Re: [Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello Mitch

It looks like my problem was an apache issue (apart from the bioperl issue).
I just unpacked the tarball from github and it works like a charm. Apologies
for wasting your time.

I have one question: I am creating one track from a GFF file at a time, e.g.
a CDS track:

./bin/gff-to-json.pl -gff lmajor_chr1.gff3 --cssclass feature --tracklabel
CDS --featlabel

This creates a track that shows the invidual CDSs, as expected, but it also
displays an element that spans the entire chromosome (see attachment). How
do I only display the CDSs without hacking into the json output? Is there
something like a 'skip top parent feature' option?


Thanks

Isabelle

On 3/18/09 7:51 PM, "Mitch Skinner" <mit...@be...> wrote:

> iphan wrote:
>> installing the latest jbrowse using the tar and the zip file fails because it
>> looks like the dnd directory is missing from the archives: Apache returns the
>> error
>> 
>> File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
>> http://localhost/~iphan/jbrowse/index.html
>>   
> 
> Two questions:
> * The zip file you're using is the one from github, right?
> 
> * Does the HTML (index.html) file have a reference to jbrowse_dojo.js?
> Also, there should be a jbrowse_dojo.js file in the jslib/dojo directory.
> 
> I used the dojo custom build tools to create a js file (jbrowse_dojo.js)
> that should include all of the JBrowse dojo dependencies, including
> dnd.  That change should make the whole thing a lot faster to load; I've
> tested it with firefox and I think IE but not with safari so far; I'll
> check that later tonight.
> 
> As always, if I can look at the installation over the internet I can
> probably diagnose things faster, although given that it's your laptop I
> can see how that would be tough to do.
> 
>> I don't have git, so would very much appreciate it if I could use the
>> alternative downloads.
>>   
> 
> The tar and zip files from github should be the same as what's in the
> git repository, the last time I tried it, it was the same but I haven't
> checked it lately.  When we make a release I'll also put a zip file on
> jbrowse.org.
> 
> Mitch