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Documentations

Last Updated: March 8, 2025 by Derrick Cheng

To set up CompbioAgent on your own server, some familiarity with Linux is necessary. If you're new to Linux, we're happy to host the dataset for you. Please contact us for details.

Requirements

Category	Details
Operating System:	RHEL 7 or RHEL 9 (CompbioAgent has not been tested on other operating systems)
Hardware Requirement:	At least 10GB free space available for web applications and database. Additional space may be needed for your dataset files.
Webserver Requirement:	Apache 2.4.X, PHP 7.4 or 8.4 (CompbioAgent has not been tested with other PHP versions)
Databases:	MySQL/MariaDB
Other Applications:	Cellxgene VIP, R, Python

Apache, MariaDB/MySQL, PHP

Please follow this link to set up the application server.

Apache

Prepare a system user for Apache. This user is created by default when installing Apache (usually apache). We assume web application files will be placed in the following directories:

#Web Directory:
/var/www/html/

#Work, log directory
/var/www/html/compbioagent_share/


#Web Application
/var/www/html/compbioagent/

#Ensure the folders have the correct permissions:
chown -R apache:apache /var/www/html/compbioagent_share/
chown -R apache:apache /var/www/html/compbioagent/

chmod -R ug+rw /var/www/html/compbioagent_share/
chmod -R ug+rw /var/www/html/compbioagent/

Web Application

#Download the CompbioAgent from GitHub. We need the webapp/ folder.
cd /tmp
git clone https://github.com/interactivereport/CompBioAgent.git
rsync -avr /tmp/CompBioAgent/webapp/ /var/www/html/compbioagent/
rm -Rf /tmp/CompBioAgent/
#After copying the files, the directory structure should look something like this:
/var/www/html/compbioagent/app/
/var/www/html/compbioagent/bxaf_lite/
/var/www/html/compbioagent/bxaf_setup/

Other Requirements

• Ensure SELinux has been disabled (Link).

MySQL/MariaDB

Create a user within the MySQL system.

#Create a user within the MySQL system:
mysql -u root -p
CREATE USER mysql_user@localhost IDENTIFIED BY 'mysql_password';
exit
#Create a MySQL Database
mysql -u mysql_user -pmysql_password -e "create database db_compbioagent"
wget https://docs.bxgenomics.com/compbioagent/db_compbioagent.sql.gz
zcat db_compbioagent.sql.gz | mysql -u mysql_user -pmysql_password db_compbioagent
#Allow the MySQL user to use the database:
GRANT ALL ON . TO 'db_compbioagent'@'localhost';

Linux Packages

#Install curl
sudo yum install -y curl;

Cellxgene VIP

Install Cellxgene VIP on your server. CompBioAid will need access to the following:

• plotH5ad.sh
• slimH5ad.sh

Ensure these tools are working properly on your server.

h5ad Files

Ensure your h5ad files are accessible by CompbioAgent via the file system or network drive.

LLM Resources

Access one of the following Large Language Model (LLM) resources:

1. OpenAI / ChatGPT API Key: For access to GPT models.
2. Ollama Server: For accessing open-source LLMs like Meta Llama, DeepSeek-R1, etc., on your server.
3. Groq API Key: For accessing open-source LLMs using Groq's resources.

Config Files

Adjust the configuration files in /var/www/html/compbioagent/bxaf_setup/default/. Refer to comments in the files for instructions:

• 1-Environment.php: MySQL/MariaDB settings (username and password).
• 2-App_Language.php: Language file. Update if you prefer a different language.
• 3-Large_Language_Model.php: LLM settings (model names, API key, provider, etc.).
• 4-Disease_Database.php: Disease information and corresponding h5ad file.
• 5-Prompt.php: Prompt instruction function. Fine-tune if introducing new models or diseases.