Re: [Gmod-ajax] Trying to test jbrowse-web

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

Hi Daniel!

There are two ways you can approach this

1) Approach it as a "developer" and use our github quickstart guide
https://github.com/gmod/jbrowse-components#quick-start

This basically involves the following commands basically (must use yarn,
not npm)

git clone https://github.com/GMOD/jbrowse-components
cd jbrowse-components
yarn
cd products/jbrowse/web
yarn start

This should automatically launch a JBrowse 2 instance with demo data that
you can browse. Further work at setting up your own data will involve using
steps from (2) below

2) Approach it as a "user" that downloads a pre-built bundle
https://jbrowse.org/jb2/docs/quickstart_web and then, as a user, you can
then follow steps to use the JBrowse CLI tool


The main gist of this is to run the following commands

npm install -g @jbrowse/cli
jbrowse create /var/www/html/jbrowse2
cd /var/www/html/jbrowse2
jbrowse add-assembly ~/yourfile.fa --load copy # this will copy the
yourfile.fa to /var/www/html/jbrowse2 and create a config entry for this
genome
samtools index ~/yourfile.bam
jbrowse add-track ~/yourfile.bam --load copy # this will copy yourfile.fa
to /var/www/html/jbrowse2 and create a track entry for this genome

I hope this helps clarify!



-Colin

On Wed, Oct 14, 2020 at 10:57 AM Daniel Reyes Parrilla <
dr...@it...> wrote:

> Hello,
>
> I have been trying for some hours to use and test the jbrowse-web (
> 0.0.1-beta.26) product of JBrowse2 (
> https://github.com/GMOD/jbrowse-components/tree/master/products/jbrowse-web
> ).I do not know where I am failing and I would like you to do me a favor to
> help me. I have realized that there are a list of packages that have not
> been already published to npm.
>
>    - "@jbrowse/plugin-breakpoint-split-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-circular-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-dotplot-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-hic": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-menus": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
>    - "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-filtering": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-hic": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-menus": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
>    - "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13"
>
> Even though I have deleted them from the package.json file and the
> corePlugins.ts list. With this I suppose that it would work fine.
>
> After that, when I executed npm start it didn't recognize rescripts, so I
> added "@rescripts/cli": "0.0.14",  "@rescripts/rescript-env": "0.0.12" and
> "@rescripts/utilities": "0.0.7", to the package.json but it still gives me
> the following error:
>
> > rescripts --max-http-header-size=100000 start
>
> internal/modules/cjs/loader.js:638
>     throw err;
>     ^
>
> Error: Cannot find module 'react-scripts/config/paths'
>     at Function.Module._resolveFilename
> (internal/modules/cjs/loader.js:636:15)
>     at Function.Module._load (internal/modules/cjs/loader.js:562:25)
>     at Module.require (internal/modules/cjs/loader.js:692:17)
>     at require (internal/modules/cjs/helpers.js:25:18)
>     at Object.<anonymous>
> (/home/daniel/Documentos/jbrowse-web/node_modules/@rescripts/utilities/paths.js:2:27)
>     at Module._compile (internal/modules/cjs/loader.js:778:30)
>     at Object.Module._extensions..js
> (internal/modules/cjs/loader.js:789:10)
>     at Module.load (internal/modules/cjs/loader.js:653:32)
>     at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
>     at Function.Module._load (internal/modules/cjs/loader.js:585:3)
>
> Best regards,
>
> Daniel Reyes
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