Hi, Nate,

How are you? Last week our director attended a meeting at New York and got
some information from you. I just visited your homepage "
http://galaxy.psu.edu/"; he mentioned.  We have some question to "Use
Galaxy<http://usegalaxy.org/>"
and "Get Galaxy <http://getgalaxy.org/>". We want to figure out how our PIs
at NIH can use them. Do you have any information regarding the 2 above
issues? for example, slides, introduction, and links, etc.

1. Which servers are available for users to use right now? Are they free?
Is there any restriction? for example, file size, speed, etc.

2. Is there any difference between "local version" and "cloud version"?
What are they different and benefits?


Please let me know if you have any suggestion.


Best Wishes,

Yan




On Fri, Apr 1, 2011 at 11:12 AM, Yan Luo <luoma...@gmail.com> wrote:

> 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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