.. _backbone-label:

Busco
==============================

Introduction
~~~~~~~~
BUSCO (Benchmarking sets of Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Note: to plot BUSCO summary results, use the companion command: generate_plot.py -wd [WORKING_DIRECTORY] [OTHER OPTIONS] The plotting script is installed as a standalone executable and can be invoked directly as above. DO NOT call it 'python3 scripts/generate_plot.py' (as the user manual at https://busco.ezlab.org/busco_userguide.html#plot suggests). This change is specific to the way this container is organized.


| For more information, please check:
| Docker hub: https://hub.docker.com/r/ezlabgva/busco 
| Home page: https://gitlab.com/ezlab/busco/ Note: Augustus is a gene prediction program for eukaryotes which is required by BUSCO. Augustus requires a writable configuration directory. This installation comes with a stub of AUGUSTUS coniguration files, but you *must* copy them out from the container into a location where you have write permissions. A helper command 'copy_augustus_config' is provided to simplify the task. Follow the procedure below to put the config files in your scratch space: $ mkdir -p $RCAC_SCRATCH/augustus $ copy_augustus_config $RCAC_SCRATCH/augustus $ export AUGUSTUS_CONFIG_PATH$RCAC_SCRATCH/augustus/config

.. note::
    Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - Cluster
    - Version(s)

  * - ANVIL
    - 5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7, 5.8.2-py
  * - BELL
    - 5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7, 5.8.2-py
  * - GAUTSCHI
    - 5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7
  * - NEGISHI
    - 5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7, 5.8.2-py
  * - SCHOLAR
    - 5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7

Commands
~~~~~~~
- busco
- generate_plot.py

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load busco

Example job
~~~~~
.. warning::
    Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead.

To run busco on our clusters:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A myallocation     # Allocation name
        #SBATCH -p wholenode        # Partition name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=busco
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers busco

        # Your busco workflow...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p cpu         # Partition name
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=busco
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers busco

        # Your busco workflow...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p ai          # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=busco
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers busco

        # Your busco workflow...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p a100        # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH --mem=2G       # Memory
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=busco
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers busco

        # Your busco workflow...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A queue     # Queue name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=busco
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers busco

        # Your busco workflow...