Dear Nate and developers,
Could you please let me know if you have any solution for my questions and
several attachments sent to you last week? Someone web pages don't work
well.
Looking forward to hearing from you.
Best Wishes,
Yan
On Mon, Feb 28, 2011 at 4:45 PM, Yan Luo <luomails(a)gmail.com> wrote:
Dear Nate,
We have a new issue to use Galaxy. When we login use a general user
account, we found:
(1) When we upload six fastq files via URL, three of them can be uploaded
successfully while the other three can't be uploaded.
(2) What's more, even those files can be uploaded, we can't perform the
mapping with BWA (NGS: Mapping/Map with BWA) either single end or
paired-end. The problem is we can't select which file to do the mapping.
(3) If we use an admin account, we can find one file when we perform the
mapping and are trying uploading other one to see if we can select from
the two files list.
(4) Could you please let me know if Galaxy has some restriction for files
number, a single file size, or total files size loaded by one user(account)?
Please find the attached screenshoots for your reference.
Looking forward to hearing from you.
Best Wishes,
Yan
On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> Yan Luo wrote:
> > Dear Nate,
> >
> > Yes, you are right, for some reason, we couldn't cd to the folder. It is
> > fixed and I restart the Galaxy. The only thing is that it needs about 10
> > minutes to start. I remembered it is a little fast last week. Is there
> any
> > problem? Anyway, Galaxy works.
>
> Assuming nothing else has changed, it sounds like your NFS server is
> having some performance problems.
>
> --nate
>
> >
> > Thanks,
> >
> > Yan
> >
> > On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> >
> > > Yan Luo wrote:
> > > > Dear Nate,
> > > >
> > > > Thanks for your quick response, I got "sever error". and
just killed
> the
> > > > process. When I ran activate as follows and can't active it:
> > > >
> > > >
> > > > kangtu@dscbc-compute:~$ .
> > > > /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
> > > > bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate:
> Stale
> > > NFS
> > > > file handle
> > > > kangtu@dscbc-compute:~$
> > >
> > > It looks like the NFS mount on which Galaxy lives has gone bad,
> possibly
> > > due to an error with the NFS server. I suggest contacting a local
> > > system administrator for assistance.
> > >
> > > --nate
> > >
> > > >
> > > >
> > > > Any suggestion will be appreciate.
> > > >
> > > > Best Wishes,
> > > >
> > > > Yan
> > > >
> > > >
> > > >
> > > > On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor <nate(a)bx.psu.edu>
> wrote:
> > > >
> > > > > Yan Luo wrote:
> > > > > > Dear Nate,
> > > > > >
> > > > > > I have a new problem, last week, I restarted the Galaxy, but
it
> > > worked
> > > > > well.
> > > > > > This morning, I found I can't start it from browser, but
when I
> check
> > > "ps
> > > > > > auxwww|grep python", I still find it is running, what
is
> problem?
> > > > >
> > > > > What happens when you try to connect via a browser? Is an error
> > > message
> > > > > displayed? Connection timeout?
> > > > >
> > > > > >
> > > > > > kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11
13:43
> > > python
> > > > > > ./scripts/paster.py serve universe_wsgi.ini
> > > > >
> > > > > If you reconnect to your screen session and take a look at the
> output
> > > > > from the Galaxy server, there may be error message displayed
which
> > > would
> > > > > explain what the problem is.
> > > > >
> > > > > --nate
> > > > >
> > > > > >
> > > > > >
> > > > > > Looking forward to hearing from you.
> > > > > >
> > > > > > Best Wishes,
> > > > > >
> > > > > > yan
> > > > > >
> > > > > > On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo
<luomails(a)gmail.com>
> > > wrote:
> > > > > >
> > > > > > > Dear Nate,
> > > > > > >
> > > > > > > I just used "screen", and restarted the
galaxy, it works. It
> is
> > > > > perfect,
> > > > > > > and I also found that some features can't be used
before, when
> I
> > > > > restart it,
> > > > > > > everything is fine.
> > > > > > >
> > > > > > > Have a wonderful weekend!
> > > > > > >
> > > > > > > Best Wishes,
> > > > > > >
> > > > > > > Yan
> > > > > > >
> > > > > > >
> > > > > > >
> > > > >
> > >
>