Full installation instructions are available after accepting appropriate license for your use case. For academic use, please see the majiq download page. For commercial use, you will need to contact us, please refer to majiq commercial.

Required dependencies

MAJIQ and VOILA are best supported with a Linux-based operating system. However, they have also successfully been tested/used these tools on MacOS and Windows.

MAJIQ requires for installation:

  • Python (3.8 or later)

  • setuptools (45 or later)

  • HTSlib (1.10 or later)

  • C++ compiler with C++11 support (e.g. gcc >= 4.8.1)

In general, before starting, you should have python3.8 installed, with both python and the included pip package installation tool.

HTSlib installation

MAJIQ’s depends on HTSlib (1.10 or later) in order to efficiently parse BAM files from RNA-seq experiments.

If you are have admin rights, you can install system-wide with package managers on Linux:

  • debian-based: apt install libhts-dev,

  • rpm-based: yum install htslib-devel.

Otherwise, you can install HTSlib from source. For example, to install htslib-1.13 to ~/install/htslib-1.13, you could run:

# download htslib 1.13 archive to current directory
curl -OL
tar -xf htslib-1.13.tar.bz2  # extract archive
cd htslib-1.13  # change into htslib source directory
# configure, make, and install htslib to ~/install/htslib-1.13
./configure --prefix=$HOME/install/htslib-1.13
make install

See INSTALL from the HTSlib sources for detailed instructions.

MAJIQ installation

If HTSlib was not installed to the default system-wide location, MAJIQ installers need to know where it was installed. This is done by setting the environment variables HTSLIB_LIBRARY_DIR and HTSLIB_INCLUDE_DIR.

For example, with previous instructions, from the same directory as the README:

# change to where library/include directories are installed
export HTSLIB_LIBRARY_DIR=$HOME/install/htslib-1.13/lib
export HTSLIB_INCLUDE_DIR=$HOME/install/htslib-1.13/include

Afterwards, install MAJIQ following the full instructions available after accepting the license agreement (e.g., pip install <url to MAJIQ repository>).