Hi Dan,

You're right; it is a binary PLINK .bed file. It would be helpful to bundle
the bim bed and fam files together as a pbed item. I think the bed file is
too large to upload from the file system so I tried to upload it within a
directory of files. When I try to upload these files as a directory of
files and select "pbed" as the file format, they are not bundled together
but uploaded separately and then the bed file upload fails.

-Rob

On Fri, Jul 13, 2012 at 4:31 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> Hi Rob,
>
> The 'bed' datatype in Galaxy refers to UCSC's Browser Extensible Data
> format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
>
> Is this a binary PLINK .bed file (
> http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml)? If so, you may
> want to consider looking at/using the 'pbed' datatype in Galaxy (for
> Rgenetics tools; datatype is galaxy_root/lib/galaxy/datatypes/genetics.py).
>  It is a composite datatype that holds the .bim, .bed, and .fam files all
> together as a single Galaxy item. If you have a use for keeping the .bed
> file separate from the other two files, or if this is a different .bed
> file, then this doesn't apply.
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Jul 12, 2012, at 5:24 PM, Robert Chase wrote:
>
> Hi Nate,
>
> I don't think that it does. We get the bed files from our GWAS pipelines.
> We were able to upload the file by adding 'bed' to the list of
> unsniffable_binary_formats in binary.py and manually specifying the format.
> Do you think this could cause problems later?
>
> -Rob
>
> On Thu, Jul 12, 2012 at 4:21 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>
>> On Jul 5, 2012, at 4:15 PM, Robert Chase wrote:
>>
>> > Hello,
>> >
>> > We tried to upload a directory of files to our local data library and
>> all uploads were successful except for one. The .bed file did not upload
>> and gave an error message; The uploaded binary file contains inappropriate
>> content. We would like to be able to share our data set with other
>> researchers using galaxy but we need to be able to upload this bed file.
>>
>> Hi Rob,
>>
>> Is there any chance that the file contains Unicode?
>>
>> --nate
>>
>> >
>> > -Rob
>> > ___________________________________________________________
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