... which brings us back to a past suggestion from one of my colleagues
(you can implement his patch in your instance):

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-September/006827.html

Cheers,
Roman

On 2011-11-17 16:19, Nate Coraor wrote:
> On Nov 16, 2011, at 4:12 PM, Chorny, Ilya wrote:
> 
>> The uploaded files need grooming, so change your Copy data into Galaxy? 
>> selection to be Copy files into Galaxy instead of Link to files without 
>> copying into Galaxy so grooming can be performed.
> 
> BAMs in Galaxy must be sorted.  Since the "link to…" option can't modify the 
> source file, the BAM can't be "uploaded" unless it's sorted prior to 
> uploading.
> 
> --nate
> 
>>  
>> Thoughts?
>>  
>> Thanks,
>>  
>> Ilya
>>  
>> Ilya Chorny Ph.D.
>> Bioinformatics Scientist I
>> Illumina, Inc.
>> 9885 Towne Centre Drive
>> San Diego, CA 92121
>> Work: 858.202.4582
>> Email: icho...@illumina.com
>> Website: www.illumina.com
>>  
>>  
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