Re: [Gmod-ajax] Challenge : Installing jbrowse

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

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