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uniclust-pipeline-slurm's Introduction

Uniclust Pipeline

Setup

Make sure to install the HH-Suite3 and MMseqs2 and adjust the paths in paths.sh. Also make sure that awk, tar, pigz, cstranslate_mpi, sed, md5deep, clustalo, kalign, timeout are all installed and available in PATH.

Usage

To build your own databases based on the uniclust pipeline you can use the following three scripts:

  • run_main.sh: Run Main does the clustering, builds the uniclust30/50/90 and does the sequence enrichment of the uniboost10/20/30 databases.
  • run_hhdatabase.sh: Builds the uniclust30_hhsuite database
  • run_annotate.sh: Builds the annotation files

Make sure to run the scripts in this order.

SLURM

This pipeline has been adopted to use the SLURM workflow manager and can be submit using sbatch run_mpi.sh

uniclust-pipeline-slurm's People

Contributors

milot-mirdita avatar jboktor avatar

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