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Installation and quick start

Installation guide

  1. Clone this repository to your desktop

    git clone https://github.com/gabefoley/asr_curation.git

  2. Create a conda environment

    conda create -n asr_curation python=3.9

  3. Activate the conda environment

    conda activate asr_curation

  4. Install the required Python packages

    pip install -r requirements.txt

  5. Install the following so that they are callable from the command line

    1. mafft - callable as mafft

    2. FastTree - callable as FastTree

    3. GRASP - callable as grasp

    4. FigTree (Optional - for viewing trees with generated annotation files)

Quick start

To run an asr_curation pipeline you need to define -

  • a config.yaml file that defines where to look for the fasta and subset files. See Defining the config files for further details. )
  • a fasta file containing all the sequences you wish to include in the pipeline
  • a subset file containing rules for subsetting the data. See Defining the subset files for further details.

You can then run snakemake directly by calling it from within the asr_curation environment we created and activated earlier.

You need to specify the number of cores to run snakemake with and point to the config.yaml file. 

snakemake --cores 1 --configfile ./asr_curation/config/example_config.yaml