Installation

Aevol can run on Linux and MacOS X. Windows users can run it using e.g. a Docker container.

Install Prerequisites

Before you dive into installing Aevol, make sure you have installed the prerequisites:

Installation Instructions

TL;DR (see below for detailed instructions):

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wget https://gitlab.inria.fr/aevol/aevol/-/archive/9.4.0/aevol-9.4.0.tar.gz
tar zxf aevol-9.4.0.tar.gz
cd aevol-9.4.0
mkdir build && cd build
cmake ..
cmake --build .         # add option --parallel to speed up
sudo cmake --install .  # optional (requires sudo privileges)

Detailed Instructions

Download

We recommend you to download the latest release. Please refer to the download page for more options.

Compile

Open a terminal and cd into the directory where you’ve downloaded the source code. Extract the files and cd into the extracted directory:

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tar zxf aevol-9.4.0.tar.gz
cd aevol-9.4.0

Create a build dir and cd into it:

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mkdir build && cd build

Now you’re ready to configure the build. If you want the default build just go for it:

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cmake ..
cmake --build .         # add option --parallel to speed up

NB: To speed up the installation, you might want to use make -j X, where X is the number of threads to use for compilation. If the installation is interrupted, we recommand deleting the build directory altogether, and starting again from line 4.

Special note for Mac OS users

Please be aware that the default configuration (with a simple cmake ..) will assume there is a brew-installed llvm and use the corresponding clang compiler. If you wish to use another compiler (e.g. gcc), please visit the Mac OS Prerequisites page for special instructions.

Compilation output

The instructions detailed above will build the aevol libraries and place a bunch of binaries (programs) in the build/bin directory. For a complete list of these binaries and what they do, see the list of programs generated at compile-time.
For a more structured presentation, please visit this page.

Install

Finally, if you have administration privileges, you can make the Aevol programs available to all users on the computer by typing:

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sudo cmake --install .  # optional (requires sudo privileges)

List of programs generated at compile-time

Program	Explanation
aevol_create_2b	Create a new simulation (Standard Aevol)
aevol_create_4b	Create a new simulation (4-Bases Aevol)
aevol_create_eukaryote_2b	Create a new simulation (Eukaryote Aevol)
aevol_run_2b	Run a simulation (Standard Aevol)
aevol_run_4b	Run a simulation (4-Bases Aevol)
aevol_run_eukaryote_2b	Run a simulation (Eukaryote Aevol)
aevol_post_lineage_2b	Reconstruct the lineage of a given individual (Standard Aevol)
aevol_post_lineage_4b	Reconstruct the lineage of a given individual (4-Bases Aevol)
aevol_post_ancestor_stats_2b	Compute statistics on ancestry described in lineage file (Standard Aevol)
aevol_post_ancestor_stats_4b	Compute statistics on ancestry described in lineage file (4-Bases Aevol)
aevol_post_extract_genomes_2b	Extract genome(s) in fasta format from aevol checkpoints (Standard Aevol)
aevol_post_extract_genomes_4b	Extract genome(s) in fasta format from aevol checkpoints (4-Bases Aevol)
aevol_post_extract_genomes_eukaryote_2b	Extract genome(s) in fasta format from aevol checkpoints (Eukaryote Aevol)
aevol_post_mutagenesis_2b	Generate single-mutants of the provided individuals (Standard Aevol)
aevol_post_mutagenesis_4b	Generate single-mutants of the provided individuals (4-Bases Aevol)
aevol_post_replicative_robustness_2b	Generate offsprings of the provided individuals (Standard Aevol)
aevol_post_replicative_robustness_4b	Generate offsprings of the provided individuals (4-Bases Aevol)
aevol_post_make_ui_output_from_checkpoint_2b	Generate visualization output files from aevol checkpoints (Standard Aevol)
aevol_post_make_ui_output_from_checkpoint_4b	Generate visualization output files from aevol checkpoints (4-Bases Aevol)
aevol_post_make_ui_output_from_checkpoint_eukaryote_2b	Generate visualization output files from aevol checkpoints (Eukaryote Aevol)
aevol_post_make_ui_output_from_fasta_2b	Generate visualization output files from from fasta and parameter file (Standard Aevol)
aevol_post_make_ui_output_from_fasta_4b	Generate visualization output files from from fasta and parameter file (4-Bases Aevol)
aevol_post_make_ui_output_from_fasta_eukaryote_2b	Generate visualization output files from from fasta and parameter file (Eukaryote Aevol)