Colin Diesh 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"

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.

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.

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


	▝▜▄ 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. │

	#!/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

	#!/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

	#!/bin/bash

	# Build a 3-genome Helicobacter pylori synteny demo for JBrowse 2.
	# Requires: datasets (NCBI), samtools, minimap2, bgzip, tabix, and @jbrowse/cli.
	set -euo pipefail

	## this should be an absolute path. this one is a web accessible directory for apache2
	export OUT=/var/www/html/jbrowse2

	## download and unzip NCBI genomes (filenames match the strain each accession is renamed to below)

	[
	{
	"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