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Re: [Gmod-ajax] JBrowse2 with JBrowse1
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From: Colin <col...@gm...> - 2021-02-02 00:21:09
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> 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 > |
