Re: [Gmod-ajax] Challenge : Installing jbrowse

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

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