How to migrate smrt analysis to a different server - dyim42/SMRT-Analysis GitHub Wiki

Migrating SMRT Analysis to another server is a manual process - there is no automated way to do this. You need to perform a fresh install and import all the old SMRT cells, jobs, and references. You also need to recreate all users.

Step 1: Note old job IDs

Make a list of all the old job IDs, references, and users that you wish to keep.

Step 2: Install the latest SMRT Analysis on the new server

Use the SMRT Analysis installation procedure for the version you are installing. See [Official Documentation] (https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Official-documentation) for details.

Step 3: Import SMRT Cells

In SMRT Portal, go to Design Job > Import and Manage > Import SMRT Cells.

Enter the path to the directory that contains all the SMRT Cells. Click Save, select the new path, then click Scan.

Note that if you are moving the SMRT Cells to a new location, you should do that before the import. If you need to move the SMRT Cells after this step, just reimport them again from the new location. (This will update the paths to the cells.)

Step 4: Import SMRT Portal Jobs

In SMRT Portal, go to Design Job > Import and Manage > Import SMRT Pipe Jobs.

Copy or link the old job directories to the $SMRT_ROOT/userdata/jobs_dropbox directory - you must define SMRT_ROOT to point to the root directory of your new installation or replace it with the actual path. Then, select the jobs and click Scan.

Note that the individual job directories must be copied or linked directly into the jobs_dropbox directory. For example: you can do something like this:

ln -s /opt/oldsmrtanalysis/current/common/jobs/016/016437 /opt/newsmrtanalysis/current/common/jobs_dropbox/016437

but not this:

ln -s /opt/oldsmrtanalysis/current/common/jobs/016 /opt/newsmrtanalysis/current/common/jobs_dropbox/016

Step 5: Recreate References

Create the references you need on the new server the same way as with the previous server: In SMRT Portal, go to Design Job > Import and Manage > Manage Reference Sequences.

Step 6: Recreate Users

Create the users you need on the new server the same way as with the previous server.

###Note:

  • Many of the steps below can be automated using the web services API which is documented for each release. See [Official Documentation] (https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Official-documentation) for details.

  • If you install the new SMRT Analysis on the same server as the old version, you will have to do the following:

    • Shutdown the old SMRT Analysis installation before installing the new version.
    • If you intend to use both versions simultaneously you also need to:
      • Choose different ports for the new servers
      • Choose different paths for the userdata

  • There is no distinction between importing unarchived and archived jobs from the old server.

    • Archiving is nothing more than relocating to a different location specified in your config.xml file.
    • To have jobs archived in the new installation, import the jobs and then archive them.

  • The job ids will change when imported to the new server.