Assaf Gordon wrote:
> 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...
This has come up enough times that I've just committed a script that
will return the filename if provided a numeric or encoded HDA. I've
posted it to the list before as galaxythinger.py, it's in the source as
galaxy-dist/scripts/helper.py as of 5919:0f878ea61e98.
It will also decode and encode IDs. More functionality for common
sysadmin tasks would be welcomed.
> hope this helps,
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