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pipeFSC - Pipeline for Fastsimcoal demographic simulations

This is a Python pipeline for running Fastsimcoal (FSC). It automates the process of setting up and running FSC models, selecting the best run for each model, calculating AIC scores, and generating files for posterior confidence intervals estimations.

Table of Contents

Installation

To use the pipeFSC pipeline, follow these steps:

  1. Clone this repository to your local machine:

    git clone https://github.com/niconm89/pipeFSC.git

  2. Navigate to the cloned directory:

    cd pipeFSC

  3. Make sure you have the required dependencies installed:

  1. Add pipeFSC path to your $PATH variable

    To add a folder to the system's PATH in a Linux/Unix system, you can follow these steps:

  • Open a Terminal: You'll need to use the command line.

  • Identify the Folder: Ensure you know the full path to the folder you want to add to the PATH. For example, let's say your folder is located at /path/to/your/folder.

  • Edit the .bashrc or .bash_profile File: You'll typically edit your user-specific configuration file. This file is located in your home directory, and you can use a text editor like nano or vi to open it. For example, use:

    nano ~/.bashrc

    or

    nano ~/.bash_profile

  • Add the Folder to PATH: Add the following line to the file, replacing /path/to/your/folder with the actual folder path:

    export PATH=$PATH:/path/to/your/folder

    This line appends your folder to the existing PATH.

  • Save and Exit: If you're using nano, press Ctrl + O to save, and Ctrl + X to exit.

  • Source the File: To apply the changes immediately, run:

    source ~/.bashrc

    or

    source ~/.bash_profile

    This step is necessary to refresh your terminal with the updated PATH.

  • Verify the Change: You can check if the folder has been added to the PATH by running:

    echo $PATH

    You should see your folder's path in the list.

    Your folder should now be part of the system's PATH, making it easier to run executables and scripts located within that folder from any directory in your terminal.

    This process is common on Linux/Unix systems, but please note that the specific file you need to edit (.bashrc or .bash_profile) can vary depending on your shell (e.g., Bash, Zsh, etc.). If you're using a different shell, you may need to modify a different configuration file.

    Note: Ensure that you have the necessary permissions to edit these configuration files. If you're not the system administrator, you might need to use sudo to gain the required permissions.

  1. Run the pipeline using the provided Python script:

    python pipeFSC.py -m /path/to/model/files -o /output/directory -n 100 -t 2

    Replace /path/to/model/files with the path to the directory containing the necessary FSC model files (*.est, *.tpl, and *_MSFS.obs).

    Note that you must place all the three files for each model you want to run in the same directory (-m /path/to/model/files, see below). You can also specify the number of replicates (-n) and the number of threads (-t) for running the models.

    $ ls pipeFSC/examples/test_SingleC_n3/
SingleC0.est
SingleC1.est
SingleC2A.est
SingleC2B.est
SingleC2N.est
SingleC0_MSFS.obs
SingleC1_MSFS.obs
SingleC2A_MSFS.obs
SingleC2B_MSFS.obs
SingleC2N_MSFS.obs
SingleC0.tpl
SingleC1.tpl
SingleC2A.tpl
SingleC2B.tpl
SingleC2N.tpl

Usage

pipeFSC part1

Aca va la descripcion del analisis

  • -m or --modeldir: Path to the directory containing the three required files (*.est, *.tpl, and *_MSFS.obs) for each model selected.
  • -o or --outdir: Path to the directory where the results will be saved. If the output directory does not exist, it will be created. (Default: 03_phylogenetic_tree)
  • -n or --nruns: Number of model run replicates. (Default: 1000)
  • -t or --threads: Number of threads to run. (Default: 8)

pipeFSC part2

Aca va la descripcion del analisis

  • -m or --modeldir: Path to the model directory.
  • -n or --nruns: Number of independent runs. (Default: 1000)
  • -t or --threads: Number of threads. (Default: 8)

Examples

Part1

./pipeFSC.P1.py -m /path/to/model/files -o /output/directory -n 100 -t 4

Part2

./pipeFSC.P2.py -m /path/to/modeldir -n 100 -t 8

You can find usage examples and more information in the examples directory.

Examples

If you encounter any issues or have questions, please open an issue on the GitHub repository.

License

This pipeline is distributed under the MIT License.