small updates

.github/workflows/website.yml

@@ -50,7 +50,7 @@ jobs:
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v1
-      - name: Push offline mode to master
+      - name: Push Offline Mode to Master
         env: 
           VITE_OFFLINE_VERSION: true
         run: |  

README.md

@@ -4,6 +4,6 @@ A client-side WebAssembly pipeline for viral consensus sequence calling.
 
 Visit: https://niema-lab.github.io/ViralWasm-Consensus/ to run the pipeline.
 
-To run the pipeline locally without internet, download the **offline** version of ViralWasm-Consensus. To do so, download the latest release / repository (https://github.com/Niema-Lab/ViralWasm-Consensus/archive/master.zip) and run the following command:
+To run the pipeline locally without internet, download the **offline** version of ViralWasm-Consensus. To do so, download the latest release / repository (https://github.com/Niema-Lab/ViralWasm-Consensus/archive/master.zip), extract the folder, and click on the `run_website.py` file.
 
-```python3 run_website.py```
+Note: You may be prompted with a firewall warning. Click "Allow Access" to run the pipeline.

run_website.py

@@ -2,9 +2,11 @@
 import socketserver
 import subprocess
 import socket
+import os
 
 PORT = 5000
-DIRECTORY = "dist"
+# get current directory and set it as the directory to serve
+DIRECTORY = os.path.dirname(os.path.realpath(__file__)) + "/dist"
 
 def kill_port_unix(port):
     command = f"lsof -i :{port} -t"

src/App.jsx

@@ -1,4 +1,4 @@
-// TODO: automatically create dist/
+// TODO: is manual release creation okay?  
 // TODO: PWA? 
 import React, { Component } from 'react'
 import Pako from 'pako';
@@ -575,7 +575,7 @@ export class App extends Component {
 		return (
 			<div className="App pb-5">
 				<h2 className="mt-5 mb-2 w-100 text-center">ViralWasm-Consensus</h2>
-				<p className="my-3 w-100 text-center">A serverless WebAssembly-based pipeline for consensus genome generation.<br /> Uses minimap2 v{MINIMAP2_VERSION}, fastp v{FASTP_VERSION}, and ViralConsensus v{VIRAL_CONSENSUS_VERSION} via <a href="https://biowasm.com/" target="_blank" rel="noreferrer">Biowasm</a>. <br /><br /></p>
+				<p className="my-3 w-100 text-center">A serverless WebAssembly-based pipeline for consensus genome generation.<br /> Uses minimap2 v{MINIMAP2_VERSION}, fastp v{FASTP_VERSION}, and ViralConsensus v{VIRAL_CONSENSUS_VERSION} via <a href="https://biowasm.com/" target="_blank" rel="noreferrer">Biowasm</a>. <br />Source code & offline version: <a href="https://github.com/niema-lab/ViralWasm-Consensus/" target="_blank" rel="noreferrer">github.com/niema-lab/ViralWasm-Consensus</a>.<br /></p>
 				<div className="mt-3" id="container">
 					<div id="input" className={`ms-5 me-4 ${this.state.expandedContainer === 'input' && 'full-width-container'} ${this.state.expandedContainer === 'output' && 'd-none'}`}>
 						<div id="input-header" className="mb-3">

src/constants.js

@@ -1,3 +1,4 @@
+// TODO: auto download the versions during the github action? 
 export const VIRAL_CONSENSUS_VERSION = "0.0.3";
 export const MINIMAP2_VERSION = "2.22";
 export const FASTP_VERSION = "0.20.1";