diff --git a/01_deploy_via_Docker.sh b/01_deploy_via_Docker.sh
index 2146cc0..ae823e1 100644
--- a/01_deploy_via_Docker.sh
+++ b/01_deploy_via_Docker.sh
@@ -3,7 +3,24 @@
 source scripts/colored_print.sh
 source scripts/check_and_set_email_credentials.sh
 source scripts/check_CPU_number.sh
+
+# Function to extract port number from configuration file
+extract_port() {
+    local file=$1
+    grep -Eo "listen\s+[0-9]+" "$file" | grep -Eo "[0-9]+"
+}
+
+# Function to format and display elapsed time
+show_time() {
+    local elapsed_time=$1
+    local hours=$((elapsed_time / 3600))
+    local minutes=$(( (elapsed_time % 3600) / 60))
+    local seconds=$((elapsed_time % 60))
+    printf "\rElapsed time: %02d:%02d:%02d" $hours $minutes $seconds
+}
+
 set -e
+chmod -R 766 data result
 
 #################### 1 email
 print_green "1. Configurations of email to send results"
@@ -13,7 +30,56 @@ check_and_set_email_credentials
 print_green "2. Configuration of CPU number"
 check_cpu_number
 
-#################### 3. Docker build
-print_green "3. Docker building"
-chmod  777 logs result
-docker-compose up -d
+
+#################### 3. Update shiny and nginx configuration files
+print_green "3. Update shiny and nginx configuration files"
+
+SHINY_CONF="conf/shiny-server.conf"
+NGINX_CONF="conf/nginx.conf"
+
+rm -rf $SHINY_CONF
+rm -rf $NGINX_CONF
+
+print_green "Generating shiny-server.conf..."
+bash scripts/create_shiny_server_conf.sh start
+print_green "\nGenerating nginx.conf..."
+bash scripts/create_nginx_conf.sh start
+
+# remove line with run_as
+sed -i '/^run_as/d' $SHINY_CONF
+
+# Extract port numbers
+NGINX_PORT=$(extract_port "$NGINX_CONF")
+SHINY_PORT=$(extract_port "$SHINY_CONF")
+
+# update nginx link
+echo "http://localhost:$NGINX_PORT/result/" > data/nginx_link.txt
+
+#################### 4. Update dockerfiles and docker-compose.yml
+print_green "4. Update dockerfiles and docker-compose.yml"
+
+# update dockerfiles
+sed -i "s|EXPOSE [0-9]*|EXPOSE $NGINX_PORT|" dockerfiles/Dockerfile.nginx
+sed -i "s|EXPOSE [0-9]*|EXPOSE $SHINY_PORT|" dockerfiles/Dockerfile.shiny
+
+# update docker-compose.yml
+bash scripts/create_docker_compose.sh $SHINY_PORT $NGINX_PORT
+
+#################### 5. Docker build
+print_green "5. Docker building"
+
+start_time=$(date +%s)
+
+docker-compose up -d > logs/docker_img_build.log 2>&1 &
+
+build_pid=$!
+# While the build process is running, display the elapsed time
+while kill -0 $build_pid 2> /dev/null; do
+    current_time=$(date +%s)
+    elapsed_time=$((current_time - start_time))
+    show_time $elapsed_time
+    sleep 1
+done
+
+print_green "\n\nYou are safe to colse this console."
+wait
diff --git a/R/app.R b/R/app.R
index 72228bd..1079533 100644
--- a/R/app.R
+++ b/R/app.R
@@ -1,5 +1,5 @@
-Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
-.libPaths(new = "/usr/local/lib/R/library")
+# Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
+# .libPaths(new = "/usr/local/lib/R/library")
 
 source("R/global.R")
 
diff --git a/R/global.R b/R/global.R
index c071a88..a625a2e 100644
--- a/R/global.R
+++ b/R/global.R
@@ -1,5 +1,5 @@
-Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
-.libPaths(new = "/usr/local/lib/R/library")
+# Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
+# .libPaths(new = "/usr/local/lib/R/library")
 
 options(shiny.maxRequestSize = 30000 * 1024^2)
 
diff --git a/R/utils/send_mail.R b/R/utils/send_mail.R
index f93ab0e..9167edb 100644
--- a/R/utils/send_mail.R
+++ b/R/utils/send_mail.R
@@ -39,6 +39,9 @@
 
 # SendResultMail(recipient = recipient, result_link = result_link)
 
+library(dplyr)
+library(emayili)
+
 SendResultMail <- function(recipient = NULL, result_link = NULL) {
 
   email_credential <- readLines("data/email_credential.txt")
diff --git a/app.R b/app.R
index 6ebdb0a..737e456 100644
--- a/app.R
+++ b/app.R
@@ -1,5 +1,5 @@
-Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
-.libPaths(new = "/usr/local/lib/R/library")
+# Sys.setenv(R_LIBS_USER = "/usr/local/lib/R/library")
+# .libPaths(new = "/usr/local/lib/R/library")
 
 source("R/app.R")
 
diff --git a/01_deploy_via_bash.sh b/archive/01_deploy_via_bash.sh
similarity index 100%
rename from 01_deploy_via_bash.sh
rename to archive/01_deploy_via_bash.sh
diff --git a/archive/test_nginx.sh b/archive/test_nginx.sh
new file mode 100644
index 0000000..e54c218
--- /dev/null
+++ b/archive/test_nginx.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+source scripts/colored_print.sh
+
+rm -rf conf/nginx_singularity.conf
+
+print_green "生成nginx_singularity.conf..."
+bash scripts/create_nginx_conf_singularity.sh start
+
+# 定义文件和镜像名称
+DEF_FILE="Singularities/Singularity_nginx.def"
+SIMG_FILE="Singularities/nginx.simg"
+
+rm -f "$SIMG_FILE"
+print_orange "已删除 $SIMG_FILE 文件，并重现构建镜像。"
+singularity build --fakeroot $SIMG_FILE $DEF_FILE
+
+#################################### 运行镜像 ####################################
+singularity run                           \
+    --bind ./result:/etc/nginx/html \
+    $SIMG_FILE
\ No newline at end of file
diff --git a/conf/nginx.conf b/conf/nginx.conf
index dbf6cfa..eedf255 100644
--- a/conf/nginx.conf
+++ b/conf/nginx.conf
@@ -1,12 +1,12 @@
 server {
-    listen       84;
-    listen  [::]:84;
+    listen       19258;
+    listen  [::]:19258;
     server_name  localhost_pmet;
 
-    # access_log  /var/log/nginx/localhost.access.log;
+    # access_log  /var/log/nginx/localhost_pmet.access.log;
 
     location /result {
         # autoindex on;
-        alias /usr/share/nginx/pmet;
+        alias /etc/nginx/html;
     }
 }
diff --git a/conf/shiny-server.conf b/conf/shiny-server.conf
index 68d48a1..ff21a45 100644
--- a/conf/shiny-server.conf
+++ b/conf/shiny-server.conf
@@ -1,13 +1,10 @@
-# Instruct Shiny Server to run applications as the user "shiny"
-run_as shiny;
-
-# Define a server that listens on port 3838
+run_as wang;
 server {
-  listen 3838;
+  listen 4615;
 
   # Define a location at the base URL
   location / {
-    app_idle_timeout 0;
+
     # Host the directory of Shiny Apps stored in this directory
     site_dir /srv/shiny-server;
 
@@ -17,5 +14,8 @@ server {
     # When a user visits the base URL rather than a particular application,
     # an index of the applications available in this directory will be shown.
     directory_index on;
+
+    # keep shiny app alive
+    app_idle_timeout 0;
   }
 }
diff --git a/data/nginx_link.txt b/data/nginx_link.txt
index a1491b2..dc393eb 100644
--- a/data/nginx_link.txt
+++ b/data/nginx_link.txt
@@ -1 +1 @@
-https://bar.utoronto.ca/pmet_result/
+http://localhost:84/result/
\ No newline at end of file
diff --git a/docker-compose.yml b/docker-compose.yml
index b8ab219..2281a70 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -5,11 +5,15 @@ services:
     build:
       context: .
       dockerfile: dockerfiles/Dockerfile.shiny
+    container_name: shiny
+    user: "1000:1000"
     volumes:
-      - ./result:/home/shiny/PMET_docker/result
-      - ./logs:/var/log/shiny-server
+      # - ./data/indexing:/home/shiny/PMET_docker/data/indexing
+      # - ./result:/home/shiny/PMET_docker/result
+      # - ./logs:/var/log/shiny-server
+      - ./result:/srv/shiny-server/pmet/result
     ports:
-      - "3838:3838"
+      - "4615:4615"
     networks:
       - app-network
 
@@ -17,16 +21,15 @@ services:
     build:
       context: .
       dockerfile: dockerfiles/Dockerfile.nginx
-    container_name: test_nginx
+    container_name: nginx
     volumes:
-      - ./result:/usr/share/nginx/pmet
+      - ./result:/etc/nginx/html
     ports:
-      - "84:84"
+      - "19258:19258"
     restart: always
     networks:
       - app-network
 
-
 volumes:
   logs:
   result:
diff --git a/dockerfiles/Dockerfile.nginx b/dockerfiles/Dockerfile.nginx
index 0af436e..38d57bc 100644
--- a/dockerfiles/Dockerfile.nginx
+++ b/dockerfiles/Dockerfile.nginx
@@ -2,13 +2,13 @@
 FROM nginx:latest
 
 # 创建结果目录
-RUN mkdir -p /usr/share/nginx/pmet && \
-    chmod -R 777 /usr/share/nginx/pmet
+RUN mkdir -p /etc/nginx/html && \
+    chmod -R 777 /etc/nginx/html
 
 COPY ./conf/nginx.conf /etc/nginx/conf.d/pmet.conf
 
 # Expose Nginx's default port
-EXPOSE 84
+EXPOSE 19258
 
 # Start Nginx service
 CMD ["nginx", "-g", "daemon off;"]
diff --git a/dockerfiles/Dockerfile.shiny b/dockerfiles/Dockerfile.shiny
index c973767..3f5e9ae 100644
--- a/dockerfiles/Dockerfile.shiny
+++ b/dockerfiles/Dockerfile.shiny
@@ -1,11 +1,17 @@
 FROM rocker/shiny:4.3.3
 
 ############################## 1. shiny setting ###############################
+# 添加 shiny 用户到 sudo 组
+RUN usermod -aG sudo shiny
+
 COPY ./conf/shiny-server.conf /etc/shiny-server/shiny-server.conf
 
 ENV work_dir="/home/shiny/PMET_docker"
+WORKDIR $work_dir
 COPY . $work_dir
 
+RUN chown -R shiny:shiny $work_dir  && \
+    chmod -R 777         $work_dir
 RUN ln -sf $work_dir /srv/shiny-server/pmet
 
 # Use the find command to find all .sh, .r, .py, .pl files and grant them 755 permissions
@@ -17,28 +23,31 @@ RUN $work_dir/scripts/install_apt_tools.sh
 
 
 # ############################## 3. R libs settings ###############################
-ENV R_LIBS_USER=/usr/local/lib/R/library
-# Set the directory owner and permissions
-RUN mkdir -p     $R_LIBS_USER      && \
-    chmod -R 777 $R_LIBS_USER
-# Set environment variables in respective user profiles
-RUN echo "export R_LIBS_USER='$R_LIBS_USER'" >> /root/.bashrc         && \
-    echo "export R_LIBS_USER='$R_LIBS_USER'" >> /home/shiny/.bashrc   && \
-    echo "R_LIBS_USER='$R_LIBS_USER'"        >> /root/.Renviron       && \
-    echo "R_LIBS_USER='$R_LIBS_USER'"        >> /home/shiny/.Renviron
+# ENV R_LIBS_USER=/usr/local/lib/R/library
+
+# RUN chown -R shiny:shiny $R_LIBS_USER && \
+#     chmod -R 755 $R_LIBS_USER
+# # # Set the directory owner and permissions
+# # RUN mkdir -p     $R_LIBS_USER      && \
+# #     chmod -R 777 $R_LIBS_USER
+# # # Set environment variables in respective user profiles
+# # RUN echo "export R_LIBS_USER='$R_LIBS_USER'" >> /root/.bashrc         && \
+# #     echo "export R_LIBS_USER='$R_LIBS_USER'" >> /home/shiny/.bashrc   && \
+# #     echo "R_LIBS_USER='$R_LIBS_USER'"        >> /root/.Renviron       && \
+# #     echo "R_LIBS_USER='$R_LIBS_USER'"        >> /home/shiny/.Renviron
 
 
 ############################## 4. install R libs ###############################
-# # Configure Java using R CMD javareconf
+# Configure Java using R CMD javareconf
 RUN sudo R CMD javareconf
 
 # # renv for package management
 # RUN Rscript -e "install.packages(c('remotes', 'littler', 'docopt', 'renv', 'jsonlite'))"
-# RUN Rscript -e "renv::restore()"
+# RUN Rscript -e "Sys.setenv(R_INSTALL_STAGED = FALSE);renv::restore();renv::install('jsonlite')"
 RUN Rscript  $work_dir/R/utils/install_packages.R
 
-RUN rsync -av --ignore-existing /usr/local/lib/R/library/ /usr/local/lib/R/site-library/ && \
-    rsync -av --ignore-existing /usr/local/lib/R/site-library/ /usr/local/lib/R/library/
+# RUN rsync -av --ignore-existing /usr/local/lib/R/library/ /usr/local/lib/R/site-library/ && \
+#     rsync -av --ignore-existing /usr/local/lib/R/site-library/ /usr/local/lib/R/library/
 
 
 ############################## 5. install python libs ###############################
@@ -51,18 +60,18 @@ RUN $work_dir/scripts/install_python_libs.sh
 RUN apt -y install bedtools
 
 # Samtools 1.3.1 #
-ENV SAMTOOLS_INSTALL_DIR=/opt/samtools
-ENV HTSLIB_INSTALL_DIR=/opt/htslib
-
 WORKDIR /tmp
 RUN wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2 && \
     tar -xjf samtools-1.17.tar.bz2 && \
     cd samtools-1.17 && \
-    ./configure --disable-lzma --prefix=$SAMTOOLS_INSTALL_DIR && \
+    ./configure --disable-lzma --prefix=/opt/samtools && \
     make && \
     make install && \
     cd / && \
     rm -rf /tmp/samtools-1.17 /tmp/samtools-1.17.tar.bz2
+
+RUN echo "export PATH=/opt/samtools/bin:$PATH" >> /root/.bashrc        && \
+    echo "export PATH=/opt/samtools/bin:$PATH" >> /home/shiny/.bashrc
 # Set the working directory back to the root directory
 WORKDIR $work_dir
 
@@ -104,6 +113,11 @@ RUN cd $work_dir/PMETdev/src/pmet \
 ############################# 8. download homotypic data ##############################
 RUN $work_dir/scripts/download_pmet_indexing.sh
 
+# RUN chmod -R 777  $work_dir/data $work_dir/result
+
+
+# Clean apt cache to reduce image size
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*
 
-EXPOSE 3838
+EXPOSE 4615
 CMD ["/usr/bin/shiny-server"]
diff --git a/logs/.gitkeep b/logs/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/scripts/create_docker_compose.sh b/scripts/create_docker_compose.sh
new file mode 100644
index 0000000..04fc56f
--- /dev/null
+++ b/scripts/create_docker_compose.sh
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+# 检查是否提供了两个参数
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <SHINY_CONF> <NGINX_CONF>"
+    exit 1
+fi
+
+SHINY_CONF=$1
+NGINX_CONF=$2
+
+# 生成 docker-compose.yml 文件
+cat <<EOF > docker-compose.yml
+x-yml-version: '3.8'
+
+services:
+  shiny-app:
+    build:
+      context: .
+      dockerfile: dockerfiles/Dockerfile.shiny
+    container_name: shiny
+    user: "$(id -u):$(id -g)"
+    volumes:
+      # - ./data/indexing:/home/shiny/PMET_docker/data/indexing
+      # - ./result:/home/shiny/PMET_docker/result
+      # - ./logs:/var/log/shiny-server
+      - ./result:/srv/shiny-server/pmet/result
+    ports:
+      - "$SHINY_CONF:$SHINY_CONF"
+    networks:
+      - app-network
+
+  nginx-server:
+    build:
+      context: .
+      dockerfile: dockerfiles/Dockerfile.nginx
+    container_name: nginx
+    volumes:
+      - ./result:/etc/nginx/html
+    ports:
+      - "$NGINX_CONF:$NGINX_CONF"
+    restart: always
+    networks:
+      - app-network
+
+volumes:
+  logs:
+  result:
+
+networks:
+  app-network:
+EOF
diff --git a/scripts/create_nginx_conf.sh b/scripts/create_nginx_conf.sh
new file mode 100644
index 0000000..ba7d800
--- /dev/null
+++ b/scripts/create_nginx_conf.sh
@@ -0,0 +1,96 @@
+#!/bin/bash
+
+usage() {
+    echo "Usage:
+          --------------------------------------------------------------------------
+          1. Use this script to generate your nginx.conf configuration
+
+             /bin/bash create_nginx_conf.sh
+
+          --------------------------------------------------------------------------
+          2. If needed, you can provide the following arguments
+
+          Commands:
+            help: show help and exit
+
+          Options:
+           --port: the port for the application (default is 84)
+           --base: base folder with applications (default is /etc/nginx/html)
+           --server-name: server name for Nginx configuration (default is localhost_pmet)
+
+          --------------------------------------------------------------------------
+          3. The generated nginx.conf will be saved to the current directory.
+         "
+}
+
+# Default values
+NGINX_PORT=84
+NGINX_BASE=/etc/nginx/html
+NGINX_SERVER_NAME=localhost_pmet
+
+while true; do
+    NGINX_PORT=$(( ( RANDOM % 60000 )  + 1025 ))  # 选择一个 1025 到 65535 之间的随机端口
+    (echo > /dev/tcp/localhost/$NGINX_PORT) >/dev/null 2>&1
+    result=$?
+    if [ $result -ne 0 ]; then  # 如果返回非0值，表示端口未被占用
+        echo "Selected free port: $NGINX_PORT"
+        break
+    fi
+done
+
+if [ $# -eq 0 ]; then
+    usage
+    exit
+fi
+
+while true; do
+    case ${1:-} in
+        -h|--help|help)
+            usage
+            exit
+        ;;
+        -p|--port|port)
+            shift
+            NGINX_PORT="${1:-}"
+            shift
+        ;;
+        -b|--base|base)
+            shift
+            NGINX_BASE="${1:-}"
+            shift
+        ;;
+        -sn|--server-name|server-name)
+            shift
+            NGINX_SERVER_NAME="${1:-}"
+            shift
+        ;;
+        -*)
+            echo "Unknown option: ${1:-}"
+            exit 1
+        ;;
+        *)
+            break
+        ;;
+    esac
+done
+
+# Generate nginx.conf
+cat <<EOF > conf/nginx.conf
+server {
+    listen       ${NGINX_PORT};
+    listen  [::]:${NGINX_PORT};
+    server_name  ${NGINX_SERVER_NAME};
+
+    # access_log  /var/log/nginx/${NGINX_SERVER_NAME}.access.log;
+
+    location /result {
+        # autoindex on;
+        alias ${NGINX_BASE};
+    }
+}
+EOF
+
+echo "conf/nginx.conf has been generated with the following settings:"
+echo "Port: ${NGINX_PORT}"
+echo "Base directory: ${NGINX_BASE}"
+echo "Server name: ${NGINX_SERVER_NAME}"
\ No newline at end of file
diff --git a/scripts/create_shiny_server_conf.sh b/scripts/create_shiny_server_conf.sh
new file mode 100644
index 0000000..a545f16
--- /dev/null
+++ b/scripts/create_shiny_server_conf.sh
@@ -0,0 +1,195 @@
+#!/bin/bash
+
+usage () {
+
+    echo "Steps:
+          ----------------------------------------------------------------------
+          1. Use this script to prepare your shiny-server.conf (configuration)
+
+               /bin/bash prepare_template.sh
+
+          ----------------------------------------------------------------------
+          2. If needed, you can provide the following arguments
+
+          Commands:
+             help: show help and exit
+             start: the generation of your config
+
+          Options:
+           --port:  the port for the application (e.g., shiny default is 3737)
+           --user:  the user for the run_as directive in the shiny configuration
+           --base: base folder with applications
+           --logs: temporary folder with write for logs (not required)
+           --disable-index: disable directory indexing
+
+          ----------------------------------------------------------------------
+          3. Make sure Singularity is loaded, and run the container using
+             the commands shown by the template.
+
+         "
+}
+
+# Start the application
+SHINY_START="no";
+
+# # Port for Flask
+# # Find an unused port number
+# CHECK_PORT="notnull"
+# while [[ ! -z $CHECK_PORT ]]; do
+#     SHINY_PORT=$(( ( RANDOM % 60000 )  + 1025 ))
+#     CHECK_PORT=$(netstat -atn | grep $SHINY_PORT)
+# done
+while true; do
+    SHINY_PORT=$(( ( RANDOM % 60000 )  + 1025 ))  # 选择一个 1025 到 65535 之间的随机端口
+    (echo > /dev/tcp/localhost/$SHINY_PORT) >/dev/null 2>&1
+    result=$?
+    if [ $result -ne 0 ]; then  # 如果返回非0值，表示端口未被占用
+        echo "Selected free port: $SHINY_PORT"
+        break
+    fi
+done
+
+
+# Base for apps
+SHINY_BASE=/srv/shiny-server;
+
+# Log folder assumed to be bound to
+# SHINY_LOGS=$(mktemp -d /tmp/shiny-server.XXXXXX) && rmdir ${SHINY_LOGS};
+SHINY_LOGS=/var/log/shiny-server
+
+# Disable indexing (on, default, is not disabled)
+DISABLE_DIRINDEX="on";
+
+# User to run_as, defaults to docker
+SHINY_USER="${USER}"
+
+if [ $# -eq 0 ]; then
+    usage
+    exit
+fi
+
+while true; do
+    case ${1:-} in
+        -h|--help|help)
+            usage
+            exit
+        ;;
+        -s|--start|start)
+            SHINY_START="yes"
+            shift
+        ;;
+        -p|--port|port)
+            shift
+            SHINY_PORT="${1:-}"
+            shift
+        ;;
+        -b|--base|base)
+            shift
+            SHINY_BASE="${1:-}"
+            shift
+        ;;
+        -u|--user)
+            shift
+            SHINY_USER="${1:-}"
+            shift
+        ;;
+        -di|--disable-index|disable-index)
+            DISABLE_DIRINDEX="off"
+            shift
+        ;;
+        -l|logs|--logs)
+            shift
+            SHINY_LOGS="${1:-}"
+            shift
+        ;;
+        -*)
+            echo "Unknown option: ${1:-}"
+            exit 1
+        ;;
+        *)
+            break
+        ;;
+    esac
+done
+
+# Functions
+
+function prepare_conf() {
+    SHINY_PORT=$1
+    SHINY_BASE=$2
+    SHINY_LOGS=$3
+    DISABLE_DIRINDEX=$4
+    SHINY_USER=$5
+    CONFIG="run_as ${SHINY_USER};
+server {
+  listen ${SHINY_PORT};
+
+  # Define a location at the base URL
+  location / {
+
+    # Host the directory of Shiny Apps stored in this directory
+    site_dir ${SHINY_BASE};
+
+    # Log all Shiny output to files in this directory
+    log_dir ${SHINY_LOGS};
+
+    # When a user visits the base URL rather than a particular application,
+    # an index of the applications available in this directory will be shown.
+    directory_index ${DISABLE_DIRINDEX};
+
+    # keep shiny app alive
+    app_idle_timeout 0;
+  }
+}"
+    echo "${CONFIG}";
+}
+
+
+# Are we starting the server?
+
+if [ "${SHINY_START}" == "yes" ]; then
+
+    echo "Generating shiny configuration...";
+    echo "port: ${SHINY_PORT}";
+    echo "logs:" ${SHINY_LOGS};
+    echo "base: ${SHINY_BASE}";
+    echo "run_as: ${SHINY_USER}";
+
+    # Prepare the template
+
+    CONFIG=$(prepare_conf $SHINY_PORT $SHINY_BASE $SHINY_LOGS $DISABLE_DIRINDEX $SHINY_USER);
+
+    # # Temporary directories, if don't exist
+    # mkdir -p "${SHINY_LOGS}";
+    # mkdir -p ${SHINY_LOGS}/logs;
+    # mkdir -p ${SHINY_LOGS}/lib;
+
+    # Configuration file
+    echo "${CONFIG}" > "conf/shiny-server.conf";
+    echo "Server logging will be in ${SHINY_LOGS}";
+#     echo
+#     echo  "To run your server:
+
+#     $ module load singularity
+#     $ singularity run                          \\
+#          --bind ./logs:/var/log/shiny          \\
+#          --bind ./lib:/var/lib/shiny-server    \\
+#          --bind ./conf/shiny-server.conf:/etc/shiny-server/shiny-server.conf \\
+#          shiny_server.simg
+
+#     ---------------------------------------------------------------------------
+#     For custom applications, also add --bind $SHINY_BASE:/srv/shiny-server
+#     To see your applications, open your browser to http://127.0.0.1:$SHINY_PORT or
+#     open a ssh connection from your computer to your cluster.
+# "
+    exit
+else
+    usage
+fi
+
+
+# $ module load singularity
+# $ singularity run --bind $SHINY_LOGS/logs:/var/log/shiny \\
+#      --bind $SHINY_LOGS/lib:/var/lib/shiny-server       \\
+#      --bind ./conf/shiny-server.conf:/etc/shiny-server/shiny-server.conf \\
+#      shiny_server.simg
diff --git a/scripts/install_apt_tools.sh b/scripts/install_apt_tools.sh
index 1dcfeb7..51dd3e5 100644
--- a/scripts/install_apt_tools.sh
+++ b/scripts/install_apt_tools.sh
@@ -57,7 +57,7 @@ apt -y install gfortran
 apt -y install rsync
 
 wget http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.0g-2ubuntu4_amd64.deb
-sudo dpkg -i libssl1.1_1.1.0g-2ubuntu4_amd64.deb
+dpkg -i libssl1.1_1.1.0g-2ubuntu4_amd64.deb
 rm libssl1.1_1.1.0g-2ubuntu4_amd64.deb
 
 export JAVA_HOME=$(dirname $(dirname $(readlink -f $(which java))))
diff --git a/scripts/pmet_binary_compile.sh b/scripts/pmet_binary_compile.sh
new file mode 100644
index 0000000..5711960
--- /dev/null
+++ b/scripts/pmet_binary_compile.sh
@@ -0,0 +1,118 @@
+#!/bin/bash
+
+print_red(){
+    RED='\033[0;31m'
+    NC='\033[0m' # No Color
+    printf "${RED}$1${NC}\n"
+}
+
+print_green(){
+    GREEN='\033[0;32m'
+    NC='\033[0m' # No Color
+    printf "${GREEN}$1${NC}\n"
+}
+
+print_orange(){
+    ORANGE='\033[0;33m'
+    NC='\033[0m' # No Color
+    printf "${ORANGE}$1${NC}\n"
+}
+
+print_fluorescent_yellow(){
+    FLUORESCENT_YELLOW='\033[1;33m'
+    NC='\033[0m' # No Color
+    printf "${FLUORESCENT_YELLOW}$1${NC}\n"
+}
+
+print_white(){
+    WHITE='\033[1;37m'
+    NC='\033[0m' # No Color
+    printf "${WHITE}$1${NC}"
+}
+
+rm -rf PMETdev/scripts/pmetindex
+rm -rf PMETdev/scripts/pmetParallel_linux
+rm -rf PMETdev/scripts/pmet
+rm -rf PMETdev/scripts/fimo
+
+############################# fimo with pmet index ##############################
+print_fluorescent_yellow "Compiling FIMO with PMET homotopic (index) binary..."
+cd PMETdev/src/meme-5.5.3
+
+make distclean
+
+currentDir=$(pwd)
+echo $currentDir/build
+
+if [ -d "$currentDir/build" ]; then
+    rm -rf "$currentDir/build"
+fi
+
+mkdir -p $currentDir/build
+
+chmod a+x ./configure
+./configure --prefix=$currentDir/build  --enable-build-libxml2 --enable-build-libxslt
+make
+make install
+cp build/bin/fimo ../../scripts/
+make distclean
+rm -rf build
+print_fluorescent_yellow "make distclean finished...\n"
+
+
+################################### pmetindex ####################################
+print_fluorescent_yellow "Compiling PMET homotopic (index) binary...\n"
+cd ../indexing
+chmod a+x build.sh
+bash build.sh
+mv bin/pmetindex ../../scripts/
+
+
+################################## pmetParallel ##################################
+print_fluorescent_yellow "Compiling PMET heterotypic (pair) binary...\n"
+cd ../pmetParallel
+chmod a+x build.sh
+bash build.sh
+mv bin/pmetParallel_linux ../../scripts/
+
+# pmet
+print_fluorescent_yellow "Compiling PMET heterotypic (pair) binary...\n"
+cd ../pmet
+chmod a+x build.sh
+bash build.sh
+mv bin/pmet ../../scripts/
+
+
+cd ../../
+pwd
+################### Check if the compilation was successful ########################
+exists=""
+not_exists=""
+
+for file in scripts/pmetindex scripts/pmetParallel_linux scripts/pmet scripts/fimo; do
+    if [ -f "$file" ]; then
+        exists="$exists $file"
+    else
+        not_exists="$not_exists $file"
+    fi
+done
+
+if [ ! -z "$exists" ]; then
+    print_green "Compilation Success:$exists"
+fi
+
+
+if [ ! -z "$not_exists" ]; then
+    print_red "Compilation Failure:$not_exists"
+fi
+
+
+############# Give execute permission to all users for the file. ##################
+chmod a+x scripts/pmetindex
+chmod a+x scripts/pmetParallel_linux
+chmod a+x scripts/pmet
+chmod a+x scripts/fimo
+
+# print_green "\n\npmet, pmetParallel_linux, pmetindex and NEW fimo are ready in 'scripts' folder.\n"
+
+print_green "DONE"