Hi Cyril,

Jen's response includes the correct information about how symlinks are handled, 
and why.  Changing the symlink underlying a dataset is not a great idea since 
it will cause the dataset's metadata to be incorrect and break Galaxy's concept 
of reproducibility.  I would suggest that you utilize the library dataset 
versioning features to accomplish what you're trying to do.

Hope this helps,
--nate

On Dec 14, 2012, at 10:07 AM, Jennifer Jackson wrote:

> Hello,
> 
> The original question/reply is posted here:
> http://lists.bx.psu.edu/pipermail/galaxy-user/2012-December/005665.html
> 
> But the dev community is welcomed to add in additional comments/advice to 
> this re-post!
> 
> Thanks,
> 
> Jen
> Galaxy team
> 
> On 12/14/12 6:49 AM, MONJEAUD wrote:
>> Hi all, 
>> 
>> I created data libraries using options "Upload files from filesystem paths" 
>> and "Link to files without copying into Galaxy". 
>> It worked but I use symbolic links because my data are frequently updated 
>> 
>> The problem is that Galaxy takes the real link (inside "external_filename" 
>> column in "dataset" table) and doesn't find the 
>> files when it is deleted. 
>> 
>> For example, I uploaded a dataset for a data library without copying : 
>> /databank/uniprot/current/fasta/all.fasta -> 
>> /databank/uniprot/01_12_2012/fasta/all.fasta
>> The real path is put in the database and it's a problem when it is deleted.
>> 
>> Is there a way for galaxy to take the symbolic link directly in the database 
>> instead of the real path. 
>> 
>> Thanks in advance! 
>> Cheers, 
>> -- 
>> 
>> Cyril Monjeaud
>> Equipe Symbiose / Plate-forme GenOuest
>> Bureau D156
>> IRISA-INRIA, Campus de Beaulieu
>> 35042 Rennes cedex, France
>> Tél: +33 (0) 2 99 84 74 17
>> 
>> 
>> 
>> ___________________________________________________________
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> 
> -- 
> Jennifer Jackson
> 
> http://galaxyproject.org
> ___________________________________________________________
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