1 Overview | 2 Using | 2.1 Version colabfold/1.5.5

Overview

ColabFold: Making Protein folding accessible to all!
- https://colabfold.mmseqs.com/
- https://github.com/sokrypton/ColabFold/wiki/MSA-Server-Database-History

Using

Version colabfold/1.5.5

The example below uses the following folder structure:

input_data/
  input.fasta
output_data/

The bind (-B) commands below map your folders to those within the container image being run.

[]$ module load colabfold/1.5.5

# The following environment variables are set:
CF_CACHE=/apps/u/opt/containers/colabfold/1.5.5/cache
CF_SIF=/apps/u/opt/containers/colabfold/1.5.5/colabfold_1.5.5-cuda12.2.2.sif

[]$ apptainer run --nv \
  -B $CF_CACHE:/cache \
  -B ./input_data:/work \
  $CF_SIF \
  colabfold_batch /work/input.fasta ./output_data

Getting command help:

[]$ module load colabfold/1.5.5
[]$ apptainer run $CF_SIF colabfold_batch -h
...

Colabfold

Overview

Using

Version colabfold/1.5.5