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README.md

PLEASE NOTE THAT THE GITHUB VERSION OF SLiM IS PRERELEASE SOFTWARE THAT IS UNDER ACTIVE DEVELOPMENT!

It is strongly recommended that all end users of SLiM use the current release version, available at http://messerlab.org/slim/.

 

License

Copyright (c) 2016-2018 Philipp Messer. All rights reserved.

SLiM is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

SLiM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with SLiM. If not, see http://www.gnu.org/licenses/.

Development & Feedback

SLiM is under active development, and our goal is to make it as broadly useful as possible. If you have feedback or feature requests, or if you are interested in contributing to SLiM, please contact Philipp Messer at messer@cornell.edu. Please note that Philipp is also looking for graduate students and postdocs.

Installation from source

We use CMake, with an out-of-source build, as described here:

https://gitlab.kitware.com/cmake/community/wikis/FAQ#out-of-source-build-trees

CMake is available with port install cmake or brew install cmake (on OS X, with MacPorts or Homebrew respectively), or with aptitude install cmake (on debian).

To compile the development version from this repository, do:

git clone https://github.com/MesserLab/SLiM.git
mkdir SLiM_build
cd SLiM_build
cmake -DCMAKE_BUILD_TYPE=Release ../SLiM
make

The resulting binaries (slim and eidos) will be located in the SLiM_build directory. You can name the build directory anything you wish; there is nothing magical about the name SLiM_build. Running make install will then attempt to install these to the default system directories, but this will probably fail unless you run it with root permissions (e.g., by doing sudo make install). To explicitly tell cmake where to install the binaries, run:

cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/path/to/install ../SLiM
make
make install

where /path/to/install is the path where you want slim and eidos installed below (they would be put in /path/to/install/bin in this example, analogous to the --user flag).

To update the build, in the SLiM_build directory run:

cmake -DCMAKE_BUILD_TYPE=Release ../SLiM
make

To build the code with debug flags turned on (i.e., optimization turned off, debugging symbols turned on, and extra runtime checking enabled), run instead:

cmake -DCMAKE_BUILD_TYPE=Debug ../SLiM
make

This could be done in a separate directory to retain both versions of the build.

See the SLiM manual for more information about building and installing, including instructions on building SLiMgui under Xcode. The manual and other SLiM stuff can be found at http://messerlab.org/slim/.

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Selection on Linked Mutations: A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference.

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