The error is gone, thank you very much!  What was the problem?

Ilya


On 11/27/12 5:34 PM, "Jim Johnson" <johns...@umn.edu> wrote:

>Ilya,
>I fixed the igvtools_tile.xml tool config and pushed it to the toolshed.
>Thanks for finding and reporting the problem.
>JJ
>
>On 11/27/12 3:18 PM, Sytchev, Ilya wrote:
>> Here's a link to one of the WIG files I am using:
>> https://www.dropbox.com/s/rv201lawduflr7j/Galaxy12-scc.wig.zip
>> I'd appreciate any pointers.
>>
>> Thanks,
>> Ilya
>>
>>
>> On 11/27/12 3:57 PM, "Jim Johnson" <johns...@umn.edu> wrote:
>>
>>>
>>>
>>> Ilya,
>>>
>>> Could you send me a failing input file, and I'll try to find out what
>>>is
>>> failing?
>>> Thanks,
>>> JJ
>>>
>>>
>>>> ------------------------------
>>>>
>>>> Message: 6
>>>> Date: Tue, 27 Nov 2012 07:22:30 +0000
>>>> From: "Sytchev, Ilya" <isytc...@hsph.harvard.edu>
>>>> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>>> Subject: [galaxy-dev] No output from IGVtools tile
>>>> Message-ID: <ccd9d465.30c7%isytc...@hsph.harvard.edu>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>>
>>>> Hi,
>>>>
>>>> I'm running IGVtools
>>>> (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in
>>>> Galaxy on a WIG file but it's failing with exit code 1 and producing
>>>>no
>>>> output file.  On the other hand, IGVtools count and sort run
>>>> successfully
>>>> in Galaxy on their respective inputs.
>>>>
>>>> Also, IGVtools tile tool runs successfully by itself from the command
>>>> line
>>>> on the same input WIG file from the same user account that runs this
>>>> Galaxy instance.
>>>>
>>>> Standard out and error from running tile in Galaxy are below.  I was
>>>> wondering if anyone had a similar problem with IGVtools in their
>>>>Galaxy
>>>> instance.
>>>>
>>>> Thanks,
>>>> Ilya
>>>>
>>>>
>>>> stdout:
>>>>
>>>> Tile.  File = input_file.wig
>>>> Max zoom = 7
>>>> Probe file = None
>>>> Window functions: mean
>>>> IGV directory: /n/galaxy/home/galaxy_scc/igv
>>>> INFO [2012-11-27 00:14:07,942]  [GenomeManager.java:118] [main]
>>>>Genome
>>>> loaded
>>>>
>>>> Processing chromosome chr19
>>>> .........10.0%
>>>> .........20.0%
>>>> .........30.0%
>>>> .........40.0%
>>>> .........50.0%
>>>> ..INFO [2012-11-27 00:14:12,778]  [Preprocessor.java:179] [main]
>>>> Ignoring
>>>> data from non-existent locus.  Probe = null  Locus =
>>>> chr19:61342442-61342477. chr19 length = 61342430
>>>> Group idx: 1
>>>> 100.0%
>>>>
>>>>
>>>>
>>>> stderr:
>>>>
>>>> cp: cannot stat
>>>>
>>>> 
>>>>`/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/databas
>>>>e/
>>>> jo
>>>> b_working_directory/000/100/output.tdf': No such file or directory
>>>>
>>>>
>


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