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Installation instructions for levioSAM2

levioSAM2 supports a variety of methods for installation:

  • Conda
  • Docker
  • Singularity
  • CMake

Conda

conda install -c conda-forge -c bioconda leviosam2

Docker

You can obtain a Docker image of the latest version from Docker hub:

docker pull naechyun/leviosam2:latest

Singularity

singularity pull docker://naechyun/leviosam2:latest

CMake

Prerequisites

Make sure the following prerequisite libraries are installed on your system.

Both libraries are available through coda:

conda install -c conda-forge sdsl-lite
conda install -c bioconda htslib

Another easy way to install these dependencies is to use your OS's existing package system:

apt-get install libhts-dev libsdsl-dev # Debian/Ubuntu
brew tap brewsci/bio; brew install htslib sdsl-lite # MacOS

If using RedHat or Fedora, then you must install sdsl-lite manually. But you can install htslib through yum:

yum install htslib

Or you can choose to install them manually by following the install instructions on their respective pages.

CMake

Once the prerequisite packages are installed and the locations of their installations are known, specify their locations to CMake by running the following commands:

mkdir build
cd build
cmake ..
make

If you installed the dependencies manually, you might have to modify the cmake command to specify their library and include directory locations like so:

cmake -D CMAKE_LIBRARY_PATH="/path/to/libsdsl/;/path/to/libhts/" \
      -D CMAKE_INCLUDE_PATH="/path/to/include/" ..

Test

We provide an end-to-end test and a set of unit tests for levioSAM.

  • The end-to-end test can be run with python leviosam-test.py. This test includes running levioSAM on several test files in testdata. We also use picard to test if the lifted SAM files are valid.

  • The unit test can be run cd build; ctest if you use cmake to build levioSAM; or make gtest; cd testdata; ../gtest if you use make to build levioSAM2.