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Talk:GBrowse 1 Configuration HOWTO

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Hello Reg. GFF file format: I was wondering if the group/region field has to be (now or in the future) of the format

 ##sequence-region

I think Apollo (but not Artemis) breaks if that is not included.

Alpapan

The current version of Apollo does require sequence-region, but I just chatted with the developer and he is removing the requirement that it be there; he thought it was required by the GFF3 spec. Of course, this question would probably have been better asked on the Apollo mailing list: http://mail.fruitfly.org/mailman/listinfo/apollo --Scott 16:21, 29 January 2008 (EST)

Ah, thanks Scott
I also was under the impression it was in the GFF3 spec.

 This element is optional, but strongly encouraged because it allows parsers to perform bounds checking on features.

So I assumed that it was GBrowse that did not follow the spec. Alpapan

* -> h3 for track properties, etc, easier on the eyes?

I ran a snippet of code...

s/^\*(.+)\n/===$1===\n/

...to produce the following output. If anyone cares, I think it lets the track properties - which are currently bulleted - stand out a bit more, making them easier to find. (check the General [SECTION] for an example.) --Stewarta 13:43, 14 March 2008 (EDT)

Declaring New Aggregators

i think it should be

 aggregators = transcript{....

not

 aggregator = transcript{....

At least with my gbrowse dev branch... I didn't edit it in case i 'm wrong. Alpapan

Agreed and fixed. Thanks. Scott 23:13, 11 June 2008 (EDT)

Renaming proposal?

Hi, I propose that this article is renamed 'Configuring GBrowse', and that we start to split it up into sub documents by heading. Each sub document would be categorized 'GBrowse configuration'. It's just so large and unwieldy - I think lots of stuff, especially advanced functionality could be split out. --DanBolser 13:41, 22 May 2009 (UTC)

So I started doing this finally (since the discussion reached consensus). If people want the mega-doc back for some reason, it can be dynamically re-created from the individual pages on the wiki by 'transcluding' content from the individual pages into another 'calling' page. For example, to include the content of GBrowse Configuration/Balloons in another page, you just type {{:GBrowse Configuration/Balloons}} on that page. Note the use of the 'noinclude' tags in the above page allows text (a header) in the individual pages that is not transcluded into the calling page. --DanBolser 01:13, 10 July 2010 (UTC)