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ksuderman / ask-galaxy.py
Created November 6, 2022 00:02
Python script to query the AskGalaxy service to generate CSV data for Observable.
#!/usr/bin/env python3
import os
import sys
import json
import requests
KB = 1024
MB = KB * KB
GB = MB * KB
@ksuderman
ksuderman / render_template.py
Created January 25, 2023 18:26
Python script to render Jinja2 templates
#!/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):
@ksuderman
ksuderman / log-timing.py
Created October 19, 2023 16:04
Compare greedy vs lazy string interpolation in log messages
# 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")
@ksuderman
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
@ksuderman
ksuderman / gist.txt
Created May 11, 2024 13:29
Pod details for failed SnpEff job
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:
@ksuderman
ksuderman / Instructions.md
Last active 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.

  1. 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
  1. Include the nfs-fix.yml file as one of the --values files in the helm install command.