Symptoms

Bitbucket Server upgrade fails with following error reported in the logs:

2012-12-06 01:19:11,743 ERROR [main]  c.a.s.i.s.g.v.PerlBinaryValidation Error validating Perl
com.atlassian.bitbucket.exception.ServerException: An error occurred while 
executing an external process: '/usr/local/git/bin/git commit -m 
Initial' exited with code 1 saying: fatal: cannot exec 
'.git/hooks/pre-commit': Permission denied          

Perl is already installed on the server.

Cause

There is a permission mismatch between the user which is running Bitbucket Server and the user which owns the Bitbucket home directory.  

Resolution

1. Ensure that the user which is running Bitbucket Server owns the home directory (and its contents).

2. If you are still running into this problem, set the following flag in your bitbucket.properties in your Bitbucket home directory. The file will need to be created, if it does not exist already:

   plugin.bitbucket-scm-git.perl.validation.enabled=false