Nate Coraor natefoo

I created this to search BioContainers images for https://github.com/NCSC-NL/OpenSSL-2022 before it turned out that the bug is probably practically unexploitable, but should be useful in the future if we have another such case:

$ $HOME/bin/scan-singularity.sh -d 2021-09-01 -i /singularity -l ./log -s $HOME '/usr/local/conda-meta/openssl-3\..*'

For my own personal notes, I ran this on a manually-created LX-Brand CentOS 7 VM (alias: singularity-scan) on rochefort with the singularity zfs dataset lofs-mounted in. From there you can install epel-release and singularity-runtime, which can work with sif files (even though it can't run them in LX). tmpfs created with:

# useradd -d /home/scan -m -s /bin/bash scan

Local conda builds

In order to test updated or new conda packages you may need to build them locally and then build the container image from those. Here's a process for doing that.

Set up conda-build as per instructions. I use a standalone Miniforge install for this.
Build your package:
```
$ cd biocnda-recpies/recipes
```

	# https://github.com/natefoo/total-perspective-vortex/tree/resource-params
	global:
	default_inherits: default

	tools:
	default:
	cores: 1
	mem: cores * 3.9
	env: {}
	scheduling:

	global:
	default_inherits: default

	tools:
	default:
	cores: 1
	mem: cores * 3.9
	env: {}
	context:
	partition: normal

	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

	#!/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)

	---
	# 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

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

	import click
	import psutil

	#!/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

	#!/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