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Re: [Gmod-ajax] Challenge : Installing jbrowse
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From: Garrett S. <ste...@gm...> - 2018-10-24 19:02:26
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The desktop version should be able to open VCF files. I was just able to open one on my computer. If you let us know what you have tried and what error you got, maybe we can help. ~Garrett On Wed, Oct 24, 2018 at 2:56 PM Beatrice Kodero <kod...@gm...> wrote: > Thanks for your continued support. I heartily appreciate. > > Desktop was my choice but could not load VCF files > > On Wed, Oct 24, 2018 at 5:09 PM Garrett Stevens < > ste...@gm...> wrote: > >> The general idea is to put the data you want to visualize in the data >> directory (probably /var/www/html/jbrowse/data for you) and then add >> track entries that reference that data to either tracks.conf or >> trackList.json in the data directory. Either the conf or json files >> work, they can do the same things. >> >> For reference, the configuration files for that site you linked can be >> viewed at http://jbrowse.igs.umaryland.edu/t_parva/data/trackList.json >> and http://jbrowse.igs.umaryland.edu/t_parva/data/tracks.conf. There are >> lots of different types of tracks, so to configure the specific types of >> tracks you want you'll have to look at our documentation >> <http://jbrowse.org/docs/reference_sequence.html> under "Configuring >> Tracks." >> >> Another option if you're only viewing locally is JBrowse Desktop >> <http://jbrowse.org/docs/jbrowse_desktop.html>, which can load your data >> and then save your session so you can come back to the same data later. >> >> ~Garrett >> >> On Tue, Oct 23, 2018 at 8:49 PM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> I am new to Linux and this is my first system to install. >>> >>> Would like to customise , have day preloaded ( like link sent before) >>> and visualize data locally of T.parva genomes >>> >>> Apologies for to many questions ;-) >>> >>> On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> >>>> Please allow me to ask, After installation and I want to preload data >>>> to my localhost ie i don't have to upload a reference gene or add track >>>> something like this here >>>> >>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>> What files will i work with? jbrowse.conf or tracks.conf or hard code? >>>> >>>> Regards >>>> Beatrice >>>> >>>> On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> Hey Scott, >>>>> >>>>> It's blank >>>>> >>>>> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: >>>>> >>>>>> Hi Beatrice, >>>>>> >>>>>> I can’t quite make out the text in the red bar (where the error >>>>>> message is). Can you tell us what it says? >>>>>> >>>>>> Thanks, Scott >>>>>> >>>>>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>> Please find attached. The error I am now getting from installation >>>>>> >>>>>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Garrett Thanks a million. >>>>>>> >>>>>>> Able to download at cd/var/www/html/jbrowse >>>>>>> >>>>>>> Please allow me to ask, After installation and I want to preload >>>>>>> data to my localhost ie i don't have to upload a reference gene or add >>>>>>> track something like this here >>>>>>> >>>>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>>>> What files will i work with? jbrowse.conf or tracks.conf or hard >>>>>>> code. >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>>>>> ste...@gm...> wrote: >>>>>>> >>>>>>>> Either should work, as long as you specify the paths to the files >>>>>>>> correctly. E.g. >>>>>>>> >>>>>>>> cd /var/www/html/jbrowse >>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>> >>>>>>>> and >>>>>>>> >>>>>>>> cd /var/www/html/jbrowse/data >>>>>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>>>>> >>>>>>>> should both work. >>>>>>>> >>>>>>>> ~Garrett >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero < >>>>>>>> kod...@gm...> wrote: >>>>>>>> >>>>>>>>> thanks for your mail again, >>>>>>>>> >>>>>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>>>>> /var/www/html/jbrowse >>>>>>>>> >>>>>>>>> Been working from /var/www/html/jbrowse/data to install content of >>>>>>>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>>>>> ste...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Ok, so looking at the error in your first message, it looks like >>>>>>>>>> you perhaps weren't in the right location when you ran the bgzip and tabix >>>>>>>>>> commands. Those are the commands that will generate the files you are >>>>>>>>>> missing. Try making sure you cd to the right directory first, >>>>>>>>>> like: >>>>>>>>>> >>>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>>> >>>>>>>>>> ~Garrett >>>>>>>>>> >>>>>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> Thanks for apt response Garrett >>>>>>>>>>> >>>>>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>>>>> . >>>>>>>>>>> >>>>>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>>>>> I used wget and downloaded above. The challenge am facing begins >>>>>>>>>>> at http://jbrowse.org/docs/tutorial.html >>>>>>>>>>> >>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>>>>> >>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>>>>> >>>>>>>>>>> I only got these files >>>>>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>>>>> >>>>>>>>>>> Instead of below files >>>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>>> /var/www/html/jbrowse/data >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>>>>> >>>>>>>>>>> I am missing >>>>>>>>>>> >>>>>>>>>>> volvox.sorted.gff3.gz >>>>>>>>>>> >>>>>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>>>>> >>>>>>>>>>> Kindly advise. >>>>>>>>>>> >>>>>>>>>>> Regards >>>>>>>>>>> >>>>>>>>>>> Beatrice >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hello, >>>>>>>>>>>> >>>>>>>>>>>> When you say the curl link is not working, what do you mean? >>>>>>>>>>>> Are you using the installation instructions found here >>>>>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>>>>>> command on that page and it worked fine for me: >>>>>>>>>>>> >>>>>>>>>>>> curl -O >>>>>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>>>>> >>>>>>>>>>>> Also the output you pasted was something with bgzip, not curl, >>>>>>>>>>>> so I'm not sure what the problem is there. If you can give some more detail >>>>>>>>>>>> we can see if we can help. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Garrett >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi , >>>>>>>>>>>>> >>>>>>>>>>>>> I trust that this email finds you well. >>>>>>>>>>>>> >>>>>>>>>>>>> I am at the point of installing jbowse and the curl link is >>>>>>>>>>>>> not working. see below installation >>>>>>>>>>>>> >>>>>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>>>>> >>>>>>>>>>>>> [bgzip] No such file or directory: >>>>>>>>>>>>> data/volvox.sorted.gff3...........error am getting. >>>>>>>>>>>>> >>>>>>>>>>>>> What could i be doing wrong? >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> Regards, >>>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>>> >>>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>>> >>>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>>>>> Gmo...@li... >>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> Beatrice Kodero >>>>>>>>>>> >>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>> >>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Beatrice Kodero >>>>>>>>> >>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>> >>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>> Skype : B.Kodero >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Regards, >>>>>>> Beatrice Kodero >>>>>>> >>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>> more than anyone else." Vince Lombardi >>>>>>> >>>>>>> Mobile : +254 726 486 077 >>>>>>> Skype : B.Kodero >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>> more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>>>> >>>>>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>>>>> >>>>>> _______________________________________________ >>>>>> Gmod-ajax mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>>> > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > |
