Hello, I am a JBrowse Dev hoping to add the ability to export data directly from JBrowse (JavaScript) to Galaxy (without exporting from JBrowse, saving locally, opening Galaxy, loading file from drive). I have looked through the wiki page on Data Sources<http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources>, but JBrowse is client-side only. I was wondering if anybody knew of a different way to do this, or had any pointers. Thanks, Erik Derohanian
Erik, 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? Thanks, J. On Oct 22, 2012, at 3:21 PM, Erik Derohanian wrote:
Hello,
I am a JBrowse Dev hoping to add the ability to export data directly from JBrowse (JavaScript) to Galaxy (without exporting from JBrowse, saving locally, opening Galaxy, loading file from drive). I have looked through the wiki page on Data Sources, but JBrowse is client-side only. I was wondering if anybody knew of a different way to do this, or had any pointers.
Thanks, Erik Derohanian
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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
Do the APIs produce the proper CORS headers? Access-Control-Allow-Origin: *, and responding to OPTIONS requests would be enough. Since this is an API protected by a key, this doesn't have any real security implications to just have hard-coded in. Rob On Oct 23, 2012 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
___________________________________________________________ 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:
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...
Yes, the Galaxy team is working on a JavaScript binding to the API, and one of the areas that we've done some work on is running tools. It's probably a little heavyweight if all your want to do is push datasets into Galaxy—HTTP posts to the API will work just fine—but it's useful if you want real integration between Galaxy and your Web application (JBrowse or otherwise), such as the ability to work with histories/datasets/tools/visualizations on the fly. J.
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
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.
This isn't possible right now, though you could imagine using FTP with the API to achieve this. J.
participants (4)
-
Brad Chapman -
Erik Derohanian -
Jeremy Goecks -
Robert Buels