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.

Activate Conda Environment

conda activate gadma_workshop_env

Platform

Choose your platform to get recommendations and installation instructions:

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

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

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

Installation

Install ATLAS using conda:

conda install bioconda::atlas

Verify Installation

  1. To verify installation first run:

    atlas simulate --chrLength 1000

    You should see the following output:

    - ATLAS terminated successfully in 0 seconds!

  2. 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 encounter the following error about libgfortran.so.3:

atlas: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

You may need to install an older version of libgfortran:

conda install conda-forge/label/cf201901::libgfortran

If you have any other problems with installation: