[Galaxy-user] 2 bug reports

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[Galaxy-user] 2 bug reports

Ross Hardison
I'm reporting two problems on the most recent Galaxy (lavender  background, http://g2.bx.psu.edu:8889/)
(The header says "logged in as [hidden email])

1. Problem running overlap:
When I ran overlap on the transcriptional regulation composite hits (Transcription Regulation (TR (20060206) [gencode_partitioned])) and a CpG island track, I got the following error message:

An error occurred running this job: ERROR: commandline error, substituting {'input2': './database/files/dataset_265.dat', 'input1': './database/files/dataset_282.dat', 'input2_strandCol': '0', 'min': 1, 'dbkey': u'hg17', 'input2_chromCol': '1', 'out_file1': './database/files/dataset_283.dat', 'input2_startCol': '2 ', 'input2_endCol': '3'} into galaxyOps3 $dbkey -chromCol=$input1_chromCol -startCol=$input1_startCol -stopCol=$input1_endCol -strandCol=$input1_strandCol -chromCol2=$input2_chromCol -startCol2=$input2_startCol -stopCol2=$input2_endCol $input1 $input2 -all -chrom=all -minSize=$min -bed=$out_file1 -> 'input1_chromCol'

Other tracks did overlap just fine.

2. Problem with "Select lines that match an expression"
I got empty files back when I tried two different things. No error was reported, but the result reports "
<A href="javascript:expand('info295')">Select on data 30

empty, format: interval, database: hg17
Info: Illegal output filename.



Ross Hardison                                             
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
phone: 814-863-0113              FAX: 814-863-7024





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Re: 2 bug reports

Dan Blankenberg
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Re: 2 bug reports

Ross Hardison
The fact that neither you nor Anton replicated the problem suggested  
to me that something was wrong with the file as I downloaded it.  
Indeed, when I downloaded TR again, it works for overlaps.

Anton had suggested that I change the name or edit the TR file, but  
neither of these solved the problem.

I could not find a difference in the two downloads of TR - same  
number of regions, and the "compare" tool did not find anything.

Thanks,
Ross

On Apr 14, 2006, at 2:16 PM, Dan Blankenberg wrote:

> It seems that when the server is shut down and then restarted, that  
> people's histories end up assigned to different people some times.  
> Loging out and Logging in seems to fix it, but a real solution  
> should be found.
>
> As for the overlap, one possibility is that TR file is not  
> technically a bed file (it has extra columns and floating point  
> numbers).  What track were you overlapping with?  Overlaping the TR  
> with itself works.  I think the current incarnation of opperations  
> may have issues when the two files have different formats?
>
> I haven't really spent any time looking at the select tool, so I  
> can say anything off of my head.
>
> Thanks for the bug reports,
>
> Dan
>
>
>
> On Fri, 14 Apr 2006, Ross Hardison wrote:
>
>> I'm reporting two problems on the most recent Galaxy (lavender  
>> background, http://g2.bx.psu.edu:8889/)
>> (The header says "logged in as [hidden email])
>>
>> 1. Problem running overlap:
>> When I ran overlap on the transcriptional regulation composite  
>> hits (Transcription Regulation (TR (20060206)  
>> [gencode_partitioned])) and a CpG island track, I got the  
>> following error message:
>>
>> An error occurred running this job: ERROR: commandline error,  
>> substituting {'input2': './database/files/dataset_265.dat',  
>> 'input1': './database/files/dataset_282.dat', 'input2_strandCol':  
>> '0', 'min': 1, 'dbkey': u'hg17', 'input2_chromCol': '1',  
>> 'out_file1': './database/ files/dataset_283.dat',  
>> 'input2_startCol': '2 ', 'input2_endCol': '3'} into galaxyOps3  
>> $dbkey -chromCol=$input1_chromCol -startCol=$input1_startCol -
>> stopCol=$input1_endCol -strandCol=$input1_strandCol -chromCol2=
>> $input2_chromCol -startCol2=$input2_startCol -stopCol2=  
>> $input2_endCol $input1 $input2 -all -chrom=all -minSize=$min -bed=
>> $out_file1 -> 'input1_chromCol'
>>
>> Other tracks did overlap just fine.
>>
>> 2. Problem with "Select lines that match an expression"
>> I got empty files back when I tried two different things. No error  
>> was reported, but the result reports "
>> Select on data 30
>>
>> empty, format: interval, database: hg17
>> Info: Illegal output filename.
>>
>>
>>
>> Ross Hardison
>> T. Ming Chu Professor of Biochemistry and Molecular Biology
>> The Pennsylvania State University
>> 304 Wartik Laboratory
>> University Park, PA 16802
>> e-mail: [hidden email]
>> phone: 814-863-0113              FAX: 814-863-7024
>>
>>
>>
>>
>>

Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: [hidden email]
phone: 814-863-0113              FAX: 814-863-7024