[Bioperl-pipeline] Re: Help! Stuck with setting up (mysql this time)

[Elia Stupka]

Hi Peter,


> OK, the server started and immediately shut down without complaining.
> (message included below as TEXT1)

this happens very often you need to look at the the data directory
(usually /usr/local/mysql/data/) and look at the log files (see also
http://www.mysql.com/doc/en/Log_Files.html). Then open the error log and
see why it couldn't start.

Most of the times the problems are actually simply associated with
permissions. You need to make sure that all the mysql directories are
readable and writable by the mysql user. If you don't have a mysql user
you should create one and give access to those files.

> mysql-test-run worked nicely. It skipped gemini, isolation and raid 
> tests,
> but otherwise it was perfect:

This indicates that you are very close to a working setup, and it probably
doesn't work just because you are starting the mysql daemon under your
user rather than the mysql user.

> hours of agony one of the manuals suggested to try the port (number
> whatever) via telnet, and that did not work either, and I am
> completely and fully unaware how to handle the ports.

Hmmm... that could also be a problem, you need to check tha the ports are
open.

> but nothing about why it immediately ends.

Look at the logs.

Elia

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