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 <chapmanb@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...
but I haven't used it myself. Hope this helps, Brad
Thanks, Erik Derohanian