New upstream version 2.2

compiler:

  - gcc

  - clang

before_script:

  - pip install --upgrade --user pip

  - pip install --user networkx

script: make; make dependencies; make test

 No newline at end of file

Ragout

======

Version: 2.1.1

Version: 2.2

[![Build Status](https://travis-ci.org/fenderglass/Ragout.svg?branch=master)](https://travis-ci.org/fenderglass/Ragout)

- [Usage](docs/USAGE.md)

Authors

-------

- Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of Sciences, UCSD)

- Pavel Avdeev (St. Petersburg University of the Russian Academy of Sciences)

- Dmitriy Meleshko (St. Petersburg University of the Russian Academy of Sciences)

- Son Pham (UCSD)

Code contributions

------------------

* Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of Sciences, UCSD)

* Pavel Avdeev (St. Petersburg University of the Russian Academy of Sciences)

* Dmitriy Meleshko (St. Petersburg University of the Russian Academy of Sciences)

* Son Pham (UCSD)

* Tatiana Malygina

Publications

------------

- Kolmogorov et al., "Chromosome assembly of large and complex genomes using multiple references",

bioRxiv preprint, 2016

* Kolmogorov et al., "Chromosome assembly of large and complex genomes using multiple references",

Genome Research, 2018

- Kolmogorov et al., "Ragout: A reference-assisted assembly tool for bacterial genomes",

* Kolmogorov et al., "Ragout: A reference-assisted assembly tool for bacterial genomes",

Bioinformatics, 2014

---------------

The work was partially supported by VP Foundation.

We would like to thank:

- Anna Liosnova (benchmarks and useful suggestions)

- Nikolay Vyahhi (testing and useful suggestions)

- Aleksey Gurevich (testing)

We also would like to thank:

* Anna Liosnova (benchmarks and useful suggestions)

* Nikolay Vyahhi (testing and useful suggestions)

* Aleksey Gurevich (testing)

Third-party

-----------

Ragout package includes some third-patry software (see INSTALL.md for details)

Ragout is using some third-patry software (see INSTALL.md for details):

* Networkx 1.8 Python library [http://networkx.github.io/]

* Newick 1.3 [http://www.daimi.au.dk/~mailund/newick.html]

* Networkx Python library [http://networkx.github.io/]

* Newick parser by Thomas Mailund [https://www.mailund.dk/]

* Sibelia [http://github.com/bioinf/Sibelia]

* HAL Tools [https://github.com/ComparativeGenomicsToolkit/hal]

License

import os

import sys

LIB_DIR = "lib"

BIN_DIR = "bin"

#Check Python version

#Setting executable paths

ragout_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))

lib_absolute = os.path.join(ragout_root, LIB_DIR)

sys.path.insert(0, lib_absolute)

sys.path.insert(0, ragout_root)

bin_absolute = os.path.join(ragout_root, BIN_DIR)

* Python 2.7

* Sibelia [http://github.com/bioinf/Sibelia]

* HAL Tools [https://github.com/glennhickey/hal] (alternatively to Sibelia)

* python-networkx >= 2.2

* HAL Tools (optionally) [https://github.com/ComparativeGenomicsToolkit/hal]

Building

--------

Local installation

------------------

To build Ragout binaries, type:

If you don't want to use bioconda release, you can build

Ragout repository clone and run it locally without installing

into system. To do this, perform:

    git clone https://github.com/fenderglass/Ragout.git

	cd Ragout

	python setup.py build

	pip install -r requirements.txt --user

    python scripts/install-sibelia.py

You will also need either Sibelia or HAL Tools installed

This will also build and install Sibelia and all Python dependencies.

See below for HAL installation instructions.

To build and install Sibelia, use:

Once installed, you can invoke Ragout from the cloned directory by using:

        python scripts/install-sibelia.py

    bin/ragout

If you already have Sibelia installed into your system, it will

be picked up automatically.

System installation

-------------------

Optionally, you may isntall Ragout into your system by typing:

To integrate Ragout into your system, run:

    git clone https://github.com/fenderglass/Ragout.git

	cd Ragout

	python setup.py build

    python setup.py install

This assumes that you already have python-networkx package

installed into your system (using the respective package manager).

Sibelia / HAL tools should also be installed / integrated separately.

HAL Tools

---------

blocks decomposition instead of Sibelia (recommended for large genomes). 

If you want to use HAL alignment as input,

you need to install HAL Tools package [https://github.com/glennhickey/hal]

you need to install HAL Tools package [https://github.com/ComparativeGenomicsToolkit/hal]

as it is described in the manual. Do not forget to properly set PATH and PYTHONPATH

environment variables.

Q: Many compilation errors, possibly with 

"unrecognized command line option '-std=c++0x'" message:

A: Probably your compiler is too old and does not support C++0x. Minimum required

versions of GCC and Clang are given in the beginning of this document.

A: Probably your compiler is too old and does not support C++0x. Make

sure you have at least GCC 4.6+ / Clang 3.2+

Q: "libstdc++.so.6: version `CXXABI_1.3.5' not found" or similar error when running

__version__ = "2.1.1"

__version__ = "2.2"