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Building megSAP Container Version

Dependencies

These instructions are for Ubuntu 20.04, but as long as you can install Apptainer, the container should work on other systems as well.

Install Apptainer (Ubuntu 20.04)

sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer

Downloading

Download the megSAP Apptainer container:

wget --no-check-certificate -O megSAP_master.sif https://megsap.de/download/container/megSAP_master.sif

Initial Setup

Although megSAP is encapsulated within an Apptainer container, some required tools, genomes, and databases must be downloaded separately.

Create a Data Folder

First, create a folder on your host system to store the downloaded data:

mkdir -p <path-to-host-data-folder>

Download Tools and Containers

Next, download a few tools and Apptainer containers for the rest of the tools:

apptainer exec --pwd /megSAP/data -B <path-to-host-data-folder>:/megSAP/data/data_folder/ megSAP_[version].sif ./download_tools.sh
apptainer exec --pwd /megSAP/data -B <path-to-host-data-folder>:/megSAP/data/data_folder/ megSAP_[version].sif ./download_container.sh

Download and Index the Reference Genome

apptainer exec --pwd /megSAP/data -B <path-to-host-data-folder>:/megSAP/data/data_folder/ megSAP_[version].sif ./download_GRCh38.sh

Download and Convert Databases

apptainer exec --pwd /megSAP/data -B <path-to-host-data-folder>:/megSAP/data/data_folder/ megSAP_[version].sif ./download_dbs.sh
apptainer exec -B <path-to-host-data-folder>:/megSAP/data/data_folder/ megSAP_[version].sif php /megSAP/src/Install/db_download.php -data_folder /megSAP/data/data_folder/

Note: OMIM, HGMD, and COSMIC databases are not downloaded automatically due to licensing restrictions. If you have the required licenses, follow the instructions for the containerized megSAP version in the download_dbs.sh script to download and convert them manually.

Settings

Changing the settings is optional, as most entries have default values. If needed, copy the default settings file from within the container to your host system:

apptainer exec megSAP_[version].sif cp /megSAP/settings.ini.default ./settings.ini

Now, edit settings.ini as needed. Do not change any paths—they reference directories inside the megSAP container. Once modified, bind your settings file when invoking the container:

-B <path-to-new-settings.ini>:/megSAP/settings.ini

For a detailed description of settings, refer to settings.md.

NGSD Initialization

If you plan to use NGSD and it is not initialized yet, follow these steps:

  1. Install a MariaDB server.

  2. Create a database and user in the SQL database.

  3. Add NGSD connection details to settings.ini.

  4. Create tables using:

    apptainer exec -B <path-to-new-settings.ini>:/megSAP/settings.ini,<path-to-host-data-folder>:/megSAP/data/data_folder/ megSAP_[version].sif php /megSAP/src/Install/db_init.php

    During this step, a ngsbits_settings.ini is created from the megSAP settings.ini and saved under <path-to-host-data-folder>/tools/ngsbits_settings.ini. This ngsbits_settings.ini file is required to run the ngs-bits container independently of the megSAP container.

  5. Import base genomic data using ngs-bits tools:

    NGSDImportQC --help  
NGSDImportHGNC --help  
NGSDImportEnsembl --help  
NGSDImportHPO --help  
NGSDImportGeneInfo --help  
NGSDImportOMIM --help  
NGSDImportORPHA --help

Note: To call ngs-bits tools, use: apptainer exec -B <path-to-host-data-folder>/tools/ngsbits_settings.ini ngs-bits_[version].sif [tool] [parameters] --settings <path-to-host-data-folder>/tools/ngsbits_settings.ini. The ngs-bits container is downloaded to <path-to-host-data-folder>/tools/apptainer_container.

Note: To annotate variants with NGSD in-house counts, classifications, etc., NGSD data has to be exported regularly. To do so, adapt the file data\dbs\NGSD\Makefile and execute make export once a week using a cronjob. To do so in the megSAP container version you have to copy the Makefile to your host system, change it and mount it when executing the make export.

Execution

Now, all required tools and data are ready. You can list available pipelines:

apptainer exec megSAP_[version].sif ls /megSAP/src/Pipelines

Refer to the documentation for more details.

Running a Pipeline

Execute a pipeline with the following command:

apptainer exec -B \
    <path-to-host-data-folder>:/megSAP/data/data_folder/, \
    <path-to-new-settings.ini>:/megSAP/settings.ini, \
    </tmp/folder/>:/tmp/local_ngs_data/, \
    </path/to/input_data/>:/working_dir/ \
    megSAP_[version].sif \
    php /megSAP/src/Pipelines/analyze.php \
        -folder /working_dir \
        -name [processed-sample-name] \
        -steps ma,vc,cn,sv,re \
        -threads [number-of-threads]

Explanation of Bind Mounts:

  • <path-to-host-data-folder> → /megSAP/data/data_folder/: Mounts the data folder containing the downloaded data.
  • <path-to-new-settings.ini> → /megSAP/settings.ini: Mounts your modified settings file.
  • </tmp/folder/> → /tmp/: Mounts your tmp folder for intermediate and locally stored files.
  • </path/to/input_data/> → /working_dir/: Mounts the folder with input data.

Note: If your host system's temporary directory is not /tmp change tmp folder mounting to </tmp/folder/> → </tmp/folder/> and change local_data = /tmp/local_ngs_data/ to local_data = </tmp/folder/>/local_ngs_data in your settings.ini

Note: This example shows how to run analyze.php. To check other pipelines, use: apptainer exec megSAP_[version].sif php /megSAP/src/Pipelines/[pipeline_name].php --help