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 https://github.com/bioinfo-core-BGU/neatseq-flow.git
    
  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 https://github.com/bioinfo-core-BGU/neatseq-flow-modules.git
    

Tip

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

Note

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/neatseq_flow.py                         \
    --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

Attention

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:

    neatseq_flow.py \
        --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
    

Note

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

Attention

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