gmod-ajax — JBrowse list

Re: [Gmod-ajax] Formats supported by JBrowse 2

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

Hi Charan,

I'm not sure I understand what you are describing. Where are these error
messages you see? Screenshots could help. Also, can you describe how you
are adding the tracks (e.g. via CLI add-track, or admin-server, etc.)?

JBrowse does support tabix-indexed GFF3 files (e.g. myfile.gff3.gz with
myfile.gff3.gz.tbi), so it seems like the files you want to use would be
supported.

Also, make sure the bucket serving the files has the correct CORS
configuration (see here
<https://github.com/GMOD/jbrowse-components/discussions/2216> for more
details).

Best,
Garrett

On Mon, Aug 30, 2021 at 12:22 PM Sunny Charan <cha...@gm...> wrote:

> Hi,
>
> I am in the process of setting up JBrowse 2 (1.3.5) on AWS EC2 instance.
>
> So far I installed the JBrowse 2 but when I was trying to "Add Tracks"
> using the Object URL from S3 bucket which are in the .gff3 and .gz
> extension.  I see a prompt saying either one of the following:
>
>    1. Error: TypeError: NetworkError when attempting to fetch resources.
>    2. This format is not supported by this version and is supported in
>    the latest version. I am reiterating again that I am using the latest
>    release 1.3.5.
>
> So, please help me further in doing the setup in a successful way where I
> can upload the tracks without any issues. And also if there are any
> specific file formats JBrowse 2 is supported which I am unaware of.
>
> --
> Thanks,
> Charan
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Formats supported by JBrowse 2

[Sunny C. <cha...@gm...>]

Hi,

I am in the process of setting up JBrowse 2 (1.3.5) on AWS EC2 instance.

So far I installed the JBrowse 2 but when I was trying to "Add Tracks"
using the Object URL from S3 bucket which are in the .gff3 and .gz
extension.  I see a prompt saying either one of the following:

   1. Error: TypeError: NetworkError when attempting to fetch resources.
   2. This format is not supported by this version and is supported in the
   latest version. I am reiterating again that I am using the latest release
   1.3.5.

So, please help me further in doing the setup in a successful way where I
can upload the tracks without any issues. And also if there are any
specific file formats JBrowse 2 is supported which I am unaware of.

-- 
Thanks,
Charan

Re: [Gmod-ajax] JBrowse Update 1.3.3 to 1.3.5(latest release)

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

Ah, sorry there was some misunderstanding. The jbrowse/cli is can be
upgraded using

    npm install -g @jbrowse/cli


Note that the CLI tool is basically only used to fetch the latest version
of jbrowse-web. The @jbrowse/cli tool doesn't run on your server in the
background or anything like that. It's only purpose is to download e.g.
this file
https://github.com/GMOD/jbrowse-components/releases/download/v1.3.5/jbrowse-web-v1.3.5.zip
and unzip it, and then it has the additional tools to add-track,
add-assembly, etc. It's good to keep the @jbrowse/cli tool up to date just
since you will get bugfixes and stuff but it's not critical to upgrade
to @jbrowse/cli to get the latest jbrowse-web release.

I will try to make a FAQ entry on this since it is a little confusing, but
hope that helps.



-Colin

On Fri, Aug 27, 2021 at 11:13 AM Sunny Charan <cha...@gm...> wrote:

> Hi Colin, no luck again :-(
>
> I cleared the cache with:
> ubuntu@ip-***-***-*-***:~$ sudo sysctl vm.drop_caches=3
>
> And checked the Jbrowse version:
> ubuntu@ip-***-***-*-***:~$ jbrowse --version
> @jbrowse/cli/1.3.3 linux-x64 node-v10.19.0
>
>
> Am I missing anything here? Please let me know.
>
> On Fri, Aug 27, 2021 at 10:38 AM Colin <col...@gm...> wrote:
>
>> When I tried this locally, it upgraded successfully. You might try
>> clearly your cache and refresh page
>>
>> # start with v1.3.3
>> jbrowse create -t v1.3.3 foldername
>> # upgrade to latest
>> jbrowse upgrade foldername
>>
>> Note that v1.3.5 misreports as v1.3.4 (due to
>> https://github.com/GMOD/jbrowse-components/issues/2256) but it if you
>> had v1.3.3 and it now says v1.3.4 then it was a successful upgrade :)
>>
>> -Colin
>>
>> On Fri, Aug 27, 2021 at 10:13 AM Sunny Charan <cha...@gm...>
>> wrote:
>>
>>> Hi Colin,
>>>
>>> Thanks for responding so quickly.
>>>
>>> I ran "jbrowse upgrade jbrowse2/" and checked the JBrowse version, it
>>> still shows 1.3.3.
>>>
>>> Do I need to follow any other steps further?
>>>
>>> Please let me know with details.
>>>
>>> On Thu, Aug 26, 2021 at 6:14 PM Colin <col...@gm...> wrote:
>>>
>>>> Hi Sunny,
>>>>
>>>> Thanks for asking. If you have previously run e.g.
>>>>
>>>>     jbrowse create yourdirectory
>>>>
>>>> And this downloaded e.g. 1.3.3
>>>>
>>>> Then you should be able to now run
>>>>
>>>>     jbrowse upgrade yourdirectory
>>>>
>>>> And it will download the latest release and install it over your old
>>>> version
>>>>
>>>>
>>>> Alternatively, you could run
>>>>
>>>>     jbrowse create newdirectory
>>>>
>>>> And manually move some of the files (e.g. bam, bigwig, and config.json
>>>> file from the old directory) over into newdirectory
>>>>
>>>> Hope that helps
>>>> -Colin
>>>>
>>>> On Thu, Aug 26, 2021 at 5:55 PM Sunny Charan <cha...@gm...>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> How to update Jbrowse 1.3.3 to 1.3.5 without uninstalling the
>>>>> existing version(1.3.3)?
>>>>>
>>>>> Please share with me detailed instructions. Thanks in advance!
>>>>>
>>>>> --
>>>>> Thanks,
>>>>> Charan
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>>
>>> --
>>> Thanks,
>>> Charan
>>>
>>
>
> --
> Thanks,
> Charan
>

Re: [Gmod-ajax] JBrowse Update 1.3.3 to 1.3.5(latest release)

[Sunny C. <cha...@gm...>]

Hi Colin, no luck again :-(

I cleared the cache with:
ubuntu@ip-***-***-*-***:~$ sudo sysctl vm.drop_caches=3

And checked the Jbrowse version:
ubuntu@ip-***-***-*-***:~$ jbrowse --version
@jbrowse/cli/1.3.3 linux-x64 node-v10.19.0


Am I missing anything here? Please let me know.

On Fri, Aug 27, 2021 at 10:38 AM Colin <col...@gm...> wrote:

> When I tried this locally, it upgraded successfully. You might try clearly
> your cache and refresh page
>
> # start with v1.3.3
> jbrowse create -t v1.3.3 foldername
> # upgrade to latest
> jbrowse upgrade foldername
>
> Note that v1.3.5 misreports as v1.3.4 (due to
> https://github.com/GMOD/jbrowse-components/issues/2256) but it if you had
> v1.3.3 and it now says v1.3.4 then it was a successful upgrade :)
>
> -Colin
>
> On Fri, Aug 27, 2021 at 10:13 AM Sunny Charan <cha...@gm...> wrote:
>
>> Hi Colin,
>>
>> Thanks for responding so quickly.
>>
>> I ran "jbrowse upgrade jbrowse2/" and checked the JBrowse version, it
>> still shows 1.3.3.
>>
>> Do I need to follow any other steps further?
>>
>> Please let me know with details.
>>
>> On Thu, Aug 26, 2021 at 6:14 PM Colin <col...@gm...> wrote:
>>
>>> Hi Sunny,
>>>
>>> Thanks for asking. If you have previously run e.g.
>>>
>>>     jbrowse create yourdirectory
>>>
>>> And this downloaded e.g. 1.3.3
>>>
>>> Then you should be able to now run
>>>
>>>     jbrowse upgrade yourdirectory
>>>
>>> And it will download the latest release and install it over your old
>>> version
>>>
>>>
>>> Alternatively, you could run
>>>
>>>     jbrowse create newdirectory
>>>
>>> And manually move some of the files (e.g. bam, bigwig, and config.json
>>> file from the old directory) over into newdirectory
>>>
>>> Hope that helps
>>> -Colin
>>>
>>> On Thu, Aug 26, 2021 at 5:55 PM Sunny Charan <cha...@gm...>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> How to update Jbrowse 1.3.3 to 1.3.5 without uninstalling the
>>>> existing version(1.3.3)?
>>>>
>>>> Please share with me detailed instructions. Thanks in advance!
>>>>
>>>> --
>>>> Thanks,
>>>> Charan
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>
>> --
>> Thanks,
>> Charan
>>
>

-- 
Thanks,
Charan

Re: [Gmod-ajax] JBrowse Update 1.3.3 to 1.3.5(latest release)

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

When I tried this locally, it upgraded successfully. You might try clearly
your cache and refresh page

# start with v1.3.3
jbrowse create -t v1.3.3 foldername
# upgrade to latest
jbrowse upgrade foldername

Note that v1.3.5 misreports as v1.3.4 (due to
https://github.com/GMOD/jbrowse-components/issues/2256) but it if you had
v1.3.3 and it now says v1.3.4 then it was a successful upgrade :)

-Colin

On Fri, Aug 27, 2021 at 10:13 AM Sunny Charan <cha...@gm...> wrote:

> Hi Colin,
>
> Thanks for responding so quickly.
>
> I ran "jbrowse upgrade jbrowse2/" and checked the JBrowse version, it
> still shows 1.3.3.
>
> Do I need to follow any other steps further?
>
> Please let me know with details.
>
> On Thu, Aug 26, 2021 at 6:14 PM Colin <col...@gm...> wrote:
>
>> Hi Sunny,
>>
>> Thanks for asking. If you have previously run e.g.
>>
>>     jbrowse create yourdirectory
>>
>> And this downloaded e.g. 1.3.3
>>
>> Then you should be able to now run
>>
>>     jbrowse upgrade yourdirectory
>>
>> And it will download the latest release and install it over your old
>> version
>>
>>
>> Alternatively, you could run
>>
>>     jbrowse create newdirectory
>>
>> And manually move some of the files (e.g. bam, bigwig, and config.json
>> file from the old directory) over into newdirectory
>>
>> Hope that helps
>> -Colin
>>
>> On Thu, Aug 26, 2021 at 5:55 PM Sunny Charan <cha...@gm...> wrote:
>>
>>> Hi,
>>>
>>> How to update Jbrowse 1.3.3 to 1.3.5 without uninstalling the
>>> existing version(1.3.3)?
>>>
>>> Please share with me detailed instructions. Thanks in advance!
>>>
>>> --
>>> Thanks,
>>> Charan
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
> --
> Thanks,
> Charan
>

Re: [Gmod-ajax] JBrowse Update 1.3.3 to 1.3.5(latest release)

[Sunny C. <cha...@gm...>]

Hi Colin,

Thanks for responding so quickly.

I ran "jbrowse upgrade jbrowse2/" and checked the JBrowse version, it still
shows 1.3.3.

Do I need to follow any other steps further?

Please let me know with details.

On Thu, Aug 26, 2021 at 6:14 PM Colin <col...@gm...> wrote:

> Hi Sunny,
>
> Thanks for asking. If you have previously run e.g.
>
>     jbrowse create yourdirectory
>
> And this downloaded e.g. 1.3.3
>
> Then you should be able to now run
>
>     jbrowse upgrade yourdirectory
>
> And it will download the latest release and install it over your old
> version
>
>
> Alternatively, you could run
>
>     jbrowse create newdirectory
>
> And manually move some of the files (e.g. bam, bigwig, and config.json
> file from the old directory) over into newdirectory
>
> Hope that helps
> -Colin
>
> On Thu, Aug 26, 2021 at 5:55 PM Sunny Charan <cha...@gm...> wrote:
>
>> Hi,
>>
>> How to update Jbrowse 1.3.3 to 1.3.5 without uninstalling the
>> existing version(1.3.3)?
>>
>> Please share with me detailed instructions. Thanks in advance!
>>
>> --
>> Thanks,
>> Charan
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
Thanks,
Charan

Re: [Gmod-ajax] JBrowse Update 1.3.3 to 1.3.5(latest release)

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

Hi Sunny,

Thanks for asking. If you have previously run e.g.

    jbrowse create yourdirectory

And this downloaded e.g. 1.3.3

Then you should be able to now run

    jbrowse upgrade yourdirectory

And it will download the latest release and install it over your old version


Alternatively, you could run

    jbrowse create newdirectory

And manually move some of the files (e.g. bam, bigwig, and config.json file
from the old directory) over into newdirectory

Hope that helps
-Colin

On Thu, Aug 26, 2021 at 5:55 PM Sunny Charan <cha...@gm...> wrote:

> Hi,
>
> How to update Jbrowse 1.3.3 to 1.3.5 without uninstalling the
> existing version(1.3.3)?
>
> Please share with me detailed instructions. Thanks in advance!
>
> --
> Thanks,
> Charan
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse Update 1.3.3 to 1.3.5(latest release)

[Sunny C. <cha...@gm...>]

Hi,

How to update Jbrowse 1.3.3 to 1.3.5 without uninstalling the
existing version(1.3.3)?

Please share with me detailed instructions. Thanks in advance!

-- 
Thanks,
Charan

Re: [Gmod-ajax] [apollo] an error was encountered when displaying this track

[Nathan D. <nd...@gm...>]

I’ve never tested in under that scenario. 

If you are going to be handling onClick events, I would probably configure it by hand.

Nathan 


> On Aug 9, 2021, at 2:06 AM, Michał T. Lorenc <m.t...@gm...> wrote:
> 
> Hi,
> While uploading a GFF3 file into Apollo via the GUI and adding the below onClick event, I got an error was encountered when displaying this track
> 
> <image.png>
> 
> 
> <image.png>
> What did I miss?
> 
> Thank you in advance,
> 
> Michal
> 
> -- 
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.

Re: [Gmod-ajax] an error was encountered when displaying this track

[Michał T. L. <m.t...@gm...>]

P.S. I was wrong the onClick works if I don't write Annotation into
Category. Do you think it is a bug?

On Mon, Aug 9, 2021 at 7:06 PM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi,
> While uploading a GFF3 file into Apollo via the GUI and adding the below
> onClick event, I got *an error was encountered when displaying this track*
>
> [image: image.png]
>
>
> [image: image.png]
> What did I miss?
>
> Thank you in advance,
>
> Michal
>

[Gmod-ajax] an error was encountered when displaying this track

[Michał T. L. <m.t...@gm...>]

Hi,
While uploading a GFF3 file into Apollo via the GUI and adding the below
onClick event, I got *an error was encountered when displaying this track*

[image: image.png]


[image: image.png]
What did I miss?

Thank you in advance,

Michal

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
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>>> Gmod-ajax mailing list
>>>>>>>> Gmo...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>>>
>>>>>>>

Re: [Gmod-ajax] Regarding Jbrowse Download

[Dinesh S. <ru...@gm...>]

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
>>>>>>
>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>

Re: [Gmod-ajax] Regarding Jbrowse Download

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

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
>>>>>
>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>

Re: [Gmod-ajax] Regarding Jbrowse Download

[Dinesh S. <ru...@gm...>]

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
>>
> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Regarding Jbrowse Download

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

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
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Regarding Jbrowse Download

[Dinesh S. <ru...@gm...>]

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

[Gmod-ajax] JBrowse/GMOD Birds of a Feather at BOSC

[Scott C. <sc...@sc...>]

Hi,

Here's a reminder that "today" (that is, tomorrow morning for me) there is
a Birds of a Feather meeting to discuss GMOD topics at ISMB/BOSC, including
JBrowse but other GMOD topics as well. The BoF starts at 15:20 UTC (7:20
PDT, 10:20 EDT) on July 28. If you are attending ISMB, please feel free to
drop in and chat about good stuff you're doing or want to do:

https://ismbeccb2021.showcare.io/sessions/28-3-bof/

Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Jbrowse2

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

Hi there, I imagine this is connected to the question at
https://github.com/GMOD/jbrowse-components/discussions/2150

Sorry for the delay in answering


I think that this will basically depend on your server setup. jbrowse 2
will not really try to do anything fancy here so it is just trying to
request a file that you specified, so if you are using a dev server for
flask that is on port 5000 (not really familiar with flask personally, but
just guessing) then if flask has a static files directory
https://flask.palletsprojects.com/en/2.0.x/tutorial/static/ you could maybe
put this GRCh38.aliases.txt file in there

Let me know if that helps
-Colin

On Mon, Jul 26, 2021 at 1:37 PM Vikash Pandey <vik...@um...> wrote:

> Dear developers
>
>
> I would like to embed Jbrowse2 in my flask app.
>
>
> I am getting this problem and was wondering if you know how to fix it.
>
>
>
> jbrowse-linear-view.js:46 GET http://127.0.0.1:5000/GRCh38.aliases.txt
> 404 (NOT FOUND)
>
>
> Thank you.
>
>
> Best
>
> Vikash
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Jbrowse2

[Vikash P. <vik...@um...>]

Dear developers


I would like to embed Jbrowse2 in my flask app.


I am getting this problem and was wondering if you know how to fix it.



jbrowse-linear-view.js:46 GET http://127.0.0.1:5000/GRCh38.aliases.txt 404 (NOT FOUND)


Thank you.


Best

Vikash

[Gmod-ajax] GMOD/JBrowse Birds of a Feather at BOSC

[Scott C. <sc...@sc...>]

Hello,

If you are attending BOSC or any other ISCM meeting next week, please feel
free to come to the GMOD/JBrowse Birds of a Feather on Wednesday, July 28
from 15:20 to 16:20 UTC (yes, that is 7:20 AM west coast US time). Several
GMOD folks will be there; you can talk about new developments with JBrowse
2 or discuss any of several other GMOD components.

https://www.iscb.org/ismbeccb2021-program/bof#bof4

The meeting will take place in the Research Exchange Forum, which hopefully
will make sense when attending the meeting!  :-)

See you all next week!

Scott



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] onClick problem with URL

[Michał T. L. <m.t...@gm...>]

Hi,
I usually use the below *onClick* event to redirect the user to NCBI side.


















*      {           "compress" : 1,         "key" :
"XPonly-besthit_addNoXP-keep-clean2",         "label" :
"XPonly-besthit_addNoXP-keep-clean2",         "onClick" : {
"action" : "newWindow",            "label" : "search at NCBI",
"url" : "http://www.ncbi.nlm.nih.gov/protein/{NCBI}
<http://www.ncbi.nlm.nih.gov/protein/{NCBI}>"         },
 "storeClass" : "JBrowse/Store/SeqFeature/NCList",         "style" : {
      "className" : "feature",            "label" : false         },
 "trackType" : "HTMLFeatures",         "type" : "HTMLFeatures",
 "urlTemplate" :
"tracks/XPonly-besthit_addNoXP-keep-clean2/{refseq}/trackData.jsonz"
},*

Unfortunately, we have got a new GFF3 file that does not have an NCBI field
instead the XP id is saved end the end of the Note field:

*NbLab350C00     scallop mRNA    1275635 1284161 .       +       .
ID=NbL00g00020.1;Parent=NbL00g00020;RPKM=3.9972;Note=armadillo
repeat-containing protein 8 LOC109230773
XP_019251743.1;evalue=0.00;cov=325.3290*

How could the XP id be extracted and added to the URL?

Thank you in advance,

Michal

[Gmod-ajax] Apollo 2.6.5 released

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

Apollo 2.6.5 has been released:
https://github.com/GMOD/Apollo/releases/tag/2.6.5

This release contains a fix that caused users to not be able to build due
to a change to the Grails servers. See grails/grails-core#11825
<https://github.com/grails/grails-core/issues/11825>. If you are not able
to upgrade Apollo to this version but still are experiencing build
failures, you can update your BuildConfig.groovy file as in this PR: 2624
<https://github.com/GMOD/Apollo/pull/2624>.

*Features*

   - Added method to upload bulk functional annotations from JSON in the
   interface. 2617 <https://github.com/GMOD/Apollo/pull/2617>, 2618
   <https://github.com/GMOD/Apollo/pull/2618>
   - Added a "topLevel" option to the "getFeatures" web services endpoint
   that causes the endpoint to return top-level (e.g. gene) features. 2616
   <https://github.com/GMOD/Apollo/pull/2616>

*Bug Fixes*

   - Removed deprecation from SequenceController.sequenceByName. 2619
   <https://github.com/GMOD/Apollo/pull/2619>
   - Fix contextual menu for blastview tracks. Thanks @abretaud
   <https://github.com/abretaud>. 2621
   <https://github.com/GMOD/Apollo/pull/2621>
   - Make Python libraries installed globally in Docker image. 2622
   <https://github.com/GMOD/Apollo/pull/2622>
   - Update mavenRepo to fix error grails server error during build, see
   grails/grails-core#11825
   <https://github.com/grails/grails-core/issues/11825>. 2624
   <https://github.com/GMOD/Apollo/pull/2624>

Full change long for all versions can be found here:
https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details:
http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here:
https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found.
Active mailing list (ap...@lb...) and google group
<https://groups.google.com/a/lbl.gov/g/apollo>.

Re: [Gmod-ajax] VL: JBowse

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

If you need the whole genome, it may be advisable to ask the creator of the
instance to provide you the  BED file they used to load it originally


-Colin



On Fri, May 21, 2021 at 7:46 AM Jenni Tolppanen (TAU) <
jen...@tu...> wrote:

>
>
> ------------------------------
> *Lähettäjä:* Jenni Tolppanen (TAU) <jen...@tu...>
> *Lähetetty:* torstai 6. toukokuuta 2021 9.31
> *Vastaanottaja:* Scott Cain <sc...@sc...>
> *Aihe:* VS: [Gmod-ajax] JBowse
>
> Hi,
>
> Thank you for the quick response!
>
> What should I do if I want BED files? And is it possible to obtain BED
> file from all the genome at once?
>
> -Jenni
> ------------------------------
> *Lähettäjä:* Scott Cain <sc...@sc...>
> *Lähetetty:* torstai 22. huhtikuuta 2021 23.09
> *Vastaanottaja:* Jenni Tolppanen (TAU) <jen...@tu...>
> *Kopio:* gmo...@li... <gmo...@li...>
> *Aihe:* Re: [Gmod-ajax] JBowse
>
> Hi Jenni,
>
> That is very strange--I've never seen that dialog box look like that.
> There are two options in that box: Visible region or whole reference
> sequence which correspond to the two circles you can check off (with
> visible region selected by default and selected in the picture you sent).
> Even though the text is very "smooshed" the dialog box should still work,
> so you can select either of the circles and click "Save" and it will save a
> GFF3 file with the data to your computer.
>
> Please let us know if you have any problems with this,
> Scott
>
>
> On Thu, Apr 22, 2021 at 12:42 PM Jenni Tolppanen (TAU) <
> jen...@tu...> wrote:
>
> Hi,
>
> I have a problem when I try to download data from the browser. For example
> I would like to get all common putative enhancers. Attached picture shows
> the problem. What should I do?
>
> Yours faithfully,
>
> Jenni Tolppanen
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Jbrowse 2 feature questions

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

Hi there, glad to hear the interest!

The ability to navigate with gene names and URL bar queries is currently
being worked on, shouldn't be a forever thing.

We have a search for gene name PR in the works here
https://github.com/GMOD/jbrowse-components/pull/1881 and navigating with
the URL bar here https://github.com/GMOD/jbrowse-components/pull/1798

If interested you can subscribe to those for updates...both are getting
polished up

-Colin

On Fri, May 21, 2021 at 12:40 PM <Do...@hi...> wrote:

> Dear JB2 support,
>
>
>
> We have used JB1 for some of our projects before (acknowledged and cited
> your work properly of course), and thanks for this very useful tool! We
> also tried version 2 recently but found out that the following 2 features
> are not supported in the new version, as mentioned at
> https://jbrowse.org/jb2/features :
>
> Name searching e.g. ability to type a gene name/ID to search for it
>
> ❌
>
> ✔️
>
> URL query API e.g. specifying ?loc=chr1:1-100 in URL bar
>
> ❌
>
> ✔️
>
>
>
> Are they intentional (ie JB2 will never support them) or just temporary?
> If JB2 will never support it, is there another way to allow users quickly
> to jump to a specific region on a chromosome by clicking a URL?
>
>
>
> Thanks in advance!
>
>
>
> Alex.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>