Move to Ubuntu

basic-worker/Dockerfile

@@ -1,10 +1,21 @@
-FROM continuumio/miniconda3:4.10.3
+FROM ubuntu:24.04
 MAINTAINER Mingxun Wang "[email protected]"
 
-RUN apt-get update && apt-get install -y build-essential
+RUN apt-get update && apt-get install -y build-essential libarchive-dev wget vim curl
+
+# Install Mamba
+ENV CONDA_DIR /opt/conda
+RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O ~/miniforge.sh && /bin/bash ~/miniforge.sh -b -p /opt/conda
+ENV PATH=$CONDA_DIR/bin:$PATH
+
+# Adding to bashrc
+RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc
+
+# Forcing version of Python
+RUN mamba create -n python312 python=3.12 -y
 
 COPY requirements.txt .
-RUN pip install -r requirements.txt
+RUN /bin/bash -c 'source activate python312 && pip install -r requirements.txt'
 
 COPY . /app
-WORKDIR /app
+WORKDIR /app

basic-worker/docker-compose.yml

@@ -13,12 +13,17 @@ services:
       - default
       - nginx-net
     restart: unless-stopped
-    command: /app/run_server.sh
+    command: /bin/bash -c "source activate python312 && /app/run_server.sh"
     environment:
-      VIRTUAL_HOST: template.ucsd.edu
+      VIRTUAL_HOST: template.gnps2.org
       VIRTUAL_PORT: 5000
-      LETSENCRYPT_HOST: template.ucsd.edu
-      LETSENCRYPT_EMAIL: [email protected]
+      LETSENCRYPT_HOST: template.gnps2.org
+      LETSENCRYPT_EMAIL: [email protected]
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
   template-worker:
     build:
@@ -27,26 +32,42 @@ services:
     container_name: template-worker
     volumes:
       - ./logs:/app/logs:rw
-    command: /app/run_worker.sh
+    command: /bin/bash -c "source activate python312 && /app/run_worker.sh"
     restart: unless-stopped
     depends_on: 
       - template-redis
       - template-rabbitmq
     networks:
       - default
       - nginx-net
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
   template-rabbitmq:
     container_name: template-rabbitmq
     image: rabbitmq
     networks:
       - default
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
+
 
   template-redis:
     container_name: template-redis
     image: redis
     networks:
       - default
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
 
 networks:

basic-worker/requirements.txt

@@ -1,6 +1,7 @@
 Flask
 gunicorn
 plotly
+numpy>=2.0
 pandas
 requests
 tqdm
@@ -12,5 +13,5 @@ dash-core-components
 dash-html-components
 dash-renderer
 dash-table
-celery==5.0.5
+celery==5.5.3
 celery_once==3.0.1

basic/Dockerfile

@@ -1,7 +1,7 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 MAINTAINER Mingxun Wang "[email protected]"
 
-RUN apt-get update && apt-get install -y build-essential libarchive-dev wget vim
+RUN apt-get update && apt-get install -y build-essential libarchive-dev wget vim curl
 
 # Install Mamba
 ENV CONDA_DIR /opt/conda
@@ -12,10 +12,10 @@ ENV PATH=$CONDA_DIR/bin:$PATH
 RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc
 
 # Forcing version of Python
-RUN mamba create -n python310 python=3.10 -y
+RUN mamba create -n python312 python=3.12 -y
 
 COPY requirements.txt .
-RUN /bin/bash -c 'source activate python310 && pip install -r requirements.txt'
+RUN /bin/bash -c 'source activate python312 && pip install -r requirements.txt'
 
 COPY . /app
-WORKDIR /app
+WORKDIR /app

basic/docker-compose.yml

@@ -13,7 +13,7 @@ services:
       - default
       - nginx-net
     restart: unless-stopped
-    command: /app/run_server.sh
+    command: /bin/bash -c "source activate python312 && /app/run_server.sh"
     environment:
       VIRTUAL_HOST: template.gnps2.org
       VIRTUAL_PORT: 5000
@@ -23,6 +23,11 @@ services:
       resources:
         limits:
           memory: 32GB
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
 networks:
   nginx-net:

basic/requirements.txt

@@ -1,6 +1,7 @@
 Flask
 gunicorn
 plotly
+numpy>=2.0
 pandas
 requests
 tqdm

multiple-page/Dockerfile

@@ -1,10 +1,21 @@
-FROM continuumio/miniconda3:4.10.3
+FROM ubuntu:24.04
 MAINTAINER Mingxun Wang "[email protected]"
 
-RUN apt-get update && apt-get install -y build-essential
+RUN apt-get update && apt-get install -y build-essential libarchive-dev wget vim curl
+
+# Install Mamba
+ENV CONDA_DIR /opt/conda
+RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O ~/miniforge.sh && /bin/bash ~/miniforge.sh -b -p /opt/conda
+ENV PATH=$CONDA_DIR/bin:$PATH
+
+# Adding to bashrc
+RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc
+
+# Forcing version of Python
+RUN mamba create -n python312 python=3.12 -y
 
 COPY requirements.txt .
-RUN pip install -r requirements.txt
+RUN /bin/bash -c 'source activate python312 && pip install -r requirements.txt'
 
 COPY . /app
-WORKDIR /app
+WORKDIR /app

multiple-page/docker-compose.yml

@@ -13,17 +13,21 @@ services:
       - default
       - nginx-net
     restart: unless-stopped
-    command: /app/run_server.sh
+    command: /bin/bash -c "source activate python312 && /app/run_server.sh"
     environment:
-      VIRTUAL_HOST: template.ucsd.edu
+      VIRTUAL_HOST: template.gnps2.org
       VIRTUAL_PORT: 5000
-      LETSENCRYPT_HOST: template.ucsd.edu
-      LETSENCRYPT_EMAIL: miw023@ucsd.edu
+      LETSENCRYPT_HOST: template.gnps2.org
+      LETSENCRYPT_EMAIL: [email protected].edu
     deploy:
       resources:
         limits:
           memory: 8000M
-
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+        max-file: "3"
 
 networks:
   nginx-net:

multiple-page/requirements.txt

@@ -1,6 +1,7 @@
 Flask
 gunicorn
 plotly
+numpy>=2.0
 pandas
 requests
 tqdm