small fixes

README.md

@@ -7,6 +7,6 @@ Visit: https://niema-lab.github.io/ViralWasm-Consensus/ to run the pipeline.
 ### ViralWasm-Consensus Offline
 **Prerequisites**: Python (Can be downloaded here: https://www.python.org/downloads/)
 
-To run the pipeline locally without internet, download the latest release of ViralWasm-Consensus: https://github.com/Niema-Lab/ViralWasm-Consensus/archive/master.zip. After, extract the folder, and click on the `run_website.py` file. 
+To run the pipeline locally without internet, download the latest release of ViralWasm-Consensus: https://github.com/Niema-Lab/ViralWasm-Consensus/archive/master.zip. After, extract the folder, and right click on the `run_website.py` file and select "Open with Python". 
 
 Note: When starting the website for the first time offline, you may be prompted with a firewall warning. Click "Allow Access" to run the pipeline.

src/App.jsx

@@ -586,7 +586,7 @@ export class App extends Component {
 		}
 
 		LOG("Executing command: " + fastpCommand);
-		await CLI.exec(fastpCommand);
+		LOG((await CLI.exec(fastpCommand)).stderr);
 		// TODO: Is there a better way to append data w/o an additional read + append? 
 		return await CLI.fs.readFile(TEMP_FASTP_OUTPUT);
 	}
@@ -648,7 +648,7 @@ export class App extends Component {
 		}
 
 		await this.state.CLI.fs.truncate(file, 0);
-		await this.state.CLI.fs.unlink(file);
+		// await this.state.CLI.fs.unlink(file);
 	}
 
 	showOfflineInstructions = (e) => {
@@ -722,7 +722,7 @@ export class App extends Component {
 										</span>
 									}
 								</label>
-								<select className="form-select" aria-label="Default select example" id="common-sequences" value={this.state.preloadedRef ?? ''} onChange={this.setPreloadedRef}>
+								<select className={`form-select  ${!this.state.refFileValid && 'is-invalid'}`} aria-label="Default select example" id="common-sequences" value={this.state.preloadedRef ?? ''} onChange={this.setPreloadedRef}>
 									<option value="">Select a Reference Sequence</option>
 									{this.state.preloadRefOptions}
 								</select>