Dear Ross,
Thank you form your prompt answer.
unfortunately I still get an error message which is :
"An error occurred running this job: *A required composite data file was not
provided (RgeneticsData.ped)"
*I did exactly what you mentioned except that my ped and map files have been
uploaded using the ftp procedure.
Do you have any clues ?
Thank you so much for your help,
Sylvain

*

*
2011/2/3 Ross <ross.laza...@gmail.com>

> Hi, Sylvian,
>
> The plink/rgenetics lped and pbed (compressed) formats are special
> 'composite' Galaxy datatypes because the map and pedigree/genotype files
> need to be kept together correctly inside Galaxy. As a result, the upload
> tool requires that the file type be specified so all of the components can
> be properly uploaded and stored together.
>
> For example, to upload pbed data from your local desktop, choose 'Upload
> file' from the Get Data tools.
>
> When the upload form appears, the trick is that you *must* change the
> default 'Autodetect' in the first (filetype) select box to the specific
> rgenetics datatype - either 'pbed' as the format for compressed plink data
> (or 'lped' for uncompressed plink genotype data) as the very first step.
> Type the first few letters into the first box, and select the right one from
> the list that appears.
>
> Once this is done, you will see that the upload tool form will change to
> show three separate file upload inputs - one each for the plink xxx.bim
> xxx.bed and xxx.fam where xxx is the name you set when you ran plink to
> create the files, or for uncompressed linkage format two separate file
> upload inputs - the plink .ped and .map files.
>
> Now you can  browse for the corresponding file for each input box from your
> local machine - be careful not to mix them up as the upload tool is unable
> to tell unfortunately.
>
> At the bottom of the form, I suggest you then change the genome build to
> the appropriate one (eg hg18 or hg19).
>
> Finally, I'd recommend that you change the 'metadata value for basename'
> (which will be the new dataset name) to something that will remind you what
> the data are - something more meaningful than the default 'rgenetics'.
>
> Click 'execute' to upload the data and create the new dataset in your
> history.  Compressed (pbed) format is preferred so the upload is quicker.
>
> Note that some tools will autoconvert between lped and pbed so there is a
> delay the first time some tools are run on a new dataset. There are built in
> converters (use the pencil icon) also if you need them.
>
> I hope this helps - thanks for using Galaxy and Rgenetics - please let us
> know how you go and feel free to contact me if you have other questions.
>
> On Fri, Feb 4, 2011 at 6:20 AM, BAULANDE Sylvain 211527 Partnerchip <
> sylvain.baula...@cea.fr> wrote:
>
>> dear Galaxy users,
>> I would like to import genotyping data in Rgenetics and I can't succeed.
>> I have ped file and map file, I try to import them in lped format but it
>> didn't work ...
>> Anybody with experience can help me to solve this issue ?
>> Many thanks in advance,
>> Best regards,
>> Sylvain
>>
>>
>>
>>
>>
>> _______________________________________________
>> galaxy-user mailing list
>> galaxy-user@lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>
>
>
> --
> Ross Lazarus MBBS MPH
> Associate Professor, HMS; Director of Bioinformatics, Channing Laboratory;
> 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850
> Head, Medical Bioinformatics, BakerIDI;
> PO Box 6492, St Kilda Rd Central; Melbourne, VIC 8008, Australia; Tel: +61
> 385321444
>
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