natefoo

#!/usr/bin/env python3
import argparse
import os.path
import json
import re
import shutil
import subprocess
import sys
import urllib.parse
from collections import defaultdict

natefoo

e.g. for bisecting

1. Install prereqs

   # dnf install -y epel-release
   # dnf install --enablerepo=crb fuse-devel fuse3-devel libuuid-devel e2fsprogs-devel openssl-devel python3-devel libattr-devel libcap-devel gmock gmock-devel

2. Build

natefoo

curl from depot

Total time: 10s

[rocky@js2-gxit-medium1 ~]$ curl -o test.sif https://depot.galaxyproject.org/singularity/biobb_wf_mutations%3A0.0.6--py_0
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  572M  100  572M    0     0  14.4M      0  0:00:39  0:00:39 --:--:-- 17.1M

natefoo

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)

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"

natefoo

# 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

natefoo

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

natefoo

Still working on it

Retest in progress

None

Fixing tool data then retest

None

Fixing tool resources then retest

natefoo

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.

natefoo

---
- 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']