Re: [Gmod-ajax] using multiple sources

[Mitch S. <mit...@be...>]

Hi, sorry it took so long to get back to you; I had a big deadline that 
I had to focus on for a while instead.

I spent some time looking at this; I was thinking of changing the 
behavior of the dataRoot setting.  But I realized that that would 
require people to re-generate their JBrowse JSON.  So don't think we 
want to do that in the current "master" branch, although it might make 
sense to do it in the current development ("lazyfeatures") branch.

So, assuming you're using the master branch, then there's one more 
option that I forgot to mention in my last email, that should make the 
name searching work, without requiring you to have multiple copies of 
the JBrowse code.  It's a bit awkward, though.

Earlier, I suggested that you have multiple data directories, with 
separate html files that pointed to them, something like this:

jbrowse/
    genome1-data/
    genome2-data/
    genome1.html
    genome2.html

The awkward thing that I forgot to suggest earlier is this: take those 
genome1-data and genome2-data directories, and rename them and move them 
around so that they look like this instead:

jbrowse/
    genome1.html
    genome2.html

genome1/
    data/

genome2/
    data/

That is, take those data directories and make them into directories 
named "data", with uniquely named parent directories.  This is because 
that "data" string (unfortunately) shows up in several places both in 
the JBrowse code and also in the generated JSON.

Then update genome1.html and genome2.html so that the refSeqs.js and 
trackInfo.js links point to where you moved those data directories; e.g.:

<script type="text/javascript" src="../genome1/data/refSeqs.js"></script>
<script type="text/javascript" src="../genome1/data/trackInfo.js"></script>


And then add the "dataRoot" option to the Browser constructor in 
genome1.html and genome2.html, so that it looks something like this:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback,
                                    dataRoot: "../genome1"
                                });


and that ought to do it.  I haven't tested the specific recommendations 
in this email, though, so do let me know if it works for you.

Mitch


On 06/01/2010 08:17 AM, Adam Witney wrote:
> On 28 May 2010, at 19:13, Mitch Skinner wrote:
>    
>> So, right now you've got two options:
>>
>> 1. have separate JBrowse directories will both code and data, or
>> 2. wait a few days or a week for us to fix up the dataRoot setting to be more flexible.
>>
>> If you choose option 1, and if you originally got JBrowse using git, then you can save some disk space by using "git clone".  For example, if you originally did a "git clone" to create a "jbrowse" directory, you can clone from there to a new directory, and the clone will save some disk space (by using hard-linking).
>>
>> $ git clone jbrowse genome1
>> $ git clone jbrowse genome2
>>
>> will give you new "genome1" and "genome2" directories that don't use much extra disk space.
>>
>> Sorry about that,
>> Mitch
>>      
> ok thanks for the tips Mitch, I will try those options
>
> thanks
>
> adam
>
>
>