Re: [Gmod-ajax] JBrowse2 with JBrowse1

[Colin <col...@gm...>]

Note also that CRAM will in many cases also be faster than BAM, so if
possible I would suggest using CRAM just in case you want to make your own
usage of the app faster

Possibly a worthwhile datapoint to add when doing benchmark

-Colin

On Wed, Jan 27, 2021 at 11:35 AM Colin <col...@gm...> wrote:

>
> Echoing what Garrett said. Generally a package-lock.json will be created
> if you use "npm install" instead of "yarn".
>
>
> Also regarding JBrowse 2 being slower than JBrowse 1, this is a real issue
> that you might see, and something we are aware of
>
> Here are some factors that can make JBrowse 2 slower
>
> 1) JBrowse 2 uses webworkers, and each track gets a dedicated webworker,
> so each track needs to initialize a large (~3mb) webworker bundle before a
> track is loaded
> 2) JBrowse 2 serializes the BAM/CRAM data from the webworker back to the
> main thread, which may increase the time to render
> 3) If you are not using Chrome in JBrowse 2, it also has to serialize
> drawing commands back to the main thread, which may increase the time to
> render. Therefore, Chrome will generally be faster when using JBrowse 2.
> Chrome can do the drawing on the webworker and we take advantage of that.
> 4) If you are using the embedded mode component, it will not use a
> webworker at all, and will still do step (2) and therefore will be slower
> also.
>
>
> All these things will make JBrowse 2 slower than JBrowse 1. JBrowse 2
> ideally benefits from offloading heavy computations to the webworker, so
> the overall experience is hopefully that it feels smoother, but there is a
> tradeoff there.
>
> Anyways, all that said, there are real reasons, as listed above, that
> JBrowse 2 can be a bit slower, and we should indeed make a measured attempt
> to benchmark
>
> We would be happy to collaborate on this if you want. I have myself done
> some cursory comparisons here
> https://github.com/GMOD/jbrowse-components/issues/969
>
>
> -Colin
>
> On Tue, Jan 26, 2021 at 5:45 PM Garrett Stevens <
> ste...@gm...> wrote:
>
>> Hi Hans,
>>
>> I don't think that error is due to JBrowse 2, the two projects are
>> isolated. I'm guessing that you're cloning the GitHub repos and installing
>> from there? package-lock.json is a file that NPM uses to make sure the same
>> versions of dependencies are always installed, but we don't use that in
>> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure
>> where that file is being detected. If you let us know the commands you used
>> to get to that point, it might help us figure out what is wrong.
>>
>> Best,
>> Garrett
>>
>> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax <
>> gmo...@li...> wrote:
>>
>>> Hello JBrowse team,
>>>
>>> I recently tried to install both jbrowse1 and jbrowse2 on the same
>>> machine. It seems as though there are competing node/npm requirements.
>>>
>>> I already have jbrowse2 setup on a new machine, but it feels slower
>>> loading BAM files, so I was going to install jbrowse1 as well, to compare
>>> the load times. However, when I went to install jbrowse1, it fails during
>>> the nodejs installation because there are files locked.
>>>
>>> "Node v15.5.1 installed at
>>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0
>>> yarn install v1.22.4
>>> warning package-lock.json found. Your project contains lock files
>>> generated by tools other than Yarn. It is advised not to mix package
>>> managers in order to avoid resolution inc
>>> onsistencies caused by unsynchronized lock files. To clear this warning,
>>> remove package-lock.json."
>>>
>>>
>>> Is this due to the jbrowse2 installation?
>>>
>>> Thank you,
>>> -Hans
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