.. _backbone-label:

Basenji
==============================

Introduction
~~~~~~~~
Basenji is a tool for sequential regulatory activity predictions with deep convolutional neural networks.


| For more information, please check:
| BioContainers: https://biocontainers.pro/tools/basenji 
| Home page: https://github.com/calico/basenji

.. 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
    - 0.5.1
  * - BELL
    - 0.5.1
  * - GAUTSCHI
    - 0.5.1
  * - NEGISHI
    - 0.5.1
  * - SCHOLAR
    - 0.5.1

Commands
~~~~~~~
- akita_data.py
- akita_data_read.py
- akita_data_write.py
- akita_predict.py
- akita_sat_plot.py
- akita_sat_vcf.py
- akita_scd.py
- akita_scd_multi.py
- akita_test.py
- akita_train.py
- bam_cov.py
- basenji_annot_chr.py
- basenji_bench_classify.py
- basenji_bench_gtex.py
- basenji_bench_gtex_cmp.py
- basenji_bench_phylop.py
- basenji_bench_phylop_folds.py
- basenji_cmp.py
- basenji_data.py
- basenji_data2.py
- basenji_data_align.py
- basenji_data_gene.py
- basenji_data_hic_read.py
- basenji_data_hic_write.py
- basenji_data_read.py
- basenji_data_write.py
- basenji_fetch_app.py
- basenji_fetch_app1.py
- basenji_fetch_app2.py
- basenji_fetch_norm.py
- basenji_fetch_vcf.py
- basenji_gtex_folds.py
- basenji_hdf5_genes.py
- basenji_hidden.py
- basenji_map.py
- basenji_map_genes.py
- basenji_map_seqs.py
- basenji_motifs.py
- basenji_motifs_denovo.py
- basenji_norm_h5.py
- basenji_predict.py
- basenji_predict_bed.py
- basenji_predict_bed_multi.py
- basenji_sad.py
- basenji_sad_multi.py
- basenji_sad_norm.py
- basenji_sad_ref.py
- basenji_sad_ref_multi.py
- basenji_sad_table.py
- basenji_sat_bed.py
- basenji_sat_bed_multi.py
- basenji_sat_folds.py
- basenji_sat_plot.py
- basenji_sat_plot2.py
- basenji_sat_vcf.py
- basenji_sed.py
- basenji_sed_multi.py
- basenji_sedg.py
- basenji_test.py
- basenji_test_folds.py
- basenji_test_genes.py
- basenji_test_reps.py
- basenji_test_specificity.py
- basenji_train.py
- basenji_train1.py
- basenji_train2.py
- basenji_train_folds.py
- basenji_train_hic.py
- basenji_train_reps.py
- save_model.py
- sonnet_predict_bed.py
- sonnet_sad.py
- sonnet_sad_multi.py
- sonnet_sat_bed.py
- sonnet_sat_vcf.py
- tfr_bw.py
- tfr_hdf5.py
- tfr_qc.py
- upgrade_tf1.py

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

    module load biocontainers
    module load basenji

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 basenji 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=basenji
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers basenji

        # Your basenji 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=basenji
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers basenji

        # Your basenji 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=basenji
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers basenji

        # Your basenji 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=basenji
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers basenji

        # Your basenji 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=basenji
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers basenji

        # Your basenji workflow...