[Gmod-ajax] staged "prepare_refseq.pl" approach

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[Gmod-ajax] staged "prepare_refseq.pl" approach

Ramón Fallon
Hi Rob!

(forgive first-time familiarity: I'm a GMOD13 course alumnus!)

I have my references sequences (contigs actually) in groups (a GFF file for each group).

I wanted to keep appending new refseqs to the jbrowse instance payload (i.e. jbrowse's data directory) by running "prepare-refseqs.pl" then "biodb-to-json.pl" on each group at different times. The possibly misplaced reason for this is that "biodb-to-json.pl" takes a long time, and one or two of my groups don't have annotations so don't need them. Now, because I know there's hashing going on, with the risk of conflicts and overwritings, is this safe to do or is it something you would not recommend?

Cheers / Ramón.

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Re: staged "prepare_refseq.pl" approach

Robert Buels-2
Unfortunately, prepare-refseqs.pl and biodb-to-json.pl don't support
incremental updates.

Have you considered serving the data differently, like from a web app
that you control?  Depending on how extensive your computing
infrastructure is, that could be a good option.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/10/2014 12:59 PM, Ramón Fallon wrote:

> Hi Rob!
>
> (forgive first-time familiarity: I'm a GMOD13 course alumnus!)
>
> I have my references sequences (contigs actually) in groups (a GFF file
> for each group).
>
> I wanted to keep appending new refseqs to the jbrowse instance payload
> (i.e. jbrowse's data directory) by running "prepare-refseqs.pl
> <http://prepare-refseqs.pl>" then "biodb-to-json.pl
> <http://biodb-to-json.pl>" on each group at different times. The
> possibly misplaced reason for this is that "biodb-to-json.pl
> <http://biodb-to-json.pl>" takes a long time, and one or two of my
> groups don't have annotations so don't need them. Now, because I know
> there's hashing going on, with the risk of conflicts and overwritings,
> is this safe to do or is it something you would not recommend?
>
> Cheers / Ramón.
>
>
> ------------------------------------------------------------------------------
> Android&trade; apps run on BlackBerry&reg;10
> Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
> Now with support for Jelly Bean, Bluetooth, Mapview and more.
> Get your Android app in front of a whole new audience.  Start now.
> http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: staged "prepare_refseq.pl" approach

Ramón Fallon
Hi Rob,

Thanks for the quick answer. Is there an example of an idea like that which you can refer me to?

Cheers / Ramón.


On Mon, Feb 10, 2014 at 7:07 PM, Robert Buels <[hidden email]> wrote:
Unfortunately, prepare-refseqs.pl and biodb-to-json.pl don't support incremental updates.

Have you considered serving the data differently, like from a web app that you control?  Depending on how extensive your computing infrastructure is, that could be a good option.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org


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Get your Android app in front of a whole new audience.  Start now.
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