PASA Web Portal - Configuration on Gannet Using Synology Container Manager

gannet
MySQL
PASA
2026
Author

Sam White

Published

February 27, 2026

INTRO

METHODS

1. Build the image (if not already done)

cd /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/00.30-E-Peve-transcriptome-assembly-Trinity/PASA sudo docker build -t pasapipeline-fixed:latest -f Dockerfile.pasaweb .

2. Save the image to a tar file

sudo docker save pasapipeline-fixed:latest > /home/sam/pasapipeline-fixed.tar

3. Transfer to Synology (replace with your Synology details)

rsync -avP pasapipeline-fixed.tar gannet:/volume2/docker/PASA_web_portal/

On Synology, load the image into Docker:

Load the pre-built image

cd /volume2/docker/PASA_web_portal sudo docker load -i pasapipeline-fixed.tar

  1. In Container Manager, create a new container with these settings:

In Container Manager:

Go to the “Image” tab You should see pasapipeline-fixed:latest in the list of images Click on the image, then click “Launch” or “Run” This opens the container creation wizard where you configure: Container name Port mappings Volume mounts Environment variables Execution Command: bash -c "cp /pasa_data/conf.txt /usr/local/src/PASApipeline/pasa_conf/conf.txt && /usr/local/src/PASApipeline/run_PasaWeb.pl 9000" Port Settings:

Local Port: 9000 Container Port: 9000 Type: TCP Volume Mappings:

Host: /volume1/path/to/PASA/directory Container: /pasa_data Network:

Use bridge mode

Working Directory:

  1. Grant MySQL permissions (if not already done):
mysql -u root -p<password>
GRANT SELECT ON peve_pasa.* TO 'pasa_access'@'localhost';
GRANT SELECT ON apul_pasa.* TO 'pasa_access'@'localhost';
GRANT SELECT ON ptua_pasa.* TO 'pasa_access'@'localhost';
FLUSH PRIVILEGES;
  1. Create/import databases (if not already done):
mysql -u root -p -h127.0.0.1 -P3307 <<'EOF'
CREATE DATABASE IF NOT EXISTS peve_pasa;
EOF

Fix collation issue in the SQL dump file (if needed):

sed -i 's/utf8mb4_0900_ai_ci/utf8mb4_general_ci/g' '/volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/00.30-E-Peve-transcriptome-assembly-Trinity/PASA/peve_pasa_backup.sql'

Load the SQL dump into the database:

mysql -u root -p<password> -h127.0.0.1 -P3307 peve_pasa \
  < /volume2/web/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/00.30-E-Peve-transcriptome-assembly-Trinity/PASA/peve_pasa_backup.sql
  1. Access:
Important

http is used instead of https because the PASA web portal does not support SSL/TLS. Ensure that your network is secure and consider using a VPN if accessing remotely.

http://gannet.fish.washington.edu:9000 Enter database name when prompted (e.g., peve_pasa)