The error is gone, thank you very much! What was the problem?
Ilya
On 11/27/12 5:34 PM, "Jim Johnson" 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" 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 +
>>>> From: "Sytchev, Ilya"
>>>> To: "galaxy-dev@lists.bx.psu.edu"
>>>> Subject: [galaxy-dev] No output from IGVtools tile
>>>> Message-ID:
>>>> 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
>>>>
>>>>
>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
