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
>