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Installation and Quick Start

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Michael Alonge edited this page Jan 23, 2019 · 1 revision

Dependencies

RaGOO depends on Python3 as well as the following packages:

  1. intervaltree
  2. numpy
  3. Minimap2

The first two packages will be installed automatically when installing RaGOO. Minimap2 is straightforward to install following the instructions on its website. Place the minimap2 executable in your path, or specify its location with the -m paramter.

Installation

Currently, the only way to install RaGOO is from source. Set up a virtualenv if desired, just be sure to make a python3 environment. Then, enter the following command to install RaGOO and its dependencies:

$ python setup.py install

Example Run

Both the assembly and the reference must be in the current workding directory, so please either copy them or create a symbolic link. For example:

$ cd /path/to/current/working/directory
$ ln -s /path/to/contigs.fasta
$ ln -s /path/to/reference.fasta
$ ragoo.py contigs.fasta reference.fasta

The associated output will be in ragoo_output.

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