error erased history?
by Ross Hardison
The error that just occurred appears to have erased my history - is
there any way to recover the history?
- 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
14 years, 10 months
error at Galaxy
by Ross Hardison
This occurred while getting phastOdds scores:
exceptions.ValueError at /history
I/O operation on closed file
Python
/usr/lib/python2.4/cgi.py in __getattr__, line 541
Web
GET http://test.g2.bx.psu.edu/history
Traceback (innermost first)
/usr/lib/python2.4/cgi.py in __getattr__
self.file.seek(0)
...
▶ Local vars
/usr/lib/python2.4/cgi.py in __repr__
return "FieldStorage(%r, %r, %r)" % (
...
▶ Local vars
/var/opt/universe/trunk-test/modules/Cheetah/Filters.py in filter
filtered = str(val)
...
▶ Local vars
in respond
▶ Local vars
/var/opt/universe/trunk-test/galaxy/interfaces/common.py in
fill_template
return str(template)
...
▶ Local vars
/var/opt/universe/trunk-test/galaxy/interfaces/root.py in history
return self.fill_template(template, history=history,
mode=mode )
...
▶ Local vars
build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in main
▶ Local vars
build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in run
▶ Local vars
Response so far
HEADERS
Date: Sat, 25 Feb 2006 18:52:04 GMT
Set-Cookie: []
Content-Length:
Content-Type: text/html
Server: CherryPy/2.1.1
BODY
Request information
INPUT
No input data.
COOKIES
Variable
Value
universe
Set-Cookie: universe=6488ab1b7e827b13fd5e85de2ef78ab7;
session
Set-Cookie: session=2e41ce0777a1fcf0a6a2f9019dbec55f95e37934;
universe_prefs
Set-Cookie: universe_prefs=three;
universe_ui
Set-Cookie: universe_ui=info66;
14 years, 10 months
[Genecats] what is an efficient way to combine data tracks? (fwd)
by Belinda M. Giardine
Does someone want to tell this person about the benefits of Galaxy?
UCSC has already told him about featureBits.
Belinda
---------- Forwarded message ----------
Date: Thu, 23 Feb 2006 17:54:49 -0800
From: Jing Zhu <jzhu(a)soe.ucsc.edu>
To: genecats(a)soe.ucsc.edu
Subject: [Genecats] what is an efficient way to combine data tracks?
Hi everyone,
I need some help on a browser-related frustration
I have been performing intersections of data from more than two tables
(combining repeatmasker, simple repeats and pseudogene tracks) by using the
TABLE BROWSER. But each step of this process takes a very long time to
finish, mostly displaying "loading ... " on web browser. Although I manage
to finish it, I would prefer a faster method. Can anyone give me a pointer
for an alternative approach? I am currently working on combining tracks of
functional annotation (Affy's gene expression track, refseq, mRNA, ESTs, and
RNAs) for the whole human genome.
Thanks in advance.
Jing
_______________________________________________
Genecats maillist - Genecats(a)soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genecats
14 years, 11 months
error message
by Ross Hardison
While using Galaxy ( http://test.g2.bx.psu.edu/) , the following
error message appeared:
Application Error
An unexpected error occurred in the Galaxy framework. The error has
been logged.
Show details? (for developers)
exceptions.NameError at /tool_runner/index
global name 'httptools' is not defined
Python
/var/opt/universe/trunk-test/galaxy/interfaces/tool_runner.py in
index, line 24
Web
GET http://test.g2.bx.psu.edu/tool_runner/index
Traceback (innermost first)
/var/opt/universe/trunk-test/galaxy/interfaces/tool_runner.py in index
return httptools.redirect( "/static/welcome.html" )
...
▶ Local vars
build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in main
▶ Local vars
build/bdist.cygwin-1.5.12-i686/egg/cherrypy/_cphttptools.py in run
▶ Local vars
Response so far
HEADERS
Date: Sat, 18 Feb 2006 12:07:10 GMT
Set-Cookie: []
Content-Length:
Content-Type: text/html
Server: CherryPy/2.1.1
BODY
Request information
INPUT
No input data.
COOKIES
Variable
Value
universe
Set-Cookie: universe=6488ab1b7e827b13fd5e85de2ef78ab7;
session
Set-Cookie: session=bd876117f1d3062e5902bbdf9e98e8533bc230ce;
universe_ui
Set-Cookie: universe_ui=info1%3Ainfo2;
14 years, 11 months
Problem using tools in local installation
by Sigurjón Axel Guðjónsson
Hi Galaxy team,
Thanks for developing great platform for interactive large-scale genome
analysis.
We installed local mirror of Galaxy on linux machine. This mirror works
well in connecting and getting data. But many of the tools are not
working.
It seems to be looking for binary files i.e. file named "galaxyOps3". Were
can we find source code for that tool or any other tools using compiled
binary files.
best regards,
Sigurjon
--------------------------
Sigurjon Axel Gudjonsson
Data Analysis and Management
deCode genetics, Inc
sigurjon.gudjonsson(a)decode.is
Tel: +354 570 1871
14 years, 11 months
error in plotting tools for Galaxy
by Ross Hardison
The histogram-plotting tool and the scatter plot tool in Galaxy now
return files that looks like pdf instructions but does not display
as a graph.
Here is the "traceback":
tion Error
An unexpected error occurred in the Galaxy framework. The error has
been logged.
Show traceback? (for developers)
NameError
Python 2.4.2: /usr/bin/python2.4
Mon Feb 13 14:51:32 2006
A problem occurred in a Python script. Here is the sequence of
function calls leading up to the error, in the order they occurred.
/var/opt/universe/trunk-encode/build/bdist.cygwin-1.5.12-i686/egg/
cherrypy/_cphttptools.py in run(self=<cherrypy._cphttptools.Request
object>)
/var/opt/universe/trunk-encode/build/bdist.cygwin-1.5.12-i686/egg/
cherrypy/_cphttptools.py in main(path='/tool_runner/index')
/var/opt/universe/trunk-encode/galaxy/interfaces/tool_runner.py in
index(self=<galaxy.interfaces.tool_runner.ToolRunner object>,
tool_id=None, **kwd={})
23 # No tool id passed, redirect to main page
24 if tool_id is None:
25 return httptools.redirect( "/static/welcome.html" )
26 # Load the tool
27 toolbox = self.get_toolbox()
httptools undefined
NameError: global name 'httptools' is not defined
args = ("global name 'httptools' is not defined",)
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
14 years, 11 months
yet another test
by Anton Nekrutenko
test
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
14 years, 11 months
test
by Anton Nekrutenko
testing
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
14 years, 11 months
