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,
On Dec 14, 2012, at 10:07 AM, Jennifer Jackson wrote:
> The original question/reply is posted here:
> But the dev community is welcomed to add in additional comments/advice to
> this re-post!
> 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 ->
>> 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!
>> 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
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: