Re: [Gmod-ajax] Regarding Jbrowse Download

[Colin <col...@gm...>]

Yes, the .conf is just another syntax and can express the same type of
things as the .json format (see
https://jbrowse.org/docs/faq.html#what-are-the-different-config-file-formats
)


-Colin

On Wed, Aug 4, 2021 at 12:42 PM Dinesh Sharma <ru...@gm...> wrote:

> can we use the .conf instead of the .json ?
>
>
> On Wed, Aug 4, 2021 at 10:11 PM Dinesh Sharma <ru...@gm...> wrote:
>
>> Awesome, thanks!
>>
>> On Wed, Aug 4, 2021 at 10:08 PM Colin <col...@gm...> wrote:
>>
>>> You would need a VCF file to load the SNPs
>>>
>>> Then you would create a "tabix" index of the VCF
>>>
>>> bgzip yourfile.vcf
>>> tabix yourfile.vcf.gz
>>>
>>> These two commands create yourfile.vcf.gz and yourfile.vcf.gz.tbi
>>>
>>>
>>> Then see
>>>
>>> https://jbrowse.org/docs/variants.html
>>>
>>>
>>> You can hand-edit your trackList.json file to say
>>>
>>> {
>>>   "tracks": [
>>> ... other tracks here ....
>>>     {
>>>       "label": "mysnps",
>>>       "urlTemplate": "yourfile.vcf.gz",
>>>       "type": "CanvasVariants",
>>>       "storeClass": "JBrowse/Store/SeqFeature/VCFTabix"
>>>     }
>>>   ]
>>> }
>>>
>>> To put it on the web, you would need a web server probably. See
>>> https://jbrowse.org/docs/faq.html#what-webserver-is-needed-for-jbrowse
>>>
>>> You can also use "static hosting" like github pages or amazon s3 to host
>>> jbrowse
>>>
>>> -Colin
>>>
>>>
>>> On Wed, Aug 4, 2021 at 11:56 AM Dinesh Sharma <ru...@gm...> wrote:
>>>
>>>> Hi Colin
>>>> I again got stuck on some tasks over Jbrowse.
>>>> This time I am working on integrating SNP (single nucleotide
>>>> polymorphism) track in Jbrowse, so while going through the various
>>>> tutorials I am not able to find a solution for the integration of SNPs, can
>>>> you please help me out with this?
>>>> Further I want this Jbrowser to be made available on www, how can I do
>>>> that?
>>>> Please help me out as I am totally new to these things.
>>>> Thanks and regards
>>>> Dinesh Sharma
>>>>
>>>>
>>>> On Wed, Aug 4, 2021 at 9:22 PM Dinesh Sharma <ru...@gm...> wrote:
>>>>
>>>>> Hi Colin
>>>>>
>>>>> On Sat, Jul 31, 2021 at 10:38 AM Dinesh Sharma <ru...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Thank you for the information.
>>>>>>
>>>>>> On Fri, 30 Jul 2021 at 11:19 PM, Colin <col...@gm...> wrote:
>>>>>>
>>>>>>> Hi Dinesh,
>>>>>>>
>>>>>>> You can probably ignore this dependency
>>>>>>>
>>>>>>> The use of libgd2 is a very old feature which sometimes pre-prepares
>>>>>>> "image tiles" for example for a wiggle track into PNG files for jbrowse to
>>>>>>> load. These days, this is not needed, as we have a special bigwig parser
>>>>>>> that runs on the client side
>>>>>>>
>>>>>>> You can even use jbrowse without even installing dependencies in
>>>>>>> some cases: if you only use indexed file formats you do not even need to
>>>>>>> run perl scripts
>>>>>>>
>>>>>>> See https://jbrowse.org/docs/tutorial.html
>>>>>>>
>>>>>>> If you want more info let me know
>>>>>>>
>>>>>>> Thanks,
>>>>>>> -Colin
>>>>>>>
>>>>>>> On Fri, Jul 30, 2021 at 11:19 AM Dinesh Sharma <ru...@gm...>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hello
>>>>>>>> to introduce myself. I am Dinesh Sharma, A Bioinformatics PhD
>>>>>>>> Scholar at IIT Delhi, India.
>>>>>>>> I have been working on a genomics problem where at last I need to
>>>>>>>> showcase my results on a genome browser.
>>>>>>>> Since i had already used Jbrowse in past (version 1.16) and was
>>>>>>>> hoping that it will still work for me this time too, i tried installing the
>>>>>>>> Jbrowse 1.16 on my linux system, however as a prerequisite I need to
>>>>>>>> install the libgd2-noxpm-dev on linux 18.04, since the aforementioned
>>>>>>>> package is no longer available, I am not able to process with the
>>>>>>>> installation.
>>>>>>>> The new version Jbrowse 2 is a bit difficult for me to grasp and
>>>>>>>> hence i request you to please help me with the issue.
>>>>>>>>
>>>>>>>> Thanks and Regards
>>>>>>>> Dinesh Sharma
>>>>>>>> PhD Scholar
>>>>>>>> KSBS, SCFBio
>>>>>>>> IIT Delhi
>>>>>>>>
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>>>>>>>> Gmo...@li...
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>>>>>>>>
>>>>>>>