Currently only Linux is supported!
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.
Ubuntu 20.04
> sudo apt-get install -y rsync bzip2 default-jre bioperl libset-intervaltree-perl libjson-xs-perl libcarp-assert-perl libgd-dev libdb-dev libxml2-dev libxml2-utils php7.4-cli php7.4-xml php7.4-mysql tabix unzip wget build-essential cmake cpanminus git libbz2-dev liblzma-dev libncurses5-dev libqt5sql5-mysql libpng-dev libqt5xmlpatterns5-dev libssl-dev qt5-default qt5-qmake qtbase5-dev libcurl4-openssl-dev libhts-dev libtabixpp-dev libtabixpp0 meson ninja-build gnumeric numdiff libpcre2-dev libreadline-dev libffi-dev libharfbuzz-dev libfribidi-dev libgit2-dev pybind11-dev libsqlite3-dev openjdk-17-jdk openjdk-17-jre gfortran
Ubuntu 22.04
> sudo apt-get install -y rsync bzip2 default-jre bioperl libset-intervaltree-perl libjson-xs-perl libcarp-assert-perl libgd-dev libdb-dev libxml2-dev libxml2-utils php8.1-cli php8.1-xml php8.1-mysql tabix unzip wget build-essential cmake cpanminus git libbz2-dev liblzma-dev libncurses5-dev libqt5sql5-mysql libpng-dev libqt5xmlpatterns5-dev libssl-dev qtbase5-dev qt5-qmake qtbase5-dev libhts-dev libtabixpp-dev libtabixpp0 meson ninja-build gnumeric numdiff libpcre2-dev libreadline-dev libffi-dev libharfbuzz-dev libfribidi-dev libgit2-dev pybind11-dev libsqlite3-dev openjdk-17-jdk openjdk-17-jre gfortran
RHEL 8.3
Add LANGUAGE and LC_ALL to /etc/locale.conf
Example:
LANGUAGE="en_US.UTF-8"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
> subscription-manager repos --enable codeready-builder-for-rhel-8-x86_64-rpms
> yum groupinstall "Development Tools" -y
> yum install zlib-devel bzip2-devel xz-devel ncurses-devel libcurl-devel cpan cpanminus gd-devel libdb-devel -y
> dnf install php-cli php-xml php-mysqlnd R-core R-core-devel -y
> yum install qt5-qtcharts.x86_64 qt5-qtbase-odbc.x86_64 qt5-qtbase-mysql.x86_64 qt5-qtxmlpatterns.x86_64 libcurl-devel.x86_64 qt5-devel.x86_64
Clone the latest release of megSAP:
> git clone -b 2024_09 https://github.com/imgag/megSAP.git
Or, if you want to test the current development version:
> git clone https://github.com/imgag/megSAP.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]
To install the required tools and data you will need to execute custom script delivered with the repository. If you work in a security critical environment it is advised that you use a chroot environment as the scripts will attempt to install software with administrative privileges.
First, we make sure the privileges of the installation scripts are correct:
> cd megSAP/data
> chmod 755 *.sh
Next, we install all required tools
> ./download_tools.sh
> ./download_tools_somatic.sh #only needed for somatic analysis
> ./download_tools_rna.sh #only needed for RNA analysis
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
> ./download_dbs_rna.sh #only needed for RNA analysis
Note: OMIM and HGMD 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 script.
Note: The use of the optional NGSD annotation requires an export of the variants to VCF files. These files should be updated on a regular basis. For example code take a look at the NGSD section in the download script.
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
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.