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Re: [Gmod-ajax] Challenge : Installing jbrowse
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From: Beatrice K. <kod...@gm...> - 2018-10-26 07:28:30
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Thanks, I am tying to open it in http://jbrowse.org/jbrowse-1-12-1/ but getting an error message. On Wed, Oct 24, 2018 at 10:02 PM Garrett Stevens < ste...@gm...> wrote: > 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 >> > -- 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 |
