUB_PAT
 ENV GITHUB_PAT=$GITHUB_PAT
-RUN R -e 'install.packages("Seurat")'
 RUN R -e 'install.packages("clustree", dependencies=TRUE)'
 RUN R -e 'install.packages("ggpubr", dependencies=TRUE)'
 RUN R -e 'remotes::install_github("velocyto-team/velocyto.R")'
@@ -82,8 +81,15 @@ RUN R -e 'BiocManager::install("EnsDb.Hsapiens.v86")'
 # Custom cache invalidation
 ARG CACHEBUST=1
 
+RUN R -e 'remotes::install_version("Matrix", version = "1.6.4")'
+RUN R -e 'install.packages("SeuratObject")'
+RUN R -e 'BiocManager::install("LoomExperiment")'
+RUN R -e 'BiocManager::install("velociraptor")'
+
+# Custom cache invalidation
+ARG CACHEBUST=1
 RUN R -e 'remotes::install_github("whtns/seuratTools")'
-RUN R -e 'install.packages("formattable")'
+# RUN R -e 'install.packages("formattable")'
 RUN mkdir /root/dockerapp
 COPY dockerapp /root/dockerapp
 # copy the app to the image

application.yml

@@ -1,8 +1,9 @@
 proxy:
   title: Open Analytics Shiny Proxy
   logo-url: https://www.openanalytics.eu/shinyproxy/logo.png
-  landing-page: /app/seuratApp
+  landing-page: /
   port: 8080
+  container-wait-time: 90000
   authentication: none
   hide-navbar: true
   container-log-path: /etc/shinyproxy/container-logs
@@ -30,15 +31,17 @@ proxy:
     container-cmd: ["R", "-e", "shiny::runApp('/root/euler')"]
     container-image: whtns/seurattools
     access-groups: admins
-    container-volumes: ["/dataVolume/storage/single_cell_projects/shinyproxy/dockerdata:/root/dockerdata"]
+    # container-volumes: ["/dataVolume/storage/single_cell_projects/shinyproxy/dockerdata:/root/dockerdata"]
+    container-volumes: ["/home/kstachelek/cobrinik_seuratApp_dockerdata:/root/dockerdata"]
     container-network: seurattools-net
   - id: seuratApp
     container-cmd: ["R", "-e", "shiny::runApp('/root/dockerapp')"]
     container-image: whtns/seurattools
-    access-groups: scientists
-    container-volumes: ["/dataVolume/storage/single_cell_projects/shinyproxy/dockerdata:/root/dockerdata"]
+    access-groups: admins
+    # container-volumes: ["/dataVolume/storage/single_cell_projects/shinyproxy/dockerdata:/root/dockerdata"]
+    container-volumes: ["/home/kstachelek/cobrinik_seuratApp_dockerdata:/root/dockerdata"]
     container-network: seurattools-net
 
 logging:
   file:
-    name: shinyproxy.log
+    name: shinyproxy.log