some questions
by Iris Vargas Jentzsch
Dear GalaxyTeam members,
I'm a PhD student at the University of Canterbury and I have been using Galaxy for about 3 weeks... It is an excellent program! Actually it is the kind of tool I was looking for many months and an awesome complement for the UCSC Genome Browser
Until now I have worked mostly using the interface at http://test.g2.bx.psu.edu/ which I guess is the test version. I have also installed the program in my linux session, however, I work more often in windows. Therefore I would like to know if you have a binary (or if you plan to make one) to run the program in windows?
And a curiosity: where are the files from the history saved? What is the size limit for all the history files?
Many thanks for your cool tool!
Iris
======================================
Iris M. Vargas Jentzsch
PhD Student
School of Biological Sciences
University of Canterbury
Private Bag 4800
Christchurch - New Zealand
phone: +64 (0) 3 364 2987 (7048)
e-mail: imj15(a)student.canterbury.ac.nz
16 years, 1 month
Fwd: Fwd: Galaxy2.2 Test retrieving DNA sequences
by Laura Elnitski
Hi-
thanks for all of the suggestions- so far we've had no luck in
obtaining our sequences.
One thing I remember is that different browsers have different
settings for how long they take until they time-out- maybe we should
try something other than Safari?
Laura
Begin forwarded message:
> From: "Yang, Mary \(NIH/NHGRI\) [F]" <yangma(a)mail.nih.gov>
> Date: July 28, 2006 2:45:22 PM EDT
> To: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski(a)mail.nih.gov>
> Subject: Re: [Galaxy-user] Fwd: Galaxy2.2 Test retrieving DNA
> sequences
>
> Laura:
> Ben and I tried the suggested options, none of them work. Also Ben
> tried the other ways, like curl, did not work either.
>
> Mary
>
>
16 years, 2 months
test galaxy not working
by Ross Hardison
I only get errors when I try to load in data to
http://test.g2.bx.psu.edu/
Attempt to upload a file gives:
An error occurred running this job: upload failed, the url specified
is invalid or you have not specified a file
delete
Attempt to get data from UCSC gives:
An error occurred running this job: ERROR:
Attempt to get ENCODE data from Galaxy gives:
An error occurred running this job: ERROR:
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8(a)psu.edu
phone: 814-863-0113 FAX: 814-863-7024
16 years, 2 months
Fwd: Galaxy2.2 Test retrieving DNA sequences
by Laura Elnitski
More- continued from Thursday's message:
The error we receive has to do with receiving the data that Galaxy is
trying to send.
Is there another way to retrieve the data? We cannot display it to
screen either.
Is has something to do with the time-out settings on our browser, right?
Thanks very much,
Laura
Begin forwarded message:
> From: "Yang, Mary \(NIH/NHGRI\) [F]" <yangma(a)mail.nih.gov>
> Date: July 28, 2006 10:39:43 AM EDT
> To: "Elnitski, Laura \(NIH/NHGRI\) [E]" <elnitski(a)mail.nih.gov>
> Subject: Galaxy2.2 Test retrieving DNA sequences
>
> Laura:
> Here is the message I got when I tried to save or display
> the file.
>
>
> Network Error (tcp_error)
>
> A communication error occurred: ""
> The Web Server may be down, too busy, or experiencing other
> problems preventing it from responding to requests. You may wish to
> try again at a later time.
>
> I think the file is too large to get it through internet. It
> will be nice if they could zip the file and send it.
> Thank you very much.
>
> Mary
>
>
16 years, 2 months
galaxy page load failure
by Erika
Hi,
Yogeshwar and I in Kateryna Makova's lab have both had trouble
loading the galaxy main page http://main.g2.bx.psu.edu/ from Mueller
Bldg. I was successfully using galaxy2.2 and first had trouble
yesterday afternoon, Thursday July 27. The browser won't refresh or
load the page. I tried using Safari 2.0.4 and internet explorer
5.2.3. Just wanted to check...
Thanks for your help!
erika
**********************************************************
E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185
16 years, 2 months
retrieving DNA sequences
by Laura Elnitski
Hi-
We've hit a problem trying to download sequence from Galaxy. Did we
ask for too many?
We can't display them nor can we save them, but the query seems to
have run fine. It reports 39,000 results.
The data are on the test browser- id 24081.
Thanks,
Laura
Laura Elnitski, Ph.D.
Head Genomic Functional Analysis Section
Genome Technology Branch
National Human Genome Research Institute
National Institutes of Health
5625 Fishers Lane, Rm. 5N-01R
Rockville, MD 20852
phone: 301-451-0265
fax: 301-435-6170
16 years, 2 months
Windows XP instalation problem
by tras sdzd
Hi there,
I have been following the instructions from the website (http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/HowToInstall) until I encountered the following problems:
1 There was missing file named universe.conf.sample but there was universe_wsgi.ini.sample. I renamed it together with the rest to universe.conf ( after that I tried and universe_wsgi.conf)
2. When I tried to run python universe_wsgi.py I've got something like - please see the attached jpeg file.
Please can somebody help me with advice.
Thanks in advance
Reymon
---------------------------------
Try the all-new Yahoo! Mail . "The New Version is radically easier to use" The Wall Street Journal
16 years, 2 months
how to share the history?
by Ying Zhang
Hi, all,
Today, Ross and I tried to share our histories. And Ross told me, he
had made his history accessible to me.
I assume here when somebody made his history shared with me, I would
automatically receive an email containing the link of the shared page.
But in fact, I have not received such an email by now, one hour later
than Ross shared his history.
So could someone give me some instructions on how to access a shared
history?
Best,
Ying
By the way, I tried to share my history with Ross, but seems
rch8(a)psu.edu is not a valid user. I am wondering when you update
Galaxy to version 2.2, have you also transferred the user
registrations to the new version? Because the first time I used
Galaxy 2.2, I need re-register for myself again.
Another concern is that Galaxy 2.2 should be our best galaxy up to
now. So why don't we update the link in UCSC table browser?
Yesterday, when I asked a result from table browser to be reported to
galaxy, I was re-directed to the oldest galaxy1.
16 years, 2 months
Re: [Galaxy-user] Problem with intersect (bx)
by Ross Hardison
Sure. The two data files are:
http://test.g2.bx.psu.edu/display?id=23602
http://test.g2.bx.psu.edu/display?id=23607
On Jul 13, 2006, at 10:33 AM, Anton Nekrutenko wrote:
> Ross:
>
> Thanks, could you provide links to the data files by clicking on
> display link and "Copy Link Location" (as shown below).
>
> <Picture 1.png>
>
> anton
>
>
>
> Anton Nekrutenko
> Assistant Professor
> Department of Biochemistry and Molecular Biology
> Center for Comparative Genomics and Bioinformatics
> 505 Wartik Building
> PennState University
> University Park, PA 16802
> 814 865-4752
> 814 863-6699 FAX
> anton(a)bx.psu.edu
> http://www.bx.psu.edu/~anton
> http://g2.bx.psu.edu
>
>
> On Jul 13, 2006, at 10:27 AM, Ross Hardison wrote:
>
>> The intersection tool under "Operate on Genomic Intervals (bx)" is
>> not working for returning either overlapping regions or
>> overlapping pieces. The intersection and overlaps in the non-bx
>> operations section are working.
>>
>> I was running intersection (bx) on a set of Mathieu Blanchette's
>> PReMods (118,402 regions) with our RP>0.05 intervals (314,040
>> regions), in hg17, requiring at least 10bp overlap. Here are the
>> error messages.
>>
>> For returning overlapping pieces:
>> An error occurred running this job: Traceback (most recent call
>> last): File "./tools/new_operations/gops_intersect.py", line 63,
>> in ? main() File "./tools/new_operations/gops_intersect.py", line
>> 56, in main for line in intersect([g1,g2], pieces=pieces,
>> mincols=mincols): File "
>>
>> For returning overlapping regions:
>> An error occurred running this job: Traceback (most recent call
>> last): File "./tools/new_operations/gops_intersect.py", line 63,
>> in ? main() File "./tools/new_operations/gops_intersect.py", line
>> 56, in main for line in intersect([g1,g2], pieces=pieces,
>> mincols=mincols): File "
>>
>> I'll leave the files and results in my history for a while in case
>> that is helpful.
>>
>> Thanks,
>> Ross
>>
>> Ross Hardison
>> T. Ming Chu Professor of Biochemistry and Molecular Biology
>> The Pennsylvania State University
>> 304 Wartik Laboratory
>> University Park, PA 16802
>> e-mail: rch8(a)psu.edu
>> phone: 814-863-0113 FAX: 814-863-7024
>>
>>
>>
>>
>>
>> _______________________________________________
>> Galaxy-user mailing list
>> Galaxy-user(a)bx.psu.edu
>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8(a)psu.edu
phone: 814-863-0113 FAX: 814-863-7024
16 years, 2 months
PS on problem with intersection (bx)
by Ross Hardison
I forgot to tell you that I'm using the test version of Galaxy
(http://test.g2.bx.psu.edu/)
- Ross
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8(a)psu.edu
phone: 814-863-0113 FAX: 814-863-7024
16 years, 2 months
