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.
galaxy.jobs.runners.gcp_batch:GoogleCloudBatchJobRunner
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.
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 viewcurl -o nfs-fix.yml https://gist.githubusercontent.com/ksuderman/7147b41832ab9434a243fbe58141a7a4/raw/c29820b60de205b0ab55d9d1c92acdaffa3894bb/nfs-fix.yml
nfs-fix.yml file as one of the --values files in the helm install command.| 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: |
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 |
| # 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): |
| #!/usr/bin/env python3 | |
| import os | |
| import sys | |
| import json | |
| import requests | |
| KB = 1024 | |
| MB = KB * KB | |
| GB = MB * KB |
| job_id | tool_id | tool_version | state | memory.max_usage_in_bytes | cpuacct.usage | process_count | galaxy_slots | runtime_seconds | ref_data_size | input_data_size | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ce4eadcc6a9dc62d | toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy7 | 2.1.0+galaxy7 | ok | 10230325248.0000000 | 1524636164586.0000000 | 32.0000000 | 1.0000000 | 1467.0000000 | 0 | 1407644464 | |
| b944eb0f5f220e64 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 | 2.24+galaxy0 | ok | 23552430080.0000000 | 1284559376976.0000000 | 32.0000000 | 1.0000000 | 1242.0000000 | 0 | 1407644464 | |
| 8510271abb9e802c | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 | 2.4.2+galaxy0 | ok | 8763760640.0000000 | 5420490778352.0000000 | 32.0000000 | 1.0000000 | 5462.0000000 | 0 | 1407644464 | |
| 7c2d1b475743f5b6 | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 | 0.7.17.1 | ok | 12500324352.0000000 | 9858370786969.0000000 | 32.0000000 | 1.0000000 | 9451.0000000 | 0 | 1407644464 |
| # 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" | |
| } |