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

Migrating SMRT Analysis to a different server while preserving SMRT Cell, Job, and user information is a manual process. Do not attempt it if you are not comfortable with any of the following steps.

Step 1. Migrate the mysql database

Perform a mysqldump on the "smrtportal" database. Move or copy the .sql file to the new host, and restore.

Backup: mysqldump -u root -p[root_password] smrtportal > dumpfilename.sql

Restore: mysql -u root -p[root_password] smrtportal < dumpfilename.sql

Step 2. Move or copy $SEYMOUR_HOME

Perform a file system move or copy of the $SEYMOUR_HOME directory and all of its subdirectories from the old host to the new host. Manually check that the following softlinks are valid in the new location:

  1. $SEYMOUR_HOME/common/userdata and subdirectories should contain data from original host

  2. $TMP folder specified in $SEYMOUR_HOME/analysis/etc/smrtpipe.rc

  3. $SHARED_DIR folder specified in $SEYMOUR_HOME/analysis/etc/smrtpipe.rc

  4. /etc/init.d/tomcatd should point to $SEYMOUR_HOME/etc/scripts/tomcatd if you have sudo

  5. /etc/init.d/kodosd should point to $SEYMOUR_HOME/etc/scripts/kodosd if you have sudo

Step 3. Move or copy the primary analysis data directory

  1. Perform file system move or copy of the primary analysis directory and all of its subdirectories from the old host to the new host.

  2. If you DO have a PacBio RS, you must update the settings in RS Remote. The primary analysis data directory (contains data directly from the instrument) is specified in RS Remote --> View --> Settings --> Output Sources, and the secondary analysis server is specified in RS Remote --> View --> Settings --> Secondary. You must update these settings in RS Remote. (If you DO NOT have an PacBio RS, this directory is likely $SEYMOUR_HOME/common/userdata/inputs_dropbox, and you do not need to do anything.)

  3. SMRT Portal does not have the ability to automatically recognize the new primary analysis path. If the path to the primary analysis data directory has changed, you need to manually delete the SMRT Cells from the database using these instructions, and then re-import all of them using the "import and manage" function on the SMRT Portal GUI. This will allow the new paths on the new host to take effect.

Step 4. Re-run configure_smrtanalysis.sh

Re-run $SEYMOUR_HOME/etc/postinstall/scripts/configure_smrtanalysis.sh and enter the hostname of the new server to configure smrtanalysis on your new server.