Analysis components from Oxford Nanopore Research
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README.md

Prototype real-time analysis components

Build Status

Pomoxis started life as a set of services to perform analysis of squiggles as they are produced in real-time. This functionality still exists although has been complemented with a number of offline analyses for generating and analysing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.

Documentation can be found at https://nanoporetech.github.io/pomoxis/.

Compatibility

Pomoxis is developed on Ubuntu 16.04, other recent linuxes should be equally compatible (see build notes below. Pomoxis is known to work on at least some MacOS High Sierra configurations, though some components (notably scrappy) are known to not work on some MacOS configurations (combinations of OS and xcode versions).

Build

Pomoxis should be installed inside a virtual environment. A Makefile is provided to create a fresh environment, and to fetch, compile and install all direct dependencies into the environment.

Before installing pomoxis is may be required to install some prerequisite packages, best installed by a package manager. On Ubuntu these are:

  • gcc-4.9
  • g++-4.9
  • zlib1g-dev
  • libncurses5-dev
  • python3-all-dev
  • libhdf5-dev
  • libatlas-base-dev
  • libopenblas-base
  • libopenblas-dev
  • libbz2-dev
  • liblzma-dev
  • libffi-dev

To setup the environment run:

git clone --recursive https://github.com/nanoporetech/pomoxis
cd pomoxis
make install
. ./venv/bin/activate

The installation of porechop (https://github.com/rrwick/Porechop) requires a newer compiler than is a available on some systems. It may therefore be necessary to install a newer compiler and set environment variables before the make install step:

# For porechop to be compiled on older systems set these, e.g.:
export CXX="g++-4.9" CC="gcc-4.9"

Note also that racon requires at least gcc>=4.8.5 to compile smoothly.

Running the above within a pre-exisiting virtual environnment may well fail; advanced may wish to simply run the setup.py file in the standard manner after compiling the third party programs as in the Makefile.

Extras

The distribution bundles some common bioinformatics tools (some of which are not currently used by pomoxis itself, but are used in the offline analysis scripts):

  • miniasm
  • minimap2
  • racon
  • bwa
  • samtools
  • porechop

These will be compiled and installed into the virtual environment created as above.