drsasp/jabaws repository overview

⁠JABAWS: Bioinformatics Web Services for Alignment and Analysis

JABAWS is a suite of bioinformatics web services for multiple sequence alignment, protein disorder prediction, and conservation analysis — packaged in a Docker image for easy deployment on your computer, server, or cluster.

The JABAWS Docker image is ideal if you need to:

• Run jobs that exceed public server limits
• Work with sensitive data under strict security policies
• Operate in offline or restricted environments

This resource was developed by the Dundee Resource for Sequence Analysis and Structure Prediction⁠. For more information or to use the public JABAWS server, visit the JABAWS web server⁠.

⁠Contents

• 🚀 Quick Start⁠
• Run a Persistent Instance⁠
• Access the Services⁠
• Use with Jalview 2.11⁠
• Services Provided⁠
• 🔍 Monitor Logs⁠
• 📁 Retrieve Job Outputs⁠
• Volume Management⁠
• 🔄 Moving to Slivka⁠
• Funding⁠

⁠🚀 Quick Start

Ensure Docker is installed on your system. If needed, refer to the Docker install docs⁠.

⁠Run a Disposable Instance

To quickly try JABAWS without saving any data or configuration, use the following command:

docker run --rm -p 8080:8080 drsasp/jabaws:latest

This will start the JABAWS web server and expose it at http://localhost:8080/jabaws. The container and any changes made within it will be discarded once it stops.

⁠Run a Persistent Instance

Choose one of the following:

⁠🔒 Option A: Docker-managed volumes (recommended)

docker run -d \
  -p 8080:8080 \
  -v jabaws-logs:/usr/local/tomcat/logs \
  -v jabaws-jobsout:/usr/local/tomcat/webapps/jabaws/jobsout \
  --name jabaws-server \
  drsasp/jabaws:latest

⁠💻 Option B: Bind mounts for local file access

mkdir -p ./logs ./jobsout
docker run -d \
  -p 8080:8080 \
  -v "$(pwd)/logs:/usr/local/tomcat/logs" \
  -v "$(pwd)/jobsout:/usr/local/tomcat/webapps/jabaws/jobsout" \
  --name jabaws-server \
  drsasp/jabaws:latest

To stop and restart the container:

docker stop jabaws-server
docker start jabaws-server

These methods are recommended for regular use or deployment on a server.

⁠Access the Services

Once started, JABAWS services will be available at:

URL: http://localhost:8080/jabaws/⁠

Open http://localhost:8080/jabaws/ServiceStatus in your web browser to see the service list and status. Services are accessible via Jalview⁠ or the JABAWS CLI⁠.

⁠Use with Jalview 2.11

To enable Jalview to use your local JABAWS instance:

• In Jalview, open Preferences → Web Services, and add your server’s JABAWS URL (e.g., http://localhost:8080/jabaws/)
• Run the tools via the Jalview Web Services menu.

⁠Services Provided

Multiple Sequence Alignment

• Clustal Omega
• Clustal W
• MAFFT
• MUSCLE
• T-Coffee
• ProbCons
• MSAProbs
• GLProbs

Disorder Prediction

• DisEMBL
• IUPred
• Jronn
• GlobPlot

Conservation Analysis

• AACon (v1.1)⁠

RNA Structure Prediction

• RNAalifold (from the Vienna RNA package)

⁠🔍 Monitor Logs

# Follow Tomcat stdout/stderr (catalina.out)
docker logs -f jabaws-server

Other log files can be tailed similarly:

# View the latest Tomcat access log
docker exec jabaws-server tail -f /usr/local/tomcat/logs/localhost_access_log.$(date +%F).txt

# Tail all .log and .txt files in the logs directory
docker exec -it jabaws-server bash -c 'tail -n 20 -f /usr/local/tomcat/logs/*.log /usr/local/tomcat/logs/*.txt'

⁠📁 Retrieve Job Outputs

# List job-output files inside the container
docker exec jabaws-server ls -la /usr/local/tomcat/webapps/jabaws/jobsout/

# Copy job-output directory to your host
docker cp jabaws-server:/usr/local/tomcat/webapps/jabaws/jobsout ./local-jobsout

⁠Volume Management

If you're using Docker-managed volumes (recommended Option A), here are some helpful commands:

# List volumes
docker volume ls

To back up volumes:

# Backup logs volume
docker run --rm -v jabaws-logs:/source -v $(pwd):/backup alpine \
  tar czf /backup/jabaws-logs-backup.tar.gz -C /source .

# Backup job outputs volume
docker run --rm -v jabaws-jobsout:/source -v $(pwd):/backup alpine \
  tar czf /backup/jabaws-jobsout-backup.tar.gz -C /source .

⁠🔄 Moving to Slivka

From Jalview 2.12 onward, JABAWS will be replaced by Slivka⁠ — a modern framework for providing bioinformatics tools as web services.

• If you're using JABAWS with Jalview 2.11 or earlier, the instructions above apply.
• If you're deploying new services or need programmatic access (e.g. Jupyter notebooks), we recommend using Slivka.

➡️ See the Slivka Docker setup⁠

⁠Funding

This work is part of the BBSRC⁠ funded Dundee Resource for Protein Structure Prediction and Sequence Analysis⁠ grant number 208391/Z/17/Z⁠.