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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