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afgane / gxrdb_plan.md
Last active August 18, 2026 21:52
gxrdb

gxrdb — a Galaxy data store

A centrally hosted store of Galaxy operational data, contributed by usegalaxy.* servers. Its job is to capture the data reliably, keep it manageable, and let consumers extract from it quickly — nothing more.

Scope

In scope. Getting job-level data out of each Galaxy database cheaply and repeatedly; normalising it once so no consumer has to; storing it so a query

@afgane
afgane / guide.md
Last active June 1, 2026 18:27
GalaxyAI setup

Run FastQC tool

  1. Install FastQC tool via the Admin panel (or on usegalaxy.org)
  2. Register and name your History (e.g., FastQC workshop)
  3. Upload a FASTQ dataset: https://zenodo.org/records/17929063/files/normal_R1.fastq.gz
  4. Search for FastQC and run it
  5. Open the HTML report (if on your VM, you'll need to add fastQC to sanitize allow list)

Configure GalaxyAI to use the Jetstream2 LLM service

@afgane
afgane / guide.md
Last active May 27, 2026 20:38
Adding a Bioconductor package to Galaxy

Wrapping Bioconductor ComplexHeatmap as a Galaxy Tool

This guide walks through a minimal, container-friendly Galaxy wrapper for the Bioconductor ComplexHeatmap package using Planemo.

The finished tool accepts a tabular numeric matrix and produces a PDF heatmap.

0. Install Planemo

Install uv, then use it to install Planemo as an isolated command-line tool.

@afgane
afgane / galaxy-debug-pod.yml
Created January 16, 2025 16:24
A manifest for a debug pod for a Galaxy deployment.
apiVersion: v1
kind: Pod
metadata:
name: gxy-debug-pod
spec:
containers:
- name: gxy-debug-pod
image: alpine:3.16
imagePullPolicy: IfNotPresent
command: ["tail"]
@afgane
afgane / inputs.txt
Last active February 8, 2024 18:26
Jupyter within Galaxy
https://zenodo.org/record/4477881/files/X_test.tsv
https://zenodo.org/record/4477881/files/X_train.tsv
https://zenodo.org/record/4477881/files/y_test.tsv
https://zenodo.org/record/4477881/files/y_train.tsv
@afgane
afgane / tvp_rules_tests.yml
Created February 6, 2023 17:59
TPV rules used for tool tests
destinations:
k8s:
max_accepted_cores: 100
max_accepted_mem: 800
max_cores: 8
max_mem: 48
@afgane
afgane / Build bonito container
Last active November 2, 2020 02:45
Add AWS GPU instance to a K8s cluster. Tested with instance type g3 on Ubuntu 20.04.
docker run --gpus all -it nvidia/cuda:10.2-devel-ubuntu18.04 /bin/bash
apt update && apt install -y python3 build-essential python3-pip libz-dev wget libncurses5 libncurses5-dev libbz2-dev liblzma-dev liblzma5
wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
tar -xf samtools-1.11.tar.bz2
cd samtools-1.11
./configure --prefix /usr/local/
make
make install
pip3 install ont-bonito cupy-cuda102
@afgane
afgane / playbook.yaml
Last active October 13, 2020 03:53
A bare-bones Ansible playbook for (re)setting a new password for Rancher Admin user.
- name: Go
hosts: all
gather_facts: no
vars:
rancher_hostname: rancher.local
pwd: pwd-from-cloudlaunch
tasks:
- name: Reset admin pwd
# kubeconfig on k3s at /etc/rancher/k3s/k3s.yaml
@afgane
afgane / keybase.md
Created January 15, 2020 20:41
keybase.md

eafgan

Keybase proof

I hereby claim:

  • I am afgane on github.
  • I am eafgan (https://keybase.io/eafgan) on keybase.
  • I have a public key ASBCgJ-Efu5HY_usIkS777EBXOwmJegBKD1nbaHH26HKZgo

To claim this, I am signing this object:

@afgane
afgane / dump.sql
Created September 30, 2019 20:09
--
-- PostgreSQL database dump
--
-- Dumped from database version 11.3 (Debian 11.3-1.pgdg90+1)
-- Dumped by pg_dump version 11.3 (Debian 11.3-1.pgdg90+1)
SET statement_timeout = 0;
SET lock_timeout = 0;
SET idle_in_transaction_session_timeout = 0;