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

cmdcolin

#!/bin/bash

## 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
datasets download genome accession GCF_000307795.1 --include gff3,genome --filename hpylori_j99.zip
datasets download genome accession GCF_000982695.1 --include gff3,genome --filename hpylori_26695.zip
datasets download genome accession GCF_025998455.1 --include gff3,genome --filename hpylori_chc155.zip
unzip -o hpylori_j99.zip

cmdcolin

import os
import re
import sys

# Check if command line argument is provided
if len(sys.argv) < 2:
    print("Usage: python script.py <input_file> [output_directory]")
    sys.exit(1)

input_file = sys.argv[1]

cmdcolin

can you remove all chakra styles and just use unstyled divs for example

I'll help you remove all Chakra UI styles from the small-card.tsx file and replace them with unstyled divs. Let me analyze what needs to be changed.

I need to check the util.ts file first to understand the arePropsEqual function that's being used in the component.

╭─  view  succeeded
│ running tool

cmdcolin

GTF to GFF conversion in bioinformatics

These are two very similar formats. But some people are still just very stuck on GTF, despite being less well defined than GFF.

CJS (commonjs) to ESM (ecmascript modules) in javascript

Just replace your require with import right? Sometimes it works, sometimes it doesn't. There is a lot of insanity that goes on, and it is really hard to do a proper technical analysis because ESM is pretty strict while CJS and the

cmdcolin

Text-editor saturday

My text editor avante.nvim is just going crazy. Previously it dumped diffs into the 'chat sidebar', and I'd accept them with "A" in the sidebar then accept all with "ca" in the main area...vibe coding. But the avante.nvim switched to running tools that run the edits instead, and is just going crazy with tool usage despite me having disable_tools enabled. I dunno. Maybe I should file a bug. But this spurred me to try to work holistically on my editing skills this morning. I just looked at my config and tweaked a million things...

Trying out rose-pine

Trying rose-pine color scheme. It is kinda funny with tons of italic but it's cute

cmdcolin

import fs from 'fs'

const tracks = JSON.parse(fs.readFileSync(process.argv[2], 'utf8')) as {
  tracks: any[]
}

const asm = 'B73'
const assemblyNames = [asm]
const base = 'https://jbrowse.maizegdb.org/B73/'
console.log(

cmdcolin

[
  { "role": "user", "type": "message", "content": "hello" },
  {
    "role": "assistant",
    "type": "message",
    "content": "Hello! How can I help you today?\n"
  },
  {
    "role": "user",
    "type": "message",

cmdcolin