Hi Ulf, Unfortunately, metadata files are assigned an id that is unrelated to the dataset id. To link the files you'll need to use the database. The numerical id you see in the filename is the id of the dataset in the `dataset` table. From this you can go backward to the history_dataset_association (hda) table, where hda.dataset_id = dataset.id. Finally, from there, hda.id can be used to find the metadata_file via metadata_file.hda_id. More succinctly: dataset.id = history_dataset_association.dataset_id history_dataset_association.id = metadata_file.hda_id --nate On Mon, Sep 15, 2014 at 6:34 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:

Dear all

For each bam file in my history I can download the associated bai (bam index) file.

I assume these files are stored somewhere under /mount/galaxy/database/files/_metadata_files. Correct? Is there an easy way to find the bam index file for a bam file, given only the internal file name of the bam (e.g. /mont/galaxy/database/files/089/dataset_89231.dat)?

I am asking because I would like to use the files_to_ftp tool to automatically download bams together with their associated indices.

Thanks Ulf

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