Re: [Gmod-ajax] Challenge : Installing jbrowse

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

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
>