Re: [Gmod-ajax] Challenge : Installing jbrowse

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

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
>