Installation¶

Requirements¶

SweepLink requires the following programs/libraries to be pre-installed:

A compiler which is compatible with C++17 or higher. We recommend gcc (version 9 or higher), you can check the pre-existing version on your system with gcc --version.
cmake, version 3.14 or higher. You can check the pre-existing version on your system with cmake --version.

Tip

Windows

It is better to install sweepLink on Windows Subsystem for Linux.

Linux

You should be able to install sweepLink without any problems.

MacOS

Use Homebrew to install cmake, autoconf and automake:

$ brew install cmake autoconf automake

Cluster

On most computing clusters, you can load recent cmake and gcc versions using modules

Download¶

SweepLink is hosted on bitbucket and can be downloaded with the command:

$ git clone --depth 1 https://bitbucket.org/wegmannlab/sweepLink.git

Compile¶

After downloading the repository, go to the directory (cd sweepLink) and compile it using cmake:

$ mkdir -p build
$ cd build
$ cmake .
$ cmake --build .

There will be a compiled program sweepLink in the directory of the repository.

Usage Options¶

You can run sweepLink without arguments

$ ./sweepLink

to obtain the usage options:

                 sweepLink 0.1
                ---------------

            University of Fribourg
  https://bitbucket.org/wegmannlab/sweepLink

Commit 79c7f6a6ab577b14f31c89be63502a6e481f9df8

  - Used executable: ./cmake-build-debug/sweepLink
  - Available tasks:
        - calculateLL   Noskova et al. (2024) SOMEWHERE
        - infer         Noskova et al. (2024) SOMEWHERE
        - simulate      Noskova et al. (2024) SOMEWHERE

  - Usage: ./cmake-build-debug/sweepLink taskName [options]
  - sweepLink terminated successfully in 0 seconds!

Quickstart¶

This is the first commands you should execute to make sure you have set up sweepLink correctly:

$  # Simulate a allele counts file with 100 loci for 1000 samples from one population
$ ./sweepLink simulate --numLoci 100 --numPop 1 --binomialN 1000
$  # Run inference of selection across loci
$ ./sweepLink infer --meta sweepLink_meta.txt --counts sweepLink_alleleCounts.txt