Requirements

• Nextflow
• Java V11
• Python3

Dependencies

• Singularity/Apptainer (-profile withsingularity)

  • Tested on Linux Server and HPC environments
  • Set common singularity image directory in nextflow.config

• Docker (-profile withdocker)

  • Tested on M2 MacBook Air (small dataset, no local structure prediction) and Linux Server
  • Start Docker before launching the pipeline

• Conda (-profile withconda)

  • Select profile server or set Linux .yml file in nextflow.config
  • Note: Due to issues with conda and t-coffee the .yml file may not be working anymore, better to try a local installation of t-coffee

• Local execution (-profile standard)

  • MAFFT
  • Biopython
  • BLAST (V2.14)
  • CD-Hit
  • Pandas
  • Matplotlib
  • secstructartist
  • DSSP (Mac: V2.2 Linux: V3.0)
  • IQ-TREE2
  • T-Coffee / EasyBuild (V13.45.61.3c310a9)
  • TM-align / EasyBuild (V20190822)
  • SAP / EasyBuild (V1.1.3)