Galaxy API question:

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Galaxy API question:

Roxanne
Hi,

I was going through the examples in the README, and everything went along fine until I tried to upload files from the import directory:

usage: library_upload_from_import_dir.py key url folder_id file_type server_dir dbkey

I don't understand what the last two arguments 'server_dir' and 'dbkey' represent, or how to determine the correct values to pass along.

I can, however, successfully upload via the import dir from the webapp.

Any help would be appreciated,


Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
LANL




___________________________________________________________
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:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Galaxy API question:

Nate Coraor (nate@bx.psu.edu)
Roxanne Tapia wrote:

> Hi,
>
> I was going through the examples in the README, and everything went along fine until I tried to upload files from the import directory:
>
> usage: library_upload_from_import_dir.py key url folder_id file_type server_dir dbkey
>
> I don't understand what the last two arguments 'server_dir' and 'dbkey' represent, or how to determine the correct values to pass along.
>
> I can, however, successfully upload via the import dir from the webapp.
>
> Any help would be appreciated,

Hi Roxanne,

server_dir is the name of the directory underneath your configured
'library_import_dir' in the Galaxy config file from which you would like
to import.  In the UI, these names appear in a drop-down list.

The dbkey is the "key" of the genome build that should be associated
with the data you're importing (e.g. 'hg18'), the full list of which is
also available on the UI upload page.

--nate

>
>
> Roxanne Tapia
> Software Developer 3
> B-6, Genome Science
> Bioscience Division
> LANL
>
>
>
>
> ___________________________________________________________
> 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:
>
>   http://lists.bx.psu.edu/
___________________________________________________________
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:

  http://lists.bx.psu.edu/