Hi Colin,

colin molter wrote, On 08/05/2011 01:54 PM:
> Is there a way to directly move/copy data from your galaxy history to a given 
> location in the filesystem of the same galaxy server?
> Said differently, there is a nice way to import data from the server to 
> galaxy, is it possible to do the reverse?
> that is ok for me.
> However, if someone has a better solution, any advices are fine for me
> thnks
> colin

If you feel comfortable meddling directly with your galaxy database, the 
following query will give you the dataset file numbers for each dataset in a 
given history.

 dataset.id as "DatasetFileNumber",
 lpad(trunc(dataset.id/1000), 3, '0') as "Directory", 
 'dataset_' || dataset.id || '.dat' as "Filename",
 history_dataset_association.hid as "Dataset Number in History",
 history_dataset_association.name as "Dataset Name"
 dataset.id = history_dataset_association.dataset_id
 history.id = history_dataset_association.history_id
 history.user_id = galaxy_user.id
 galaxy_user.email = 'gor...@cshl.edu'
 history.name = 'K9981_het'
order by

Just change the "history.name" and the "galaxy_user.email" in the query to get 
the correct history (assuming your histories' names are unique).

This SQL is for PostgreSQL, but MySQL  should be similar.

The first column (DatasetFileNumber) is the file associated with the galaxy 
dataset (e.g. 2456)
The second is the directory (e.g. "002" for dataset 2456),
The third is the file name (e.g. "dataset_2456.dat").

A simple shell script should be able to construct the correct path.
Note that for datasets larger than 100,000 there's going to be an extra 
directory of "000/" (e.g. "000/101/dataset_101123.dat").

As always, direct database access is never recommended...

hope this helps,

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