Hi Alex,

This error has been corrected, thanks for reporting it. Please let use know if 
you encounter any additional issues.


Thanks for using Galaxy,

Dan


On Aug 21, 2012, at 1:12 AM, Alex Shaw wrote:

> Hi,
> 
> I'm also interested in using bedtools with galaxy. I have found a bug.
> When I try to run "Intersect multiple sorted BED files"
> 
> Error: The requested genome file
> (/galaxy/home/g2test/galaxy_test/tool-data/shared/ucsc/chrom/hg_g1k_v37.len)
> could not be opened. Exiting!
> 
> I've used bedtools on the command line, and it is looking for a file
> that specifies the chr length for the reference genome.
> 
> Alex
> 
> On 17 August 2012 08:23, Jennifer Jackson <j...@bx.psu.edu> wrote:
>> Hello Mo,
>> 
>> This tool comes from a repository sourced from the Tool Shed:
>> http://toolshed.g2.bx.psu.edu/
>> 
>> Search for a tool named "bedtools" with owner "aaronquinlan". You could
>> examine the repository and then the tool wrapper author can be contacted
>> directly with questions about parameters or if you think there is a bug.
>> 
>> Hopefully this helps!
>> 
>> Jen
>> Galaxy team
>> 
>> 
>> On 8/16/12 10:13 AM, Mohammad Heydarian wrote:
>>> 
>>> Hi,
>>> I am using the "Count intervals in one file overlapping intervals in
>>> another file" tool (part of the bedTools package) to assess the number
>>> of RNA-seq reads that map back to a specific region. (I am using this on
>>> the Galaxy test server). I am finding that this tool returns many more
>>> reads than it should.
>>> 
>>> In reading the bedTools manual, it seems like this tool is the
>>> "windowBed" tool and it actually has many more parameters that are not
>>> shown on the Galaxy interface. What are these (hidden) settings for
>>> these parameters that are not shown?
>>> 
>>> Hopefully this can explain my incorrectly recorded reads.
>>> 
>>> Thanks in advance.
>>> 
>>> 
>>> Cheers,
>>> Mo Heydarian
>>> 
>>> 
>>> 
>>> ___________________________________________________________
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>> 
>> --
>> Jennifer Jackson
>> http://galaxyproject.org
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
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>> 
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>> please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 
> 
> 
> -- 
> Alex Shaw
> Research Officer
> 
> Neuroscience Research Australia
> 
> www.NeuRA.edu.au
> Barker Street Randwick Sydney NSW 2031 Australia
> PO Box 1165 Randwick Sydney NSW 2031 Australia
> T +61 2 9399 1112 F +61 2 9399 1005
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>  http://lists.bx.psu.edu/


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