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

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Plus, just to keep you posted. I am trying to embed the JBrowse React component in an Angular web application. I am using the following method https://medium.com/@zacky_14189/embedding-react-components-in-angular-the-easy-way-60f796b68aef , and I have gotten a React navbar to work in Angular. There are a few more methods to test. It is only to know if you are interested in knowing more about it and maybe to give punctual supports in case it is needed.

Best regards,

Daniel Reyes
________________________________
De: Daniel Reyes Parrilla
Enviado: jueves, 15 de octubre de 2020 8:29
Para: Colin
CC: gmo...@li...; Rafael Nebot Medina
Asunto: Re: [Gmod-ajax] Trying to test jbrowse-web

It worked! Thank you very much :)
________________________________
De: Colin [col...@gm...]
Enviado: miércoles, 14 de octubre de 2020 16:24
Para: Daniel Reyes Parrilla
CC: gmo...@li...; Rafael Nebot Medina
Asunto: Re: [Gmod-ajax] Trying to test jbrowse-web

Forgot to mention to run `samtools faidx yourfile.fa`, but the https://jbrowse.org/jb2/docs/quickstart_web guide should detail further :)

-Colin

On Wed, Oct 14, 2020 at 11:05 AM Colin <col...@gm...<mailto:col...@gm...>> wrote:
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...<mailto: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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