galaxy-user February 2006

galaxy-user@lists.galaxyproject.org

6 participants
8 discussions

error erased history?
by Ross Hardison 26 Feb '06

26 Feb '06

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

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error at Galaxy
by Ross Hardison 25 Feb '06

25 Feb '06

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;

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[Genecats] what is an efficient way to combine data tracks? (fwd)
by Belinda M. Giardine 24 Feb '06

24 Feb '06

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

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error message
by Ross Hardison 20 Feb '06

20 Feb '06

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;

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Problem using tools in local installation
by Sigurjón Axel Guðjónsson 17 Feb '06

17 Feb '06

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

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error in plotting tools for Galaxy
by Ross Hardison 14 Feb '06

14 Feb '06

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

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yet another test
by Anton Nekrutenko 07 Feb '06

07 Feb '06

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

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test
by Anton Nekrutenko 07 Feb '06

07 Feb '06

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

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galaxy-user February 2006