Re: [Gmod-ajax] Challenge : Installing jbrowse

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

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>
>>>>
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>>>>