Add Dynamics ports to RStudio

RStudio/4.1.1/Dockerfile

@@ -15,6 +15,13 @@ ENV http_proxy="${http_proxy}" \
 
 RUN mkdir /vizapp
 
+# Config the Rstudio
 # Allow root login. Ref. Section 3.2. https://s3.amazonaws.com/rstudio-server/rstudio-server-pro-0.99.903-admin-guide.pdf
 # Usefull for fakeroot function of singularity 
 RUN /usr/bin/bash -c "sed -i 's/^UID_MIN.*/UID_MIN                  0/g' /etc/login.defs"
+
+ARG ARG_VIZAPP_PORT=8123
+ENV VIZAPP_PORT=${ARG_VIZAPP_PORT:-8123}
+
+# Change the default port to 8123, which is the one used by Astrocyte
+RUN /usr/bin/bash -c "sed -i 's/--server-daemonize 0/--server-daemonize 0 --www-port=\${VIZAPP_PORT}/g' /etc/services.d/rstudio/run"

RStudio/4.2.2/Dockerfile

@@ -15,6 +15,13 @@ ENV http_proxy="${http_proxy}" \
 
 RUN mkdir /vizapp
 
+# Config the Rstudio
 # Allow root login. Ref. Section 3.2. https://s3.amazonaws.com/rstudio-server/rstudio-server-pro-0.99.903-admin-guide.pdf
 # Usefull for fakeroot function of singularity 
 RUN /usr/bin/bash -c "sed -i 's/^UID_MIN.*/UID_MIN                  0/g' /etc/login.defs"
+
+ARG ARG_VIZAPP_PORT=8123
+ENV VIZAPP_PORT=${ARG_VIZAPP_PORT:-8123}
+
+# Change the default port to 8123, which is the one used by Astrocyte
+RUN /usr/bin/bash -c "sed -i 's/--server-daemonize 0/--server-daemonize 0 --www-port=\${VIZAPP_PORT}/g' /etc/services.d/rstudio/run"

RStudio/run_rstudio_singularity.sh

@@ -15,7 +15,7 @@ tmpDir=/tmp/$USER/rstudio
 VIZAPP_HOME="$tmpDir/vizapp/"
 
 # dependencies libs of vizapp, space seperated
-VIZAPP_LIBS="rmarkdown"
+#VIZAPP_LIBS="rmarkdown"
 
 # user specified path to install the vizapp libs inside the container
 R_LIBS_USER="/vizapp/rlibrary"
@@ -36,7 +36,7 @@ ln -s /mnt $tmpDir/home/outputDir
 
 # version and the image to use
 PACKAGE="rstudio"
-VERSION="4.2.2"
+VERSION="4.1.1"
 IMAGE_NAME="git.biohpc.swmed.edu:5050/astrocyte/container/${PACKAGE}:${VERSION}"
 
 # name of the local image
@@ -51,6 +51,7 @@ fi
 DISABLE_AUTH=true
 PASSWORD=BioHPC
 DEFAULT_USER=root
+VIZAPP_PORT=8123
 
 # install vizapp libs to customize folder
 for lib in $VIZAPP_LIBS; do
@@ -58,22 +59,24 @@ for lib in $VIZAPP_LIBS; do
     SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
     SINGULARITYENV_PASSWORD=$PASSWORD \
     SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+    SINGULARITYENV_VIZAPP_PORT=$VIZAPP_PORT \
     singularity exec -f -C -w -e \
     -H $tmpDir/home:/root \
     -B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image} \
     R -e "if (!require('$lib', character.only=TRUE)) {install.packages('$lib', dependencies=TRUE, lib='$R_LIBS_USER')}"
 done
 
-echo -e "\nPlease visit http://localhost:8787 to connect to the RStudio server ...\n"
+echo -e "\nPlease visit http://localhost:${VIZAPP_PORT} to connect to the RStudio server ...\n"
 
 # run vizapp on localhost
 SINGULARITYENV_R_LIBS_USER=${R_LIBS_USER} \
 SINGULARITYENV_DISABLE_AUTH=$DISABLE_AUTH \
 SINGULARITYENV_PASSWORD=$PASSWORD \
 SINGULARITYENV_DEFAULT_USER=$DEFAULT_USER \
+SINGULARITYENV_VIZAPP_PORT=$VIZAPP_PORT \
 singularity run -f -C -w -e \
--H $tmpDir/home:/root \
--B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image}
+    -H $tmpDir/home:/root \
+    -B $outputDir:/mnt,$VIZAPP_HOME:/vizapp,$tmpDir/tmp:/tmp ${singularity_image} 
 
 
 ## Enable this section if run as non-root user inside the container