Haphpipe

Description

haphpipe website  

HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.

Environment Modules

Run module spider haphpipe to find out what environment modules are available for this application.

System Variables

• HPC_HAPHPIPE_DIR - installation directory
• HPC_HAPHPIPE_BIN - executable directory

Additional Information

For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default. To enable it, set the environment variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: mpiexec --mca pml ucx --mca osc ucx ... Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX. Please consult UCX's documentation for detail.

Citation

If you publish research that uses haphpipe you have to cite it as follows:

When using HAPHPIPE, please cite their article when it is available. For now, reference the GitHub website: https://github.com/gwcbi/haphpipe and the validation paper.