Nate Coraor natefoo

Untested Galaxy object store configuration with nested distributed objects stores that allow moving between permanent and scratch

type: distributed
search_for_missing: false
backends:
  - type: distributed
    search_for_missing: false
    allow_selection: true
    name: "Permanent"

Still working on it

Retest in progress

None

Fixing tool data then retest

None

Fixing tool resources then retest

I upgraded Mailman3 from <3.3.1 to >= 3.3.1 without heeding the instructions and as a result, had a ton of my list members erroneously set to disabled due to bounces.

These scripts scan your bounce log file and re-enable anyone who was disabled. You could also easily modify it to just re-enable everyone, but I didn't want to do it unilaterally just in case.

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

	from galaxy.app import GalaxyManagerApplication
	from galaxy.tool_shed.cache import ToolShedRepositoryCache


	global_conf = {
	"shed_tool_config_file": "shed_tool_conf.xml",
	}
	app = GalaxyManagerApplication(**global_conf)
	app.tool_shed_repository_cache = app._register_singleton(ToolShedRepositoryCache)
	app._configure_tool_data_tables(from_shed_config=False)

	# contents of OverlayFS upper mount (will be published)
	+ tree /home/idc/brc-cvmfs/work/upper
	/home/idc/brc-cvmfs/work/upper
	├── config
	│ ├── all_fasta.loc
	│ ├── bowtie2_indices.loc
	│ ├── bowtie_indices.loc
	│ ├── bwa_mem_index.loc
	│ ├── dbkeys.loc
	│ ├── hisat2_indexes.loc

	data_managers:
	- data_table_reload:
	- all_fasta
	- __dbkeys__
	id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4
	params:
	- dbkey_source\|dbkey: dm6
	- reference_source\|reference_source_selector: ucsc
	- reference_source\|requested_dbkey: dm6

	---
	- hosts: galaxyservers
	become: true
	become_user: root
	vars_files:
	- group_vars/secret.yml
	pre_tasks:
	- name: Install Dependencies
	apt:
	#name: ['acl', 'bzip2', 'git', 'make', 'python3-psycopg2', 'tar', 'virtualenv']

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

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