first cut of elabftw

Techops/elabftw.knownelement.com/CloudronManifest.json

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+{
+  "id": "org.elabftw.cloudron",
+  "title": "eLabFTW",
+  "author": "Nicolas CARPi",
+  "description": "Electronic laboratory notebook to track experiments, manage protocols, store laboratory inventory, communicate with others and more. Your best lab companion.",
+  "tagline": "Electronic lab notebook for researchers",
+  "version": "1.0.0",
+  "healthCheckPath": "/",
+  "httpPort": 8000,
+  "addons": {
+    "mysql": {},
+    "localstorage": {}
+  },
+  "manifestVersion": 2,
+  "website": "https://www.elabftw.net",
+  "contactEmail": "support@example.com",
+  "icon": "file://logo.png",
+  "memoryLimit": 1024,
+  "tags": ["science", "lab", "research", "notebook", "eln"],
+  "minBoxVersion": "7.4.0",
+  "postInstallMessage": "eLabFTW has been successfully installed! You will need to create a Sysadmin account when you first access the application.",
+  "documentationUrl": "https://doc.elabftw.net/",
+  "forwardedHeaders": ["X-Forwarded-For", "X-Forwarded-Proto", "X-Forwarded-Host"],
+  "tcpPorts": {},
+  "optionalSso": {
+    "ldap": {
+      "enabled": true
+    }
+  }
+}

Techops/elabftw.knownelement.com/Dockerfile

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+FROM cloudron/base:4.2.0
+
+# Install required packages
+RUN apt-get update && \
+    apt-get install -y \
+    php-cli \
+    php-fpm \
+    php-mysql \
+    php-curl \
+    php-gd \
+    php-intl \
+    php-mbstring \
+    php-xml \
+    php-zip \
+    php-bcmath \
+    nginx \
+    supervisor \
+    curl \
+    zip \
+    unzip \
+    git \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Install Composer
+RUN curl -sS https://getcomposer.org/installer | php -- --install-dir=/usr/local/bin --filename=composer
+
+# Get the latest eLabFTW release
+WORKDIR /app/code
+RUN git clone https://github.com/elabftw/elabftw.git . && \
+    composer install --no-dev --optimize-autoloader
+
+# Configure NGINX
+COPY nginx.conf /etc/nginx/sites-available/default
+
+# Prepare directory structure
+RUN mkdir -p /app/data/uploads /app/data/config /app/data/logs /run/php && \
+    chown -R cloudron:cloudron /app/data /run/php
+
+# Copy initialization data
+RUN mkdir -p /tmp/data/config /tmp/data/uploads /tmp/data/logs && \
+    cp -r /app/code/config-example.yml /tmp/data/config/config.yml && \
+    chown -R cloudron:cloudron /tmp/data
+
+# Copy start script and supervisor config
+COPY start.sh /app/code/
+COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
+RUN chmod +x /app/code/start.sh
+
+# Configure PHP-FPM
+RUN sed -i 's/www-data/cloudron/g' /etc/php/*/fpm/pool.d/www.conf && \
+    sed -i 's/listen = \/run\/php\/php[0-9]\.[0-9]-fpm.sock/listen = \/run\/php\/php-fpm.sock/g' /etc/php/*/fpm/pool.d/www.conf && \
+    echo 'catch_workers_output = yes' >> /etc/php/*/fpm/pool.d/www.conf
+
+# Create logo image
+RUN curl -o /app/code/logo.png https://raw.githubusercontent.com/elabftw/elabftw/master/src/ts/img/logo.png
+
+WORKDIR /app/code
+
+CMD ["/app/code/start.sh"]

Techops/elabftw.knownelement.com/docker-compose.yml

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-#elabftw docker compose for tsys

Techops/elabftw.knownelement.com/elabftw-BuildNotes.md

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+# eLabFTW Cloudron Package Build Notes
+
+This document provides instructions for building, testing, and deploying the eLabFTW Cloudron package.
+
+## Package Overview
+
+This package deploys eLabFTW, an open-source electronic laboratory notebook (ELN) for researchers, on Cloudron. The package:
+
+- Uses the MySQL addon for database storage
+- Uses the localstorage addon for file storage
+- Includes NGINX and PHP-FPM configuration
+- Supports optional LDAP authentication through Cloudron
+
+## Building the Package
+
+1. Create a new directory for your package:
+   ```bash
+   mkdir elabftw-cloudron
+   cd elabftw-cloudron
+   ```
+
+2. Save all the provided files to this directory:
+   - CloudronManifest.json
+   - Dockerfile
+   - start.sh
+   - nginx.conf
+   - supervisord.conf
+
+3. Make the start.sh file executable:
+   ```bash
+   chmod +x start.sh
+   ```
+
+4. Download the eLabFTW logo for the package icon:
+   ```bash
+   curl -o logo.png https://raw.githubusercontent.com/elabftw/elabftw/master/src/ts/img/logo.png
+   ```
+
+5. Build the package:
+   ```bash
+   cloudron build
+   ```
+
+## Testing the Package
+
+1. Install the package on your Cloudron for testing:
+   ```bash
+   cloudron install —location elabftw.example.com
+   ```
+
+2. After installation, visit the application URL and complete the initial setup:
+   - Create the Sysadmin account
+   - Configure your teams and user groups
+   - Set up any initial templates or protocols
+
+3. Test the following functionality:
+   - User authentication (local accounts)
+   - File uploads (should be stored in /app/data/uploads)
+   - Database connection (should be using Cloudron MySQL)
+   - LDAP authentication (if enabled)
+   - General application functionality
+
+## Deploying to Production
+
+1. Once testing is complete, you can deploy to production:
+   ```bash
+   cloudron install —location elabftw.yourdomain.com
+   ```
+
+2. For production use, consider:
+   - Setting up regular backups of the Cloudron app
+   - Configuring LDAP authentication if needed (via Cloudron UI)
+   - Adjusting memory limits in CloudronManifest.json if necessary based on usage
+
+## Post-Installation
+
+After installation, you’ll need to:
+
+1. Create a Sysadmin account when first accessing the application
+2. Configure teams and user groups
+3. Set up experiment templates and protocols as needed
+4. Consider enabling and configuring LDAP authentication for easier user management
+
+## Troubleshooting
+
+- Check logs with `cloudron logs -f elabftw`
+- If database issues occur, verify the MySQL addon is properly configured
+- For file storage issues, check permissions on /app/data directories
+- For authentication issues, verify LDAP configuration (if using LDAP)
+
+## Updates
+
+When a new version of eLabFTW is released:
+
+1. Update the git clone command in the Dockerfile to point to the latest release (or specific tag)
+2. Rebuild and update your package:
+   ```bash
+   cloudron build
+   cloudron update —app elabftw.yourdomain.com
+   ```
+
+## Customization
+
+You can customize the package by:
+
+1. Modifying the config.yml template in /tmp/data/config to set default values
+2. Adjusting PHP settings in the Dockerfile or php.ini
+3. Modifying NGINX configuration for special requirements
+4. Adjusting memory limits in CloudronManifest.json based on usage patterns

Techops/elabftw.knownelement.com/input-files/info

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-This directory contains template files for the application at FQDN indidicated by the parent directory. They will be processed using mo (bash mustache).

Techops/elabftw.knownelement.com/nginx.conf

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+server {
+    listen 8000;
+    server_name _;
+    root /app/code/web;
+    index index.php;
+
+    client_max_body_size 100M;
+
+    access_log /dev/stdout;
+    error_log /dev/stderr;
+
+    location / {
+        try_files $uri /index.php$is_args$args;
+    }
+
+    location ~ ^/index\.php(/|$) {
+        fastcgi_pass unix:/run/php/php-fpm.sock;
+        fastcgi_split_path_info ^(.+\.php)(/.*)$;
+        include fastcgi_params;
+        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
+        fastcgi_param HTTPS on;
+        
+        # Forward Cloudron proxy headers
+        fastcgi_param HTTP_X_FORWARDED_FOR $http_x_forwarded_for;
+        fastcgi_param HTTP_X_FORWARDED_PROTO $http_x_forwarded_proto;
+        fastcgi_param HTTP_X_FORWARDED_HOST $http_x_forwarded_host;
+    }
+
+    # Deny access to other PHP files
+    location ~ \.php$ {
+        return 404;
+    }
+
+    # Rewrite app routes
+    location @rewriteapp {
+        rewrite ^(.*)$ /index.php/$1 last;
+    }
+}

Techops/elabftw.knownelement.com/output-files/info

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-This directory contains final docker compose files for the application at FQDN indidicated by the parent directory. 

Techops/elabftw.knownelement.com/start.sh

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+#!/bin/bash
+set -e
+
+# Create directory structure if it doesn't exist
+if [ ! -d /app/data/uploads ]; then
+    mkdir -p /app/data/uploads
+    cp -r /tmp/data/uploads/* /app/data/uploads/ 2>/dev/null || true
+    chown -R cloudron:cloudron /app/data/uploads
+fi
+
+if [ ! -d /app/data/logs ]; then
+    mkdir -p /app/data/logs
+    cp -r /tmp/data/logs/* /app/data/logs/ 2>/dev/null || true
+    chown -R cloudron:cloudron /app/data/logs
+fi
+
+if [ ! -f /app/data/config/config.yml ]; then
+    mkdir -p /app/data/config
+    cp -r /tmp/data/config/* /app/data/config/ 2>/dev/null || true
+    
+    # Configure database connection
+    sed -i "s/host: .*/host: ${CLOUDRON_MYSQL_HOST}/" /app/data/config/config.yml
+    sed -i "s/port: .*/port: ${CLOUDRON_MYSQL_PORT}/" /app/data/config/config.yml
+    sed -i "s/database: .*/database: ${CLOUDRON_MYSQL_DATABASE}/" /app/data/config/config.yml
+    sed -i "s/username: .*/username: ${CLOUDRON_MYSQL_USERNAME}/" /app/data/config/config.yml
+    sed -i "s/password: .*/password: ${CLOUDRON_MYSQL_PASSWORD}/" /app/data/config/config.yml
+    
+    # Configure paths
+    sed -i "s|uploads: .*|uploads: /app/data/uploads|" /app/data/config/config.yml
+    sed -i "s|logs: .*|logs: /app/data/logs|" /app/data/config/config.yml
+    
+    # Configure LDAP if enabled
+    if [ "${CLOUDRON_LDAP_ENABLED}" == "true" ]; then
+        # Update LDAP settings in config
+        sed -i "s/ldap_enabled: .*/ldap_enabled: true/" /app/data/config/config.yml
+        sed -i "s/ldap_host: .*/ldap_host: ${CLOUDRON_LDAP_SERVER}/" /app/data/config/config.yml
+        sed -i "s/ldap_port: .*/ldap_port: ${CLOUDRON_LDAP_PORT}/" /app/data/config/config.yml
+        sed -i "s/ldap_username: .*/ldap_username: ${CLOUDRON_LDAP_BIND_DN}/" /app/data/config/config.yml
+        sed -i "s/ldap_password: .*/ldap_password: ${CLOUDRON_LDAP_BIND_PASSWORD}/" /app/data/config/config.yml
+        sed -i "s/ldap_base_dn: .*/ldap_base_dn: ${CLOUDRON_LDAP_USERS_BASE_DN}/" /app/data/config/config.yml
+    fi
+    
+    chown -R cloudron:cloudron /app/data/config
+fi
+
+# Create a symlink to the config file
+ln -sf /app/data/config/config.yml /app/code/config.yml
+
+# Set proper permissions
+chown -R cloudron:cloudron /app/data
+
+# Start the supervisord
+exec /usr/bin/supervisord -c /etc/supervisor/conf.d/supervisord.conf

Techops/elabftw.knownelement.com/supervisord.conf

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+[supervisord]
+nodaemon=true
+logfile=/dev/stdout
+logfile_maxbytes=0
+
+[program:nginx]
+command=/usr/sbin/nginx -g "daemon off;"
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile=/dev/stderr
+stderr_logfile_maxbytes=0
+autostart=true
+autorestart=true
+priority=10
+
+[program:php-fpm]
+command=/usr/sbin/php-fpm8.1 -F
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile=/dev/stderr
+stderr_logfile_maxbytes=0
+autostart=true
+autorestart=true
+priority=5

Techops/elabftw.knownelement.com/vendor-files/info

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-This directory contains files from the vendor unmodified. They serve as a base for the input-files sibling directory