ksuderman

ksuderman

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

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

ksuderman

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

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

# 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

#!/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

#!/usr/bin/env python3

import os
import sys
import json
import requests

KB = 1024
MB = KB * KB
GB = MB * KB

ksuderman

ksuderman

# ANSI color codes for the console.
reset="\033[0m"
bold="\033[1m"
ital="\033[3m" # does not work on OS X

# Function used to highlight text.
function hi() {
    echo -e "$bold$@$reset"
}

ksuderman

#!/usr/bin/env bash

# Use this script to update the GalaxyKubeman Helm chart versions in Leo
#
# Put this script on your path and run from the root Leonardo source directory.
# > cd /home/user/leonardo
# 
# USAGE
#   > bumpleo <new version>
#