Re: [Gmod-ajax] JBrowse2 with JBrowse1

[Hans Vasquez-G. <hav...@uc...>]

Thank you Colin. I am trying to workout firewall restrictions with campus
IT, so right now my JBrowse instance isn't publicly available.

A couple of additional questions have come up with collaborating on this
project. Is there a way to share the current view via a link that is
urlencoded? I was going to share a link with a user, but noticed the share
option requires a session parameter.

 Also, is there a way to add tracks via a urlencoded link like jbrowse1? I
was able to write a php script that takes blast results to dynamically
display BLAST hits on a given reference on JBrowse1. I would like to port
this functionality to JBrowse2.

Thank you,
-Hans

On Wed, Jan 27, 2021 at 4:00 PM Colin <col...@gm...> wrote:

> No worries:)
>
> We would be happy to check out the BAM file also if it is causing issue
> with JBrowse 2
>
> If there is a public web link or jbrowse instance available we can try to
> download from there
>
> Can also use a samtools view to get a slice of the region and send that
> through any file service to mine or garrett's email
>
> -Colin
>
> On Wed, Jan 27, 2021 at 3:11 PM Hans Vasquez-Gross <
> hav...@uc...> wrote:
>
>> Hi Colin,
>>
>> Thank you for your email. Converting the BAM to CRAM has definitely sped
>> up the loading. I'll do more tests and see if I notice it failing to load,
>> but so far it hasn't in my limited testing.
>>
>> Best,
>> -Hans
>>
>> On Wed, Jan 27, 2021 at 10:39 AM Colin <col...@gm...> wrote:
>>
>>> 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
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>
>> --
>> Hans Vasquez-Gross
>> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross>
>> PhD Candidate
>> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/
>> Department of Plant Science
>> University of California at Davis
>> Email: hav...@uc...
>> Skype: hansvg.ucd
>>
>

-- 
Hans Vasquez-Gross
<http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross>
PhD Candidate
Dubcovsky Website - http://dubcovskylab.ucdavis.edu/
Department of Plant Science
University of California at Davis
Email: hav...@uc...
Skype: hansvg.ucd