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

[Daniel R. P. <dr...@it...>]

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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