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']

natefoo

# https://github.com/natefoo/total-perspective-vortex/tree/resource-params
global:
  default_inherits: default
    
tools:
  default:
    cores: 1
    mem: cores * 3.9
    env: {}
    scheduling:

natefoo

global:
  default_inherits: default

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

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

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

#!/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)