Dear Nate,

Thanks a lot, I will check them.

Best Wishes,

Yan

On Fri, Apr 1, 2011 at 11:07 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
> Dear Nate,
>
> Thanks for your information, I will use it next times. By the way, how do we
> know the status of Galaxy's database (mysql)? I can't make sure if the
> database starts normally.

Do you mean the database server itself?  If you can connect with the
'mysql' command line interface, it's up.  If you are worried about
corruption, you can check the MySQL logs or use 'mysqlcheck'.

--nate

>
> Best Wishes,
>
> Yan
>
> On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor <nate@bx.psu.edu> wrote:
>
> > Yan Luo wrote:
> > > Dear Nate,
> > >
> > > Your suggestion is very important for us. You are right, there is other
> > > instance of Galaxy to use the socket. I found the ps and kill them, but
> > they
> > > are still there, then I using screen -wipe to remove it (I use screen to
> > run
> > > the galaxy). It works. Is there any possibly for Galaxy to auto release
> > the
> > > previous port and reuse it in the future version?
> >
> > It does this now.  You would need to reconnect to the screen (using
> > 'screen -r') and stop Galaxy with CTRL-C.
> >
> > Note that screen is not necessary.  You can start and stop Galaxy in the
> > background with:
> >
> > Start:
> >
> > % sh run.sh --daemon
> >
> > Stop:
> >
> > % sh run.sh --stop-daemon
> >
> > --nate
> >
> > >
> > > Have a nice weekend!
> > >
> > > Best Wishes,
> > >
> > > Yan
> > >
> > > On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor <nate@bx.psu.edu> wrote:
> > >
> > > > Yan Luo wrote:
> > > > > Dear Nate,
> > > > >
> > > > > I can't start my galaxy and got the following information, could you
> > > > please
> > > > > let me know how we can fix it as soon as possible? We were running
> > the
> > > > > system, it was down last night suddenly. Hope we can fix it today.
> > > > >
> > > > >
> > > > >
> > > > >   File
> > > > >
> > > >
> > "/mnt/gluster-vol/home/kangtu/tools/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> > > > > line 151, in server_wrapper
> > > > >     **context.local_conf)
> > > > ...
> > > > >   File "/usr/lib/python2.6/SocketServer.py", line 411, in server_bind
> > > > >     self.socket.bind(self.server_address)
> > > > >   File "<string>", line 1, in bind
> > > > > socket.error: [Errno 98] Address already in use
> > > >
> > > > Something (possibly another instance of Galaxy) is already listening on
> > > > the port you are trying to start Galaxy on.  You can determine what
> > that
> > > > process is with 'lsof -i :<PORT>' where <PORT> is the port number you
> > > > connect to Galaxy on.  You may need to use sudo for this to succeed.
> > > >
> > > > Assuming it's another Galaxy instance, you can probably find it with
> > 'ps
> > > > auxwww | grep universe' and then kill that process.
> > > >
> > > > --nate
> > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Looking forward to hearing from you.
> > > > >
> > > > > Best Wishes,
> > > > >
> > > > > Yan
> > > >
> >