Quick Start Guide for SMRT Link v25.3 Installation
This guide provides a concise overview of the steps required to install SMRT Link v25.3 or SMRT Link Lite v25.3. For detailed instructions, please refer to Installing SMRT Link .
For detailed walkthrough, check out our SMRT Link Install tutorial video.
Note
This Quick Start Guide assumes that all prerequistes are met. Please reference System Requirements and ensure the checklist below is completed before proceeding with the installation.
Installation/upgrade checklist
| ✅ | Appropriate hardware located and configuration chosen with Linux Rocky or Ubuntu OS. |
| ✅ | Installation root directory ($SMRT_ROOT) identified on shared (NFS) file system. |
| ✅ | Service account ($SMRT_USER) identified/created to install/run the SMRT Link services. |
| ✅ | $SMRT_ROOT base directory has appropriate rwx permissions for $SMRT_USER. |
| ✅ | Job Management System (JMS) and Singularity installed/setup (if using SMRT Analysis). |
| ✅ | Full path for SMRT Analysis database directory (db_datadir) chosen on the local file system on the install node. |
| ✅ | Full path for SMRT Analysis jobs output directory (jobs_root) chosen on shared (NFS) file system. |
| ✅ | Full path for SMRT Analysis temporary directory (tmp_dir) chosen on the local file system on each node. |
| ✅ | Ports 8243, 9243, and 9443 are available and open for SMRT Link web services. |
| ✅ | (Optional) LDAP settings. See Advanced Topics for details. |
| ✅ | (Optional) SSL certificate for NGINX. See Advanced Topics for details. |
Installation steps
| Step | Action |
|---|---|
| 1 | Log onto Install Host: Access the server as $SMRT_USER. |
| 2 | 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 |
| 3 | Run the Installer: Execute the following commands based on the installation type: Full SMRT Link: ./smrtlink_<version_number>.run --rootdir $SMRT_ROOTSMRT Link Lite: ./smrtlink_<version_number>.run --lite true --jmstype NONE --rootdir $SMRT_ROOT --nworkers 4For most installations the default setup options can be accepted. See Installing SMRT Link for more information on configuration options. |
| 4 | Start Services: Use the command:$SMRT_ROOT/admin/bin/services-start |
| 5 | Run Site Acceptance Test (Optional):$SMRT_ROOT/admin/bin/run-sat-services |
Note
For additional post-installation managment options please see the Post-Installation Steps.
Upgrade steps
| Step | Action |
|---|---|
| 1 | Log onto Install Host: Access the server as $SMRT_USER. |
| 2 | Download and Unzip the Installer:curl -O https://downloads.pacbcloud.com/public/software/installers/smrtlink-release_25.3.0.273777.zip unzip smrtlink-release_25.3.0.273777.zip |
| 3 | Stop Services:$SMRT_ROOT/admin/bin/services-stop |
| 4 | Run Installer with Upgrade Option:./smrtlink_<version_number>.run --rootdir $SMRT_ROOT --upgrade |
| 5 | Start Services:$SMRT_ROOT/admin/bin/services-start |
| 6 | Run Site Acceptance Test (Optional):$SMRT_ROOT/admin/bin/run-sat-services |
| 7 | Clear Browser Cache (Recomended): In Chrome, go to More Tools > Clear Browsing Data, select "All Time" for cached files, and clear. This ensures defualt settings are properly loaded. |