Tests on Windows

[tavareshugo]

WSL2

• [x] ~epi2me-labs/wf-bacterial-genomes~
  • Ran successfully using Docker (-profile standard) took 1h 55m 52s for 10 samples.
• [x] de novo assembly script (rasusa + flye + medaka_consensus + bakta)
  • successful, takes ~1h per sample downsampled to 100x (sometimes less).
• [x] ~checkm~
  • Ran successfully took around ~1h
• [x] checkM2
• [x] mash
  • ~had to downgrade to version 2.2 (conda recipe issue)~ (install it in a separate environment if needed)
  • ran successfully ~10m per set of sequences.
• [ ] busco
• [x] mlst
  • runs in less than 1 minute
• [x] panaroo
  • takes 7 hours on 63+5 samples!
• [x] funcscan
  • Ran successfully in 41m 23s

Multipass

VirtualBox

[tavareshugo]

Setup instructions draft:

1. Update and install system packages

sudo apt update && sudo apt upgrade -y && sudo apt autoremove -y
sudo apt install -y git
sudo apt install -y default-jre

2. Install Mamba

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh -b
rm Mambaforge-$(uname)-$(uname -m).sh
export PATH="$HOME/mambaforge/bin/:$PATH"
mamba init
conda config --add channels defaults; conda config --add channels bioconda; conda config --add channels conda-forge

Restart the terminal: you should see (base) at the start of your terminal.

3. Install the software environment for the workshop

# avoid timeout errors
conda config --set remote_read_timeout_secs 500
# create environment and install software
mamba create --name awd
mamba install --name awd multiqc checkm-genome busco mlst nextflow panaroo

# install mash separately due to version conflict with conda recipe
# this is unconventional and not best practice... but it works for now
wget https://github.com/marbl/Mash/releases/download/v2.3/mash-Linux64-v2.3.tar
tar -xf mash-Linux64-v2.3.tar
mv mash-Linux64-v2.3/mash $(conda info --base)/envs/awd/bin/
rm -r mash-Linux64-v2.3*

4. Install singularity

# singularity system dependencies
sudo apt install -y runc uidmap
# download deb installer
codename=$(lsb_release -cs)
wget -O singularity.deb https://github.com/sylabs/singularity/releases/download/v3.11.4/singularity-ce_3.11.4-${codename}_amd64.deb
# install and clean
sudo dpkg -i singularity.deb
rm singularity.deb

5. Nextflow setup

TODO: add some code to generate config file.

---

Other things:

• Make Excel default for opening TSV files
• Have some sensible text editor (VS Code?) as the default for opening shell scripts.
• ...

[tavareshugo]

At the moment there's a conflict between versions for the conda environment:

• mash version 2.3 has a conda recipe problem, so we need to downgrade to 2.2
• but this is incompatible with busco version 5.4.0 (the latest) and downgrading to a lower version has a bug also

~Might need to install these things in separate environments?~
(one way is to download the dependency-free binary from their repo)