I just noticed the part:  "files_0|url_paste":
http://jbrowse-server.org/path/to/file.vcf";

JBrowse is fully client-side, so there is no jbrowse server we can use. Is
there a way to pass data to galaxy directly without the server? This
functionality could also be useful for desktop applications.



On Tue, Oct 23, 2012 at 9:59 PM, Brad Chapman <chapm...@50mail.com> wrote:

>
> Erik and Jeremy;
>
> >> I am a JBrowse Dev hoping to add the ability to export data directly
> >> from JBrowse (JavaScript) to Galaxy
> >
> > The API could be used for this.
> >
> > Specifically, you could do an upload for the user from a URL via the
> > tools API. I know that Brad Chapman (cc'd) has done this successfully
> > recently. Brad, can you share the parameters used to do this?
>
> Definitely, you want to do a POST to:
>
> /api/tools?key=YOURAPIKEY
>
> with a JSON payload of:
>
> {"tool_id": "upload1",
>  "history_id": "identifier of history to use",
>  "params": {"file_type": "vcf",
>             "dbkey": "hg19",
>             "files_0|url_paste":
> http://jbrowse-server.org/path/to/file.vcf";,
>             "files_0|NAME": "file_name_for_history.vcf"}}
>
> This is all new since the last galaxy-dist release, so you'd need a
> recent galaxy-central server.
>
> Passing it back to Jeremy, there is also a Javascript wrapper around the
> tools API which might help:
>
>
> https://bitbucket.org/galaxy/galaxy-central/src/tip/static/scripts/mvc/tools.js
>
> but I haven't used it myself. Hope this helps,
> Brad
>
>

Thanks,
Erik Derohanian
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