User does not have the correct permissions to upgrade - pb-dyim/SMRT-Analysis GitHub Wiki

SMRT Analysis upgrades are very sensitive to ownership and permission settings. During upgrade, you need to make sure that you are the same user as the user who installed the previous version of SMRT Analysis. You can check this by examining the ownership of the $SEYMOUR_HOME directory:

user1@server$ ls -l /opt
lrwxrwxr-x 1 smrtanalysis smrtanalysis 32 2012-12-17 08:02 smrtanalysis -> smrtanalysis-1.4.0
drwxrwxr-x 8 smrtanalysis smrtanalysis 142 2012-05-17 21:38 smrtanalysis-1.3.1
drwxrwxr-x 8 smrtanalysis smrtanalysis 142 2012-05-17 21:38 smrtanalysis-1.3.3
drwxrwxr-x 8 smrtanalysis smrtanalysis 142 2012-05-17 21:38 smrtanalysis-1.4.0
logout

smrtanalysis@server$ /opt/smrtanalysis/etc/scripts/postinstall/upgrade_and_configure_smrtanalysis.sh

In this example, the $SEYMOUR_HOME directory is set to /opt/smrtanalysis/ and this directory is actually a softlink to smrtanalysis-1.4.0, which is owned by the user smrtanalysis belonging to the group smrtanalysis. However, you are currently logged in as user1. To proceed, you must log out and log back in as the user smrtanalysis. This user should now run upgrade_and_configure_smrtanalysis.sh

If you lost the credentials for the smrtanalysis user, you need a root user (with sudo permissions) to change the ownership of $SEYMOUR_HOME. say user1, and then run upgrade_and_configure_smrtanalysis.sh as the new user.

user1@server$ sudo chown -R user1:group1 /opt/smrtanalysis/
user1@server$ sudo chown -R user1:group1 /opt/smrtanalysis-1.4.0/
user1@server$ ls -l /opt
lrwxrwxr-x 1 user1 group1 32 2012-12-17 08:02 smrtanalysis -> smrtanalysis-1.4.0
drwxrwxr-x 8 smrtanalysis smrtanalysis 142 2012-05-17 21:38 smrtanalysis-1.3.1
drwxrwxr-x 8 smrtanalysis smrtanalysis 142 2012-05-17 21:38 smrtanalysis-1.3.3
drwxrwxr-x 8 user1 group1 142 2012-05-17 21:38 smrtanalysis-1.4.0

If you DO NOT have sudo and, you ARE NOT the same user who installed the previous version, you CANNOT upgrade smrtanalysis. You MUST either log in as the same user, or find an administrator with root privileges to reset the ownership and permissions in the $SEYMOUR_HOME directory.