From: Hans Vasquez-G. <hav...@uc...> - 2021-02-01 23:01:11
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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 |