Keith Suderman ksuderman

## helm-app.md

      
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              June 5, 2026 16:22
            
              
                Galaxy Helm Chart Release App Creation
              
          
    Creating the release GitHub App

The release workflow uses a GitHub App (rather than the default GITHUB_TOKEN)
because it must bypass branch protection to push the version-bump commit and
tag to master, publish to another repository, and trigger a downstream repo.
The default GITHUB_TOKEN cannot do these things.

Create the App. Go to the organization's
Settings → Developer settings → GitHub Apps → New GitHub App (an
org-owned App is recommended over a personal one so ownership survives


## github-app-token-setup.md

      
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                ksuderman
                / github-app-token-setup.md
            
            
              Created
              April 16, 2026 18:37
            
              
                GitHub App Token Setup for Galaxy Helm Chart Updates
              
          
    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


## comparison.html
<!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 {

## parallel-tool-loading-results.md

      
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                ksuderman
                / parallel-tool-loading-results.md
            
            
              Created
              February 3, 2026 19:06
            
              
                Parallel tool loading comparison
              
          
    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_COMPARISON.md

      
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                ksuderman
                / GCP_BATCH_COMPARISON.md
            
            
              Created
              January 15, 2026 02:14
            
              
                Compare and contrast the two options available to dispatch Galaxy jobs to Google Batch.
              
          
    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


## scikit.ipynb

      
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                ksuderman
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              August 22, 2025 13:22
            
              
                Jupyter Playbook - scikit 01
              
          
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## Instructions.md

      
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                ksuderman
                / Instructions.md
            
            
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              June 3, 2024 20:07
            
              
                Patch to fix NFS permission problems
              
          
    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.


## gist.txt
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:

## GalaxyTests1C.md

      
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                ksuderman
                / GalaxyTests1C.md
            
            
              Created
              October 30, 2023 19:37
            
              
                Galaxy Test Summary
              
          
    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


## log-timing.py
# 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")
	<!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:
Test	Number
API	1724
Client	834
Converter	109
DB Migration	92
Framework	360
Integration	889
	# 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")