Re: [Gmod-ajax] Challenge : Installing jbrowse

[Garrett S. <ste...@gm...>]

I see where you found that link in the documentation. It's not correct,
sorry about that. I'll try to get it fixed soon. To download the newest
desktop version you can go to http://jbrowse.org/blog/ and download the
file called JBrowse-1.15.4-desktop-linux-x64.zip (or the corresponding one
if you're not using linux). Unzip it and launch the file
JBrowse-1.15.4-desktop. If it doesn't work, you may need to install
libgconf, which can be installed on some linux systems by running
sudo apt install libgconf-2-4
Let us know if you still have problems.

~Garrett

On Fri, Oct 26, 2018 at 3:28 AM Beatrice Kodero <kod...@gm...> wrote:

> 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
>