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install_unix.md

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Building megSAP from sources (Linux)

Currently only Linux is supported!

Dependencies

We are providing instructions for Ubuntu 20.04 and RHEL 8.3 here. However this should be reasonably easy to port to any other Linux distribution.

Base dependencies for different operating systems:

Ubuntu 20.04

> sudo apt-get install -y rsync zlib1g bzip2 php7.4-cli php7.4-xml php7.4-mysql make unzip wget git gnumeric tabix pigz ghostscript

Ubuntu 22.04

> sudo apt-get install -y rsync zlib1g bzip2 php8.1-cli php8.1-xml php8.1-mysql make unzip wget git gnumeric tabix pigz ghostscript

Ubuntu 24.04

> sudo apt-get install -y rsync zlib1g bzip2 php8.2-cli php8.2-xml php8.2-mysql make unzip wget git gnumeric tabix pigz ghostscript

Install Apptainer

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

Downloading

Clone megSAP repository with containerized tools:

> git clone -b containerize_tools https://github.com/imgag/megSAP.git

Resolving proxy issues with git

If you are behind a proxy that block the standard git port, you see something like this:

$ git clone https://github.com/imgag/megSAP.git
Cloning into 'megSAP'...
fatal: Unable to look up github.com (port 9418) (Name or service not known)

Then you have to adapt your ~/.gitconfig file like that:

[http]
proxy = http://[user]:[password]@[host]:[port]

Initial setup

To install the required tools and databases you will need to execute some installation scripts in the order described here.

First, we make sure the privileges of the installation scripts are correct:

> cd megSAP/data
> chmod 755 *.sh

Next, we install a few tools and download apptainer containers for the rest of the tools:

> ./download_tools.sh
> ./download_container.sh

Next, we need to download and index the reference genome:

> ./download_GRCh38.sh

Finally, we need to download and convert some open-source databases for annotations:

> ./download_dbs.sh
> php ../src/Install/db_download.php # DB downloads that require apptainer containers

Note: OMIM, HGMD and COSMIC are not downloaded automatically because of license issues. If you have the license for those databases, download/convert them according to the commented sections in the download_dbs.sh script.

NGSD initialization

If you want to use the NGSD and it is not initialized already, perform the following steps:

  1. Install a MariaDB server

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

  3. Add the NGSD information to the megSAP settings.ini file.

  4. Create tables using the following script:

    php ../src/Install/db_init.php

  5. Import genomics base data (genes, transcripts, phenotypes, gene-phenotype associations, ...) using the following tools from ngs-bits:

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

Note: To call ngs-bits tools, you have to call the apptainer container like that apptainer exec data/tools/apptainer_container/ngs-bits_[version].sif [tool] [parameters].

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.

Settings

Changing the settings is not absolutely necessary as most entries have defaults set.
If you want to change the settings, copy settings.ini.default to settings.ini and adapt the settings to your needs.

Settings entries are described here

Execution

Now the pipelines with all required tools and data are installed. They can be found within the src/Pipelines folder. Go to the documentation for further details.