Keith Suderman ksuderman

GitHub App Token Setup for Galaxy Helm Chart Updates

This document explains how to create a GitHub App token for the workflow that automatically creates PRs to update the Galaxy Helm chart when new Galaxy releases are tagged.

Why Use GitHub App Tokens?

GitHub App tokens are more secure than Personal Access Tokens (PATs) because they provide:

Better Security: Scoped permissions, automatic token rotation
Better Audit Trail: Actions appear as performed by the app
No User Dependencies: Doesn't depend on individual user accounts

Parallel Tool Loading Results

Date: 2026-02-03 Cluster: ks-gcp-test (GCP) Galaxy Image: ksuderman/galaxy-guerler:26.0.dev0 Tools: ~2,776 total (~2,673 from CVMFS, 103 local)

Test Configurations

| Test | Workers | Configuration |

GCP Batch Job Runners Comparison

Galaxy supports two approaches for dispatching jobs to Google Cloud Batch: the Direct GCP Batch Runner and the Pulsar GCP Batch Runner. Each has distinct architectures and trade-offs.

Architecture Overview

Direct GCP Batch Runner (`gcp_batch`)

Runner class: galaxy.jobs.runners.gcp_batch:GoogleCloudBatchJobRunner
File access: NFS mount from Kubernetes cluster

Installations instructions

PR #314 had the unfortunate side effect of breaking some tools with permission denied or file not found errors. This affects Helms chart versions 5.10.0 through 5.14.0. Until that PR is rolled back please add the above YAML snippet when installing Galaxy to Kubernetes with the Galaxy Helm chart.

Use curl to download the nfs-fix.yml file. If you copy/paste the nfs-fix.yml file be sure to do so from the raw view

curl -o nfs-fix.yml https://gist.githubusercontent.com/ksuderman/7147b41832ab9434a243fbe58141a7a4/raw/c29820b60de205b0ab55d9d1c92acdaffa3894bb/nfs-fix.yml

Include the nfs-fix.yml file as one of the --values files in the helm install command.

The approximate number and type of each kind of tests run as GitHub actions as of Oct 30, 2023

Test	Number
API	1724
Client	834
Converter	109
DB Migration	92
Framework	360
Integration	889

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<meta name="viewport" content="width=device-width, initial-scale=1.0">
	<title>Pulsar vs GCP Batch: Runtime Comparison</title>
	<script src="https://cdn.jsdelivr.net/npm/chart.js@4.4.7/dist/chart.umd.min.js"></script>
	<style>
	* { box-sizing: border-box; margin: 0; padding: 0; }
	body {

	apiVersion: v1
	kind: Pod
	metadata:
	name: gxy-galaxy-7sfwd-bcf7s
	generateName: gxy-galaxy-7sfwd-
	namespace: galaxy
	uid: 6d31be0a-146b-498a-82ad-1cd91f99d7ac
	resourceVersion: '77286'
	creationTimestamp: '2024-05-11T08:49:46Z'
	labels:

	# A simple timing test to compare lazy and greedy string interpolation
	# in log messages

	import timeit

	# Debug messages will not be logged
	SETUP = '''
	import logging
	logging.basicConfig(level=logging.WARNING)
	log = logging.getLogger("mylogger")

	#!/usr/bin/env python3

	import os
	import sys
	import yaml
	import argparse
	from jinja2 import Template
	from pprint import pprint

	def render_template(template, values):