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Re: [Gmod-ajax] JBrowse2 with JBrowse1
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From: Hans Vasquez-G. <hav...@uc...> - 2021-02-02 17:51:44
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Hi Colin, So if I need to get BLAST -> JBrowse working, my only option right now is JBrowse1? I used to use a heavily modified viroblast php installation to generate the links to JBrowse. However, in my new lab, I have setup sequenceServer and have started configuring that for BLAST. There is some documentation on the FAQ (https://jbrowse.org/docs/faq.html) mentioning sequenceserver configuration, but I believe this is only for JBrowse1. Do you know of any talks about getting sequenceserver working with JBrowse2? Thank you, -Hans On Mon, Feb 1, 2021 at 4:21 PM Colin <col...@gm...> wrote: > > 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. > > Currently there is not yet a feature for this but we plan on making it. It > would actually be possible with the session url but it'd be a bit tedious. > If possible I'd recommend keeping track of this issue for updates > https://github.com/GMOD/jbrowse-components/issues/1464 > > > 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. > > Using the "share" button at the top of the screen is the best way to share > links with your colleagues. > > The share link that this generates is uses a URL shortener that we made > (no data on users is collected when using this, and the system can be > considered "end to end encrypted"), but you can also get an expanded link > from the gear icon in the share dialog that skips the URL shortener > > Screenshot: > > [image: > localhost_3000__config=test_data%2Fconfig_demo.json&session=local-hHHLBr_Jn > (1).png] > > > -Colin > > On Mon, Feb 1, 2021 at 4:00 PM Hans Vasquez-Gross < > hav...@uc...> wrote: > >> 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 >> > -- 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 |
