cmdcolin

Sequence ↔ structure interop: the Mol* harness prototype

Kept out of the react-msaview repo on purpose. The prototype is somebody else's unreleased work — the demo is up but the source repo does not resolve, so nothing here is published. A reverse-engineered critique of it does not belong in a public repo's history. What this argues for our own code lives in react-msaview/agent-docs/ideas/alignment-structure-mapping-layer.md, written to stand on its own without any of the below.

Read 2026-09-10 at . David

cmdcolin

Intro

I used Claude Code Opus 4.8 to generate a response to https://wren.wtf/shower-thoughts/stop-using-opencode/. My prompt: "Please read https://wren.wtf/shower-thoughts/stop-using-opencode/ it is a recent blog post trying to critique the opencode codebase. please try to debunk the post and show misunderstandings. you can cross reference ~/src/opencode source code if you want" and then a couple follow up things to clarify the cors issue, etc.

Note that I do not have a horse in the race, I do not use opencode.

This is v9. of this gist after cross checking it several times. Here is the response:

A response to "Stop Using OpenCode"

cmdcolin

Reply to Arun — odgi subcommands for JBrowse

Hi Arun,

Great to hear about the odgi clone. I'll share some of my efforts to integrate odgi and pangenomes into jbrowse. Big caveat up front: we're still pretty naive about graph/pangenome methods, and the approach we were exploring was frankly a bit weird and specific to shoehorning a graph into a linear genome browser. So please read the below as "here's what we poked at and where we got stuck," not a considered spec — and weight the parts we flag as broadly useful over the parts that are just our own oddball need.

cmdcolin

Notes from a JBrowse pangenome-visualization experiment

Measurements and friction points from ~Feb–May 2026, while trying to drive pangenome visualization in JBrowse from odgi. The prototype has since been removed from our tree; these notes are what's worth keeping.

Environment for all numbers: odgi v0.9.4-2-g405be8f6 built from source, vg v1.69.0, single 16-core box. Test data: HPRC chr20 (hprc-v1.1-mc-grch38.chr20, 919 paths, 1.13 GB .og) and a 51-path volvox toy pangenome.

cmdcolin

(((hg38:0.14961451,Mus_musculus:0.44906740000000006):0.0309181,(((Vicugna_pacos:0.0161542,Camelus_dromedarius:0.01271789):0.0985471,((Hippopotamus_amphibius:0.065968,(Balaenoptera_bonaerensis:0.01679449,((Neophocaena_asiaeorientalis:0.00884101,Delphinapterus_leucas:0.00659375):0.00365908,Tursiops_truncatus:0.01144293):0.013062240000000001):0.0297733):0.00895057,Bos_taurus:0.127401772):0.02603271):0.042973,((Canis_lupus:0.08975158,Leptonychotes_weddellii:0.06130375):0.0858961,Equus_caballus:0.11125822):0.00536403):0.04351754):0.0186332,Trichechus_manatus:0.17252018);

cmdcolin

{
  "plugins": [
    {
      "name": "MsaView",
      "url": "https://jbrowse.org/plugins/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js"
    }
  ],
  "assemblies": [
    {
      "name": "hg38",

cmdcolin

[
  {
    "role": "user",
    "parts": [
      {
        "text": "<session_context>\nThis is the Gemini CLI. We are setting up the context for our chat.\nToday's date is Wednesday, April 15, 2026 (formatted according to the user's locale).\nMy operating system is: linux\nThe project's temporary directory is: /home/cdiesh/.gemini/tmp/jbrowse-components\n- **Workspace Directories:**\n  - /home/cdiesh/src/jbrowse-components\n- **Directory Structure:**\n\nShowing up to 200 items (files + folders). Folders or files indicated with ... contain more items not shown, were ignored, or the display limit (200 items) was reached.\n\n/home/cdiesh/src/jbrowse-components/\n├───_typos.toml\n├───.editorconfig\n├───.gitignore\n├───.ignore\n├───.prettierignore\n├───.prettierrc.json\n├───babel.config.cjs\n├───CHANGELOG.md\n├───CLAUDE.md\n├───CODE_OF_CONDUCT.md\n├───codecov.yml\n├───CONTRIBUTING.md\n├───eslint.config.mjs\n├───global.d.ts\n├───integration.test.js\n├───jest.config.js\n├───LICENSE\n├───package.json\n├───pnpm-lock.yam

cmdcolin

  ▝▜▄     Gemini CLI v0.34.0
    ▝▜▄
   ▗▟▀    Signed in with Google: colin.diesh@gmail.com /auth
  ▝▀      Plan: Gemini Code Assist for individuals /upgrade

╭───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ We're making changes to Gemini CLI that may impact your workflow.                                                                                                                                         │
│ What's Changing: We are adding more robust detection of policy-violating use cases and restricting models for free tier users.                                                                            │
│ How it affects you: If you need use of Gemini pro models you will need to upgrade to a supported paid plan.                                                                                               │

cmdcolin

#!/bin/bash
export OUT=/var/www/html/jbrowse2
sudo apt-get update
sudo apt-get install nodejs wget apache2 tabix samtools minimap2
sudo service apache2 start
## confirm node.js greater than or equal to v18 is installed
node --version
sudo npm install -g @jbrowse/cli
## confirm that the jbrowse CLI is installed
jbrowse --version

cmdcolin

#!/bin/bash
export OUT=/var/www/html/jbrowse2
sudo apt-get update
sudo apt-get install nodejs wget apache2 tabix samtools minimap2
sudo service apache2 start

## confirm node.js greater than or equal to v18 is installed
node --version
sudo npm install -g @jbrowse/cli