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Re: [Gmod-ajax] Regarding Jbrowse
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From: Vijay B. <uda...@gm...> - 2016-08-23 18:42:43
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Hi GMOD As I told in the previous e-mail about the tracks.conf and trackList.json but I have not yet seen any tracks in the JBrowse page. Can anyone please help me with this. I am in real need of it. Can anyone respond quick? Thanks in advance. Regards Vijay. On Mon, Aug 22, 2016 at 2:15 PM, Vijay Bhasker <uda...@gm...> wrote: > Hi Scott > > Just to clarify the tracks.conf and trackList.json are present in both > JBrowse-1.11.0/bin/data and JBrowse-1.11.0/data. But tracks.conf in > JBrowse-1.11.0/data is empty. tracks.conf in JBrowse-1.11.0/bin/data has > [tracks.alignments] > urlTemplate = FM.01.new.chr11.bam > type = Alignments2 > > > On Monday, August 22, 2016, Scott Cain <sc...@sc...> wrote: > >> Hi Vijay, >> >> Let's back up a little. I few emails ago, you wrote that your config >> files (tracks.conf and trackList.json) are in /bin/data. That is an odd >> place for them to be, even if I assume you didn't intend to have that >> leading slash and it isn't really in the system /bin directory, rather in >> the jbrowse bin/ directory. Typically, configuration files like this would >> be in the data directory directly under the jbrowse directory, so for >> example here: >> >> /var/www/jbrowse/JBrowse-1.11.0/data >> >> (I'm guessing from other thing that you've written that this is where it >> should be). If those files aren't there, then you almost certainly have to >> edit the jbrowse.conf or jbrowse_conf.json files so that JBrowse can find >> them. In jbrowse.conf, you'd need to look for the dataRoot option. >> >> Finally, as a fairly minor side note: are you really using JBrowse >> 1.11.0? It's quite old; the newest release is 1.12.2. >> >> Scott >> >> >> On Mon, Aug 22, 2016 at 12:46 PM, Vijay Bhasker <uda...@gm...> >> wrote: >> >>> Hi >>> >>> Sure Nathan. I have attached the latest page here. >>> >>> Thanks. >>> Vijay. >>> >>> On Mon, Aug 22, 2016 at 12:22 PM, Nathan Dunn <nat...@lb...> >>> wrote: >>> >>>> >>>> Can you provide screen shots that include the new page with the URL and >>>> the track list on the left? >>>> >>>> Nathan >>>> >>>> On Aug 22, 2016, at 9:06 AM, Vijay Bhasker <uda...@gm...> >>>> wrote: >>>> >>>> Hi >>>> >>>> I have moved jbrowse folder to/var/www/html and typed in the url >>>> localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page >>>> but again with a single reference sequence. >>>> >>>> Thanks. >>>> Vijay. >>>> >>>> On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <sc...@sc...> >>>> wrote: >>>> >>>>> My recollection is that browsers generally don't behave the same when >>>>> you are looking at a file via a "file:///" versus a "http://" url. >>>>> You should really be accessing this page via a web browser. >>>>> >>>>> Scott >>>>> >>>>> On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <uda...@gm...> >>>>> wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> Could anyone please tell me which file should I edit for the >>>>>> customization of features like pop-up boxes, mouse-over behavior etc. >>>>>> >>>>>> Thanks. >>>>>> Vijay. >>>>>> >>>>>> On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <uda...@gm... >>>>>> > wrote: >>>>>> >>>>>>> Hi >>>>>>> >>>>>>> I have attached the javascript console log, datafiles directory and >>>>>>> the url i used to connect with in xubuntu in a virtualbox. >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <nat...@lb...> >>>>>>> wrote: >>>>>>> >>>>>>>> >>>>>>>> Can you post: >>>>>>>> >>>>>>>> 1 - the javascript console in the developer tools window when you >>>>>>>> reload the page (with caching turned off - see the network tab) >>>>>>>> 2 - the contents of the volvox directory so that we can see the >>>>>>>> file sizes >>>>>>>> 3 - the URL you are using to connect with >>>>>>>> 4 - the browser / OS you are using >>>>>>>> 5 - a screenshot of what you are seeing >>>>>>>> >>>>>>>> Nathan >>>>>>>> >>>>>>>> On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <uda...@gm...> >>>>>>>> wrote: >>>>>>>> >>>>>>>> Hi >>>>>>>> >>>>>>>> It was a copy paste error. It is as you mentioned it to be. Now >>>>>>>> what should I do to get back the tracks. Which file is responsible for the >>>>>>>> tracks. How can I edit those tracks? >>>>>>>> >>>>>>>> Regards. >>>>>>>> Vijay. >>>>>>>> >>>>>>>> On Monday, August 22, 2016, Nathan Dunn <nat...@lb...> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> The JSON is malformed. Using: >>>>>>>>> >>>>>>>>> http://codebeautify.org/jsonviewer >>>>>>>>> >>>>>>>>> 1 - should start with an open { (maybe just a copy and paste >>>>>>>>> error) >>>>>>>>> 2 - this is incorrect on the end: >>>>>>>>> >>>>>>>>> "trackType" : "/var/www/jbrowse/JBrowse-1.11 >>>>>>>>> .0/src/JBrowse/GenomeView.*$* >>>>>>>>> >>>>>>>>> >>>>>>>>> should be: >>>>>>>>> >>>>>>>>> "trackType" : "/var/www/jbrowse/JBrowse-1.11 >>>>>>>>> .0/src/JBrowse/GenomeView*”,* >>>>>>>>> >>>>>>>>> >>>>>>>>> This should show up in your javascript console as an error, as >>>>>>>>> well, >>>>>>>>> >>>>>>>>> Nathan >>>>>>>>> >>>>>>>>> On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <uda...@gm...> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Hi GMOD >>>>>>>>> >>>>>>>>> In /bin/data/tracks.conf I have >>>>>>>>> >>>>>>>>> [tracks.alignments] >>>>>>>>> urlTemplate = FM.01.new.sorted.chr11.bam >>>>>>>>> type = Alignments2 >>>>>>>>> >>>>>>>>> And the tracks.conf in /data is empty. >>>>>>>>> >>>>>>>>> In /bin/data/trackList.json I have >>>>>>>>> >>>>>>>>> "tracks" : [ >>>>>>>>> { >>>>>>>>> "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", >>>>>>>>> "storeClass" : "JBrowse/Store/Sequence/StaticChunked", >>>>>>>>> "key" : "Reference sequence", >>>>>>>>> "chunkSize" : 20000, >>>>>>>>> "category" : "Reference sequence", >>>>>>>>> "label" : "DNA", >>>>>>>>> "type" : "SequenceTrack" >>>>>>>>> }, >>>>>>>>> { >>>>>>>>> "storeClass" : "JBrowse/Store/SeqFeature/NCList", >>>>>>>>> "key" : "dna", >>>>>>>>> "label" : "dna", >>>>>>>>> "trackType" : "/var/www/jbrowse/JBrowse-1.11 >>>>>>>>> .0/src/JBrowse/GenomeView.$ >>>>>>>>> "urlTemplate" : "tracks/dna/{refseq}/trackData.json", >>>>>>>>> "compress" : 0, >>>>>>>>> "style" : { >>>>>>>>> "className" : "feature", >>>>>>>>> "color" : "function(feature) {return 'red'; }" >>>>>>>>> }, >>>>>>>>> "type" : "/var/www/jbrowse/JBrowse-1.11 >>>>>>>>> .0/src/JBrowse/GenomeView.js" >>>>>>>>> }, >>>>>>>>> { >>>>>>>>> "type" : "FeatureTrack", >>>>>>>>> "style" : { >>>>>>>>> "className" : "feature" >>>>>>>>> }, >>>>>>>>> "compress" : 0, >>>>>>>>> "urlTemplate" : "FM.01.new.sorted.chr11.bam", >>>>>>>>> "trackType" : null, >>>>>>>>> "label" : "vijay", >>>>>>>>> "key" : "vijay", >>>>>>>>> "storeClass" : "JBrowse/Store/SeqFeature/BAM" >>>>>>>>> } >>>>>>>>> ], >>>>>>>>> "names" : { >>>>>>>>> "url" : "names/", >>>>>>>>> "type" : "Hash" >>>>>>>>> }, >>>>>>>>> "formatVersion" : 1 >>>>>>>>> } >>>>>>>>> >>>>>>>>> This is my complete conf file. Now when I cleared the cache and >>>>>>>>> refreshed the browser, I can only find the reference sequences track and >>>>>>>>> all my previous tracks have been disappeared. Could anyone please help me >>>>>>>>> bring back the tracks and how can I edit those tracks. >>>>>>>>> >>>>>>>>> Thanks. >>>>>>>>> >>>>>>>>> Regards >>>>>>>>> Vijay. >>>>>>>>> >>>>>>>>> On Sun, Aug 21, 2016 at 11:54 AM, Lbl <nat...@lb...> wrote: >>>>>>>>> >>>>>>>>>> Please post the full error and full tracks.conf and verify that >>>>>>>>>> the older tracks.conf is not cached. You can do this under the networks >>>>>>>>>> developer tab under chrome or Firefox per Scott's earlier advice. >>>>>>>>>> >>>>>>>>>> > On Aug 21, 2016, at 8:13 AM, Vijay Bhasker < >>>>>>>>>> uda...@gm...> wrote: >>>>>>>>>> > >>>>>>>>>> > Hi GMOD >>>>>>>>>> > >>>>>>>>>> > I have changed the key name for some tracks in volvox.json but >>>>>>>>>> the track names remains the same in the browser even after refreshing it. >>>>>>>>>> Also, when I click on some tracks it shows the error message "Unable to >>>>>>>>>> fetch the ../.gff3". Could anyone please help me resolve this issue. >>>>>>>>>> > >>>>>>>>>> > Thanks. >>>>>>>>>> > >>>>>>>>>> > Regards >>>>>>>>>> > Vijay. >>>>>>>>>> > ------------------------------------------------------------ >>>>>>>>>> ------------------ >>>>>>>>>> > _______________________________________________ >>>>>>>>>> > 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 >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------ >>>>> ------------ >>>>> Scott Cain, Ph. D. scott at >>>>> scottcain dot net >>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>>> Ontario Institute for Cancer Research >>>>> >>>> >>>> >>>> >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > |