sequencetubemaps: A JavaScript module for the visualization of genomic sequence graphs.
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg.
Documentation
Important Notes
- Module Name: sequencetubemaps (see the modules page for more information)
- To start seqauencetubemap please start interactive session with 2 tunnel (see tunneling, and copy the whole directory to local.
- SEQTM sequencetubemaps installation directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=4g --gres=lscratch:10 -T -T [user@cn3144 ~]$ module load sequencetubemaps
[user@cn3144 ]$ cd /data/$USER; cp -r SEQTM . [user@cn3144 ]$ cd sequenceTubeMap [user@cn3144 ]$ npm start > sequence-tube-maps@0.1.0 start [backend] [backend] > sequence-tube-maps@0.1.0 serve [backend] > node ./src/server.mjs "42583" [backend] [backend] TubeMapServer listening on http://:::3000 [frontend] Attempting to bind to HOST environment variable: 127.0.0.1 [frontend] If this was unintentional, check that you haven't mistakenly set it in your shell. [frontend] Learn more here: https://cra.link/advanced-config [frontend] [frontend] [HPM] Proxy created: /api -> http://localhost:3000 [frontend] [HPM] Proxy created: /api/v0 -> http://localhost:3000 [frontend] (node:1074683) [DEP_WEBPACK_DEV_SERVER_ON_AFTER_SETUP_MIDDLEWARE] DeprecationWarning: 'onAfterSetupMiddleware' option is deprecated. Please use the 'setupMiddlewares' option. [frontend] (Use `node --trace-deprecation ...` to show where the warning was created) [frontend] (node:1074683) [DEP_WEBPACK_DEV_SERVER_ON_BEFORE_SETUP_MIDDLEWARE] DeprecationWarning: 'onBeforeSetupMiddleware' option is deprecated. Please use the 'setupMiddlewares' option. [frontend] Starting the development server... [frontend] [frontend] Compiled successfully! [frontend] [frontend] You can now view sequence-tube-maps in the browser. [frontend] [frontend] http://127.0.0.1:41719 [frontend] Note that the development build is not optimized. [frontend] To create a production build, use npm run build. [frontend] [frontend] webpack compiled successfully#wait until the server start successfully, then copy the url to web browser, eg: http://127.0.0.1:41719
