Dear Nate,

Thanks a lot, I will check them.

Best Wishes,

Yan

On Fri, Apr 1, 2011 at 11:07 AM, Nate Coraor <n...@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 <n...@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 <n...@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
> > > > >
> > >
>
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