gmod / jb2export

A CLI program to generate static image exports for jb2

This repo is being migrated into https://github.com/GMOD/jbrowse-components/tree/main/products/jbrowse-img

jb2export's Issues

Add ability to generate an HTML page with bulk exports and links to a live session(?)

Similar to jigv

Add ability to specify a list of files instead of using raw session.json/assemblies.json/tracks.json configs

Update to work with jexl

On branch jexl_updates and jbrowse-components branch export_svg_wiggle_jexl

I get this error

$ node dist/index.js --config data/config.json --defaultSession --out out.svg
Error: no plugin manager defined for renderer DivSequenceRenderer
    at new RendererType (/home/cdiesh/src/jb2export/node_modules/@jbrowse/core/pluggableElementTypes/renderers/RendererType.js:62:13)
    at DivSequenceRenderer.<anonymous> (/home/cdiesh/src/jb2export/node_modules/@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType.js:48:291)
    at new ServerSideRenderer (/home/cdiesh/src/jb2export/node_modules/@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType.js:59:19)
    at DivSequenceRenderer._createSuperInternal (/home/cdiesh/src/jb2export/node_modules/@jbrowse/plugin-sequence/dist/plugin-sequence.cjs.development.js:208:24)
    at new DivSequenceRenderer (/home/cdiesh/src/jb2export/node_modules/@jbrowse/plugin-sequence/dist/plugin-sequence.cjs.development.js:2122:19)
    at /home/cdiesh/src/jb2export/node_modules/@jbrowse/plugin-sequence/dist/plugin-sequence.cjs.development.js:2209:16
    at /home/cdiesh/src/jb2export/node_modules/@jbrowse/core/PluginManager.js:307:26
    at /home/cdiesh/src/jb2export/node_modules/@jbrowse/core/PluginManager.js:87:20
    at Array.forEach (<anonymous>)
    at /home/cdiesh/src/jb2export/node_modules/@jbrowse/core/PluginManager.js:86:26

Profiling results

Flamegraph from 0x

2113070.0x.tar.gz

The draw mismatches and color scale pops out significantly

command

From https://github.com/davidmarkclements/0x

0x dist/index.js > out.svg

Add a non-lgv example e.g. dotplot

Add example with using a plugin

Throws useLayoutEffect warnings

Consequence of mainthreadrrpc, but may be overcome by upgrading deps

Code doesn't work without internet

Silently fails, no error or warning
Run yarn test produces empty out.svg
To test, turn off wifi on compy

Test with local file path

Fix alignments track export

Program takes longer than the total rendering process to complete?

Running the await renderToSvg sometimes takes significantly shorter than the total program time e.g. 5 seconds vs 25 total

The program console.error logs the output to show rendering time and total program completion is printed by node by default

Not able to get a simple volvox.fa example

jb2export --fasta volvox.fa --configtracks refseq --loc ctgA:1-100

maybe it's my computer but it's causing some fuss

Fix ref renaming

Add ability to load full config and session json files

Probably allow separate ones