Re: [Gmod-ajax] I cannot use the UCSC plugin

[Colin <col...@gm...>]

And to be clear, the UCSC REST API is different from the UCSC track hubs
and the UCSCPlugin can only really  be used when you are manually editing
the config file at the moment (doesn't have any extra GUI to pick and
choose tracks, so the SegDups example above was made by editing the
config.json file, like this
https://github.com/GMOD/jbrowse-components/blob/main/test_data/config_demo.json#L268-L278
)

-Colin

On Tue, May 3, 2022 at 4:55 PM Colin <col...@gm...> wrote:

> Hi there
> Can you describe what your end goal is? Is it to access tracks from UCSC
> on hg19 or hg38 (these aren't generally available as a trackhub), or to
> access a specific trackhub?
>
> I just ask because you mention wanting to create a hub.txt but without
> knowing what you want it is hard to advise
>
> Note:
>
> The trackhubs we connect to are generally from resources that have a
> hub.txt e.g. from this list https://genome.ucsc.edu/cgi-bin/hgHubConnect
>
> Also, it is a bit confusing but the UCSCPlugin is used for accessing the
> UCSC REST API http://genome.ucsc.edu/goldenPath/help/api.html and this
> can actually access hg19 and hg38 tracks (example link showing the SegDups
> track from UCSC)
> https://jbrowse.org/code/jb2/v1.7.6/?config=test_data%2Fconfig_demo.json&session=share-P44nyEajyD&password=iO0Q7
>
> -Colin
>
> On Mon, May 2, 2022 at 1:39 PM Miri Michaeli <
> mir...@an...> wrote:
>
>> Hello Jbrowse team!
>> I tried several manuals and used almost all the info I could reach out
>> to, but I got a dead-end, so I send you this desperate email in request for
>> help.
>> I installed the UCSC plugin
>> [image: image.png]
>> then to use it I do:
>> [image: image.png]
>> but I cannot find how to create a hub.txt even on UCSC they only have an
>> example that they claim to work but I downloaded and it doesn't.
>> I would appreciate any help because I have struggled with it for a long
>> time..
>> Thanks in advance,
>> Miri
>>
>> --
>> *Miri Michaeli*, PhD
>> Bioinformatician Scientist
>>
>>
>>
>>
>> 10 Hanechoshet St., 2nd Floor
>> Tel Aviv, 6971072
>> Israel
>> mir...@an... <sh...@an...>
>> Phone Number: +972-52-4583610
>> www.animabiotech.com
>>
>>
>> --------------------------------------
>> The content of this email is confidential and intended for the recipient
>> specified in message only. It is strictly forbidden to share any part of
>> this message with any third party, without a written consent of the sender.
>> If you received this message by mistake, please reply to this message and
>> follow with its deletion, so that we can ensure such a mistake does not
>> occur in the future._______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>