Influenza

Environment recreation

Automatic Install

• conda env create -f clustering.yml
• conda activate clustering
• jupyter lab

Manual Install

• mamba create -n clustering jupyterlab jupyter-resource-usage jupyterlab-git jupyterlab-fasta jupyterlab-lsp pandas numpy scipy biopython hdbscan scikit-learn nodejs tqdm kneed rpy2 python-lsp-server r-languageserver raxml mafft r-base r-irkernel r-tidyverse r-plotly r-ggstar bioconductor-ggtree bioconductor-ggtreeextra r-phangorn bioconductor-tanggle (r-svglite)
• conda activate clustering
• jupyter lab

Pipeline execution

Nearly fully automated as of 2022/01/19 in two Juyter Notebooks.

1. Clusterer.ipynb (Python): FASTA + Settings -> CSV tables
2. Graphics.ipynb (R): CSV tables + Settings -> Grafics

Problems

• Browser tab crashes unexpectedly when starting the jupyter server
  • fix: jupyter lab --notebook-dir=/home/user/Influenza/
  • cached content makes the notebook start in the wrong root folder
  • notebook-dir lets you reset the root location