<commit_before>genomics/bcftbx
===============

Utilities for NGS and genomics-related bioinformatics developed within the
Bioinformatics Core Facility (BCF) within the Faculty of Life Sciences (FLS)
at the University of Manchester (UoM).

Overview
********

The utilities are divided into broad categories:

- Handling data from SOLiD and Illumina sequencers (`solid2cluster`,
  `illumina2cluster`)
- Performing QC and manipulation of NGS data (`QC-pipeline`)
- Setting up reference data (`build-indexes`)
- Supporting analysis of ChIP-seq, RNA-seq and microarray data (`ChIP-seq`,
  `RNA-seq`, `microarray`, `NGS-general`)
- General non-bioinformatics utilities (`utils`)

There is also a Python package called `bcftbx` which is used by many of the
programs.

Installation
************

Run::

    python setup.py install

to install the package.

To use the package without installing it first you will need to add the
directory to your `PYTHONPATH` environment.

To install directly from github using `pip`::

    pip install git+https://github.com/fls-bioinformatics-core/genomics.git@devel

Documentation
*************

Documentation based on `sphinx` is available under the `docs` directory.

To build::

    cd docs
    make html
<commit_msg>README.rst: update installation instructions to use 'pip' over invoking setup.py directly.<commit_after>genomics/bcftbx
===============

Utilities for NGS and genomics-related bioinformatics developed within the
Bioinformatics Core Facility (BCF) within the Faculty of Life Sciences (FLS)
at the University of Manchester (UoM).

Overview
********

The utilities are divided into broad categories:

- Handling data from SOLiD and Illumina sequencers (`solid2cluster`,
  `illumina2cluster`)
- Performing QC and manipulation of NGS data (`QC-pipeline`)
- Setting up reference data (`build-indexes`)
- Supporting analysis of ChIP-seq, RNA-seq and microarray data (`ChIP-seq`,
  `RNA-seq`, `microarray`, `NGS-general`)
- General non-bioinformatics utilities (`utils`)

There is also a Python package called `bcftbx` which is used by many of the
programs.

Installation
************

It is recommended to use::

    pip install .

from within the top-level source directory to install the package.

To use the package without installing it first you will need to add the
directory to your `PYTHONPATH` environment.

To install directly from github using `pip`::

    pip install git+https://github.com/fls-bioinformatics-core/genomics.git@devel

Documentation
*************

Documentation based on `sphinx` is available under the `docs` directory.

To build::

    cd docs
    make html

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