Hi Scott,

This isn't currently exposed through the API, but I'm working on implementing it at https://github.com/galaxyproject/galaxy/pull/2741, if you'd like to test it.


On Thu, Aug 4, 2016 at 10:38 AM Ouellette, Scott <Scott_Ouellette@hms.harvard.edu> wrote:
Hi all,

I have a use case where I need to programmatically download both the .bam and it's index file to run IGV outside of Galaxy, but have not found a straightforward way to do so.
It seems that Galaxy always generates this .bai file under the hood, and I can download it manually by clicking the “save” icon on the dataset in my history. Although, the application I am coding for relies on the bioblend Python library.


In bioblend I see a field returned upon a `DatasetClient(<galaxy_instance>).show_dataset(<dataset_id>)` but that is as far as I've got:

"meta_files": [
            "file_type": "bam_index"

Any help is appreciated!

Scott O.

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