From 85d120fe6453e9e1248841076151c28796402494 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Sun, 13 Jul 2025 15:34:01 -0700
Subject: [PATCH] Update Jbrowse CLI version

---
 jbrowse/package.json                |  2 +-
 jbrowse/tools/buildStandaloneCli.js | 68 -----------------------------
 2 files changed, 1 insertion(+), 69 deletions(-)
 delete mode 100644 jbrowse/tools/buildStandaloneCli.js

diff --git a/jbrowse/package.json b/jbrowse/package.json
index 3807eef04..cfe8c7aae 100644
--- a/jbrowse/package.json
+++ b/jbrowse/package.json
@@ -10,7 +10,7 @@
     "build-dev": "npm run build-no-pkg",
     "build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map webpack --config ./config/prod.config.js --progress --profile",
     "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen",
-    "prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@1.7.4 --prefix ./buildCli",
+    "prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@3.2.0 --prefix ./buildCli",
     "jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
   },
   "dependencies": {
diff --git a/jbrowse/tools/buildStandaloneCli.js b/jbrowse/tools/buildStandaloneCli.js
deleted file mode 100644
index fbfd342e9..000000000
--- a/jbrowse/tools/buildStandaloneCli.js
+++ /dev/null
@@ -1,68 +0,0 @@
-// This script is a workaround until pkg supports ES modules: https://github.com/vercel/pkg/issues/1291
-// See also: https://nodejs.org/api/single-executable-applications.html
-// This should be replaced once a better solution is available
-const fs = require('fs');
-const { exec, execSync } = require('child_process');
-
-function convertEs6ToCommonJS(packageName) {
-    const sourceFile = './buildCli/node_modules/@isaacs/cliui/node_modules/' + packageName + '/index.js';
-    const origFile = sourceFile + '.orig';
-    if (fs.existsSync(origFile)) {
-        console.log('File exists, skipping: ' + origFile);
-    } else {
-        console.log('Updating: ' + sourceFile);
-        if (!fs.existsSync(sourceFile)) {
-            throw new Error('Missing file: ' + sourceFile);
-        }
-
-        if (fs.existsSync('./buildCli/' + packageName)) {
-            console.log('Deleting existing index.js file')
-            fs.unlinkSync('./buildCli/' + packageName)
-        }
-
-        try {
-            execSync('npx esbuild --outdir=./buildCli/' + packageName + ' --target=es6 --format=cjs ' + sourceFile)
-        } catch (err) {
-            throw new Error('ERROR: ' + err.message);
-        }
-
-        try {
-            fs.renameSync(sourceFile, origFile)
-        } catch (err){
-            throw new Error('ERROR: ' + err);
-        }
-
-        try {
-            fs.renameSync('./buildCli/' + packageName + '/index.js', sourceFile)
-        } catch (err){
-            throw new Error('ERROR: ' + err);
-        }
-    }
-}
-
-convertEs6ToCommonJS('ansi-regex')
-convertEs6ToCommonJS('ansi-styles')
-convertEs6ToCommonJS('strip-ansi')
-convertEs6ToCommonJS('wrap-ansi')
-convertEs6ToCommonJS('string-width')
-
-const child = exec('npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli', (err, stdout, stderr) => {
-    if (err) {
-        throw new Error('Unable to run pkg: ' + err)
-    }
-});
-
-child.stdout.setEncoding('utf8');
-child.stdout.on('data', function(data) {
-    console.log(data);
-});
-
-child.stderr.setEncoding('utf8');
-child.stderr.on('data', function(data) {
-    console.log(data);
-});
-
-child.on('close', function(code) {
-    console.log('closing pkg: ' + code);
-});
-