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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