Upgrading SMRT Link to v25.3
This section provides detailed instructions for upgrading SMRT Link to version 25.3. Following these steps ensures a smooth transition and maintains the integrity of your data and configurations.
Supported upgrade paths
Upgrades to v25.3 from versions since 13.x are supported.
Pre-upgrade considerations
Before initiating the upgrade, ensure the following:
-
Backup: Create a complete backup of your current SMRT Link installation, including configuration files and databases.
A utility script to generate an appropriate cron server command was added at
$SMRT_ROOT/admin/bin/generate-cron-backup. This helper script makes it easy to take a pg_dump of the smrtlinkdb and keycloak databases. Ideally, these should both be backed up. -
Active Jobs: Verify that no active SMRT Link analysis jobs are running. It's crucial to complete or terminate all jobs before proceeding.
-
Disk Space: Ensure sufficient disk space is available for the upgrade process.
Upgrade steps
Follow these steps to upgrade SMRT Link to v25.3:
| Step | Action |
|---|---|
| 1 | Download and Unzip the Installer: curl -O https://downloads.pacbcloud.com/public/software/installers/smrtlink-release_25.3.0.273777.zip unzip smrtlink-release_25.3.0.273777.zip |
| 2 | Log onto Install Host: Access the server as $SMRT_USER. |
| 3 | Stop SMRT Link Services: Use the command: $SMRT_ROOT/admin/bin/services-stop Ensure that no active SMRT Link analysis jobs are running before stopping services. |
| 4 | Run the Installer with Upgrade Option: Navigate to the directory containing the downloaded installer. Execute the installer with the upgrade option: ./smrtlink_<version_number>.run --rootdir $SMRT_ROOT --upgrade The $SMRT_ROOT directory must be an existing SMRT Link installation. Several validation steps will occur to ensure that a valid $SMRT_ROOT is being updated. |
| 5 | Start SMRT Link Services: Use the command: $SMRT_ROOT/admin/bin/services-start |
| 6 | Run Site Acceptance Test (Optional): $SMRT_ROOT/admin/bin/run-sat-services. Successful completion indicates that the HPC configuration is functioning correctly. |
Post-upgrade steps
| Step | Action |
|---|---|
| 1 | Clear Browser Cache (Recommended): Open Google Chrome and navigate to More Tools > Clear browsing data. Select All Time for the time range and check Cached images and files. Click Clear data and restart the browser. |
| 2 | Configure LDAP and SSO (Optional): Set up LDAP and SSO integration and add users. See Advanced Topics. |
| 3 | Install SSL Certificate (Optional): Upon the first startup of SMRT Link, NGINX automagically generates a key and self signed certificate. To create a new certificate see Advanced Topics. |
| 4 | Change Default Passwords (Optional): Update admin and pbicsuser passwords. See Advanced Topics. |
SMRT Tools upgrade steps
SMRT Tools are the command-line tools included with SMRT Link. These are developer tools for use by bioinformaticians working with secondary analysis results.
| Step | Action |
|---|---|
| 1 | Upgrade SMRT Tools:./smrtlink_<version_number>.run --rootdir $SMRT_ROOT --smrttools-only --upgrade |
| 2 | Access Tools:$SMRT_ROOT/smrtlink/smrtcmds/bin |
Troubleshooting
If you encounter issues during the upgrade:
-
Logs: Review the installation logs located in
$SMRT_ROOT/install/logsfor error messages. -
Support: Contact PacBio support at support@pacb.com or call 1-877-920-PACB (7222) for assistance.