ATLAS Installation¶

During the workshop you will learn how to use ATLAS to prepare your sequencing data for demographic inference. We kindly ask you to install ATLAS on your system using the instructions below.

Platform¶

Choose your platform to get recommendations and installation instructions:

Linux

On Linux computers, you should be able to install ATLAS witout any difficulties.

Windows

On Windows computers, use the Windows Subsystem for Linux. Follow instructions for Linux system below.

MacOS

On Linux computers, you should be able to install ATLAS.

Dependencies¶

We will start with installation of ATLAS dependencies:

Linux

Check that gcc compiler of version 9 or higher is installed:
```
$ gcc --version
```
If not, please install gcc:
```
$ sudo apt install gcc
```
Check that cmake of version 3.14 or higher is installed:
```
$ cmake --version
```
If not, please install cmake:
```
$ sudo apt install cmake
```

MacOS

Check that clang compiler is installed:
```
$ clang --version
```

Install samtools, cmake, autoconf and automake:

$ brew install samtools cmake autoconf automake

Installation¶

Download ATLAS repository:

$ git clone --depth 1 https://bitbucket.org/WegmannLab/atlas.git

And run compilation:

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

You can add the path to atlas as an alias in your .bashrc file as follows to avoid having to indicate the path to atlas/build all the time:

alias atlas='/path/to/atlas/build/atlas'

Verify Installation¶

To verify installation first run:

$ atlas simulate --chrLength 1000

You should see the following output:

- ATLAS terminated successfully in 0 seconds!

Download example input file example_for_atlas.bam:

$ wget https://github.com/noscode/GADMA_workshops/raw/refs/heads/main/docs/source/2024_18_11/files/example_for_atlas.bam

And run:

$ atlas BAMDiagnostics --bam example_for_atlas.bam

You should see the following output:

- ATLAS terminated successfully in 0 seconds!

Let Us Know You Were Successful¶

In order for us to understand how many participants are ready for the workshop, we ask you to send us some results of your run.

Print the first three lines of file example_for_atlas_mappingQualityHistogram.txt:
```
$ head -3 example_for_atlas_mappingQualityHistogram.txt
```
Please send us these lines via the following form:

Send Your Result

Troubleshooting¶

If you have any problems with installation:

Linux

You can install ATLAS using conda

$ conda env create -f conda.yml
$ conda activate atlas 
$ mkdir build; cd build

As cmake and conda do not play together nicely, you need to tell cmake where conda puts its binnaries and libraries:

$ cmake .. -GNinja -DCONDA=ON -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++) -DCMAKE_LIBRARY_PATH=$CONDA_PREFIX/lib -DCMAKE_INCLUDE_PATH=$CONDA_PREFIX/include
$ ninja

Take a look at the official installation documentation
If you still face issues, please write to ekaterina.e.noskova@gmail.com.

MacOS

Try using gcc compiler instead of clang for compilation.

You can install ATLAS using conda

$ conda env create -f conda.yml
$ conda activate atlas 
$ mkdir build; cd build

As cmake and conda do not play together nicely, you need to tell cmake where conda puts its binnaries and libraries:

$ cmake .. -GNinja -DCONDA=ON -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++) -DCMAKE_LIBRARY_PATH=$CONDA_PREFIX/lib -DCMAKE_INCLUDE_PATH=$CONDA_PREFIX/include
$ ninja

Take a look at the official installation documentation
If you still face issues, please write to ekaterina.e.noskova@gmail.com.