galaxy 2.2 won't load
by Erika
Hi,
I'm having 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, Tuesday August
29. The browser won't refresh or load the page. I tried using
Safari 2.0.4 and internet explorer 5.2.3. However, the test site
loads just fine.
Thanks for your help with this!
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
15 years, 1 month
sum of the length of regions
by Radek Szklarczyk
hi!
i found it hard to get the sum of the length of regions. I ended up
multiplying mean (sum stats) by the number of regions, for which I
had to calculate the length with an expression first. Maybe I
overlooked a simple way of getting what i want?
radek
---
Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek
15 years, 1 month
filter crash
by Radek Szklarczyk
Hi!
I use galaxy 2.2
I extract all snps from snp125 (whole genome, hg17, i use ucsc
browser main - UCSC: snp125 (genome) 2,771,857 regions, format: bed,
database: hg17 )
and filter on expression: int(c3) - int(c2) == 1
I get an error:
"An error occurred running this job: Code for line in file(inp_file):
line = line.strip() if line and line[0] != '#': c1, c2, c3, c4, c5,
c6 = line.split('\t') c1, c2, c3, c4, c5, c6 = str(c1), float(c2),
float(c3), str(c4), float(c5), str(c6) if int(c3) - in"
radek
---
Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek
15 years, 1 month
Galaxy2.2 not accessible
by Ross Hardison
When I try to reach Galaxy2.2 (http://main.g2.bx.psu.edu/), it does
not load, and I get the message:
"Proxy Error
The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /.
Reason: Error reading from remote server"
Galaxy2.2-Test does load and work OK.
- 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
15 years, 1 month
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
15 years, 1 month
problem with gmaj
by Ross Hardison
I'm trying to use the GMAJ tool on Galaxy, but get this error:
Error loading alignments from bundled file "input.maf":
edu.psu.bx.gmaj.BadInputExceptions: Sequence length contradiction"
s baboon.1 26891 63 + 1248010
TCAG...
Current = 1248010. Previous = 550206
The maf files were extracted using the "Extract MAF blocks" tool, for
TBA ENCODE alignments.
The maf data are at
http://main.g2.bx.psu.edu/display?id=3054
15 years, 1 month
broken link
by Cathy Riemer
>From the "WhatDoIDoFirst" wiki page:
"In the second window open Galaxy by typing http://www.galaxy2.org
in the location bar or by clicking below"
Server not found
Firefox can't find the server at www.galaxy2.org.
-Cathy
15 years, 2 months
describe table schema
by Erika
Tools: Get data: UCSC Main table browser:
when you click on "describe table schema" button, rather than getting
the description of the table you get a message saying:
"This is a proxy to the data services provided by the UCSC Genome
Browser's Table Browser."
any chance we can get the table descriptions?
thanks,
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
15 years, 2 months
Problems using GALAXY via the web server
by Jamil Bacha
Hi,
I am trying to run some analyses using GALAXY but whatever I try keep
getting a message returned saying /ERROR: [Errno 12] Cannot allocate
memory/. My uploaded data files are in BED format with just the
chromosome, start, end and name entered. I cannot find any obvious
formatting problems with my files. Can you please advise.
Many thanks
Jamil
15 years, 2 months
help with maf file (upload?)
by Emmanuel Buschiazzo
Hi,
I uploaded yesterday a .maf file (pretty big, ca. 55 MB). Despite a long
waiting time, the upload did not seem to find an end (the webpage got
stucked with the 'progression-display' full), and I had to close the
window. However, the file now appears when I'm logged in.
Despite this, when trying to use gmaj, no data seems to have the proper
type.
Also, when I try to 'display' my data file, there is a server error.
Are these errors due to the file being corrupted because of the
'interrupted' upload?
Is it something else?
Thanks for your help.
Emmanuel.
<mailto:ebr26@student.canterbury.ac.nz>
15 years, 2 months
