natefoo

name: galaxy_training_material
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - binutils_impl_linux-64=2.36.1=h193b22a_2
  - ca-certificates=2022.6.15=ha878542_0
  - gcc=12.1.0=h9ea6d83_10

natefoo

Notes

Architectures/ISAs

I believe that no illumos distributions modify uname -srmpio, meaning that for all distributions this will be:

% uname -srmpio
SunOS 5.11 i86pc i386 i86pc Solaris

natefoo

#!/bin/bash
# stopgap to build mod_zip DSO for nginx-galaxy before that package goes away entirely
set -euo pipefail

nginx_version='1.12.2'
upload_module_version='2.255-nfs'
auth_pam_module_version='1.4'
mod_zip_version='808fb55e7235a201ea862e02dab612b87787d5a4'
gid=$(id -g)
uid=$(id -u)

natefoo

---
# Manage static Galaxy configuration files

- name: Static config setup
  block:

    - name: Ensure Galaxy version is set
      include_tasks: _inc_galaxy_version.yml
      when: __galaxy_major_version is undefined

natefoo

import os
import subprocess
import time
from datetime import (
    date,
    datetime,
)

import click
import psutil

natefoo

#!/usr/bin/env python3
import os
import traceback

import click
from rich import progress
from tusclient.fingerprint import fingerprint

from bioblend import ConnectionError
from bioblend.galaxy import GalaxyInstance

natefoo

#!/usr/bin/env python3
# Quick and dirty script to update usegalaxy-tools with missing tools fron GTN trainings. Note that this installs the
# newest versions of things, not necessarily the version specified in the training json.
import argparse
import os
import pathlib
import string
import subprocess
import sys

natefoo

#!/usr/bin/env python
"""
Finds datasets on disk that shouldn't be there.

This script is not object-store aware. You just point it at directories that are DiskObjectStore backends (e.g.
file_path in the Galaxy config by default).
"""
from __future__ import absolute_import, print_function

import sys

natefoo

run-pulsar-dev.sh

This script was prepared for development work at the Galaxy Community Conference 2021 CoFest. It has been superseded by a Docker Compose-based project at:

https://github.com/natefoo/galaxy-pulsar-dev/

natefoo

#!/usr/bin/env python3
# run with:
#    find topics -name \*.md -type f -print0 | xargs -0 python3 lamefix.py
import fileinput
import sys


def fix(mdfileobj):
    in_diff = False
    min_length = sys.maxsize