Thanks for your answer!!!

Cyril

On 12/14/2012 04:17 PM, Nate Coraor wrote:
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

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--

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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