NeatSeq-Flow Installation

Author: Menachem Sklarz

Affiliation: Bioinformatics Core Facility, National institute of Biotechnology in the Negev, Ben-Gurion University.

Download and Install

  1. Clone the package from github:

    git clone
  2. You may have to install two python dependencies: yaml and bunch. This can be done with:

    pip install pyyaml bunch
  3. Clone the package of modules from github:

    git clone


A NeatSeq-Flow GUI is available. See the detailed GUI tutorial.


You can also download the repository code from the following links:

Executing NeatSeq-Flow

Create a new directory anywhere, cd into it and execute the following commands ($NSF_main is the directory where NeatSeq-Flow is installed):

python $NSF_main/bin/                         \
    --sample_file $NSF_main/Workflows/Sample_sets/PE_tabular.nsfs    \
    --param_file  $NSF_main/Workflows/mapping.yaml       \
    --message     "an informative message"

Install and execute with Conda


The following instructions are for use with the bash shell!

  1. Install Miniconda (for python version 2.7).

  2. Download the NeatSeq-Flow conda environment file.

  3. Create an environment:

    conda-env create -f NeatSeq_Flow_conda_env.yaml
  4. Activate the environment:

    source activate NeatSeq_Flow
  5. Execute the following command to tell NeatSeq-Flow where the base conda installation is located:

    export CONDA_BASE=$(conda info --root)
  6. Make a dir for your project and change into it:

    mkdir first_neatseq_flow_proj; cd first_neatseq_flow_proj
  7. Execute NeatSeq-Flow: \
        --sample_file $CONDA_PREFIX/NeatSeq-Flow-Workflows/Sample_sets/PE_tabular.nsfs \
        --param_file $CONDA_PREFIX/NeatSeq-Flow-Workflows/mapping.yaml \
        --message "an informative message"
  8. When done, deactivate the environment:

    source deactivate


You don’t need to have the environment activated in order to execute the scripts!


See the NeatSeq-Flow Tutorial for a full example of how to use NeatSeq-Flow