Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[Robert B. <rb...@gm...>]

My main recommendation for reducing startup time is to upgrade to the
latest version of JBrowse.

For reducing the disk footprint and number of files in the `data/tracks`
subdirectory, I'd look at migrating your feature tracks away from
`flatfile-to-json` NCList format to an indexed format like Tabix-indexed
GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed
driver).

For the `data/names` subdirectory, there is an ElasticSearch plugin out
there that would let you store your name-searching index in ElasticSearch,
see https://github.com/elsiklab/jbrowse_elasticsearch

Hope this helps! Always happy to answer any further questions.

On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...> wrote:

> Hi Heidi,
>
> I'm cc'ing this to the JBrowse mailing list for more input.
>
> I can say that 346GB sounds like a lot to me, but nematodes have a lot
> smaller genomes than plants!  Have you looked at the javascript console to
> see what takes a lot of time?  Do you want to post a link to the one that
> performs badly?  Also, I'll point out (before Rob gets a chance to) that
> newer releases of JBrowse use webpack and thus have better startup times.
> Finally, things you might want to think about is converting some of your
> GFF-based tracks to tabix indexed files, which will be much cleaner from a
> storage perspective and probably perform better too, though I don't
> remember if tabix indexed GFF files work with 1.12 (or work well, which I
> suppose is two separate things).
>
> Scott
>
>
> On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...>
> wrote:
>
>> Hello
>>
>>
>>
>> I’d appreciate some JBrowse guidance in regards to information I can’t
>> seem to adequately locate in the documentation regarding server hardware
>> configuration.
>>
>>
>>
>> We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in
>> particular that seems to be causing poor performance with the website.  The
>> JBrowse footprint, on disk is 346G.  How does this compare with other
>> users?  Is this considered large?  We also have over 5 million files.  This
>> creates I/O issues on disk.  What configuration recommendations do you have
>> to help alleviate this problem.
>>
>>
>>
>> https://www.rosaceae.org/tools/jbrowse
>>
>> Heidi Hough
>> System/Database Administrator
>> Main Bioinformatics Lab - Department of Horticulture
>> Washington State University
>> 48 Johnson Hall
>> Pullman, WA 99164-6414
>>
>> 509-335-7093 <(509)%20335-7093>
>> hei...@ws...
>>
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
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