Re: [Gmod-ajax] Challenge : Installing jbrowse

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

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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