Re: [Gmod-ajax] JBrowse2 with JBrowse1

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

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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