Yan Luo 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.
Hi Yan,
Could you expand the history items so it's possible to see what the upload error is?
If you set the 'smtp_server' and 'error_email_to' options in the universe_wsgi.ini file, you will also get a new icon in the history item which will allow you to generate a bug report. This bug report will contain the full error message from the upload tool, if the one in the history item is truncated.
(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.
The reason the files are not showing up in the tool most likely has to do with file format. The BWA tool expects input files to be in the fastqsanger format. The best way to acheive this is to run your input file through the FASTQ Groomer tool before using it with BWA.
(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)?
Galaxy does not have any built-in limitations on file size/count.
--nate
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@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@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@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@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 > > > > > >