Re: [Gmod-ajax] Challenge : Installing jbrowse

[Beatrice K. <kod...@gm...>]

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
>>>
>>>