===============
Getting Started
===============

Setting up ChiLin
===================

install quick-start
----------------------
In order to make installation easier, we write a script,
`download.sh`, run with help instruction. This script could get access
to the required data, such as bowtie index for hg19 and mm9, and all
stable dependent program.
basicly using the command below::

test installation
---------------------
we sample down 1000 reads for testing the ChiLin installation state
the test files are in the *tests* folder

- Generating Configuration file
 To run the tests, you need simply need to run::

    Chilin gen -s hg19

.. literalinclude:: ../chilin/tests/test.conf
      :language: ini
      :linenos:

 then, replace the *ChiLin.conf basis* section with
 chilin/tests/test.conf *basis* section. Fill in the treat and control in absolute
 path in the chilin/tests/ directory, the data are sampled down for
 speed test.

- run::

    ChiLin run -c ChiLin.conf -t TF

This should be run all dependent program with dependent data.

Common usage of ChiLin modules
===============================

Analyzing single datasets
---------------------------
Here we recommend a dataset from `GSE30624` for testing whole pipeline
with :ref:`QC report` generated.

Exmaple configuration
--------------------------
Here is one of the simpest ChiLin_ workflow you can make.

.. literalinclude:: ../chilin/tests/test.conf
      :language: ini
      :linenos:

.. _Get Started
replace the line 6 to line 9 with your machine configurations.
When saved to ``test.conf``, this config file can construct a powerful pipeline via:

::

    > ChiLin run -c test.conf -t TF

detailed output and temporary files will be explained in the :ref:`Manual`

Analyzing datasets in batch
-------------------------------
For *autodc* module for running ChiLin, we provide a fork version
chilin-mvc_ with tools for auto downloading GEO data and analyzing on
server.

*Getting help*
==============
Any question on installation or runnning is appreciated, please mail
to qinqianhappy@gmail.com.

.. chilin-mvc:: https://bitbucket.org/Alvin_Qin/chilin-mvc
.. ChiLin:: https://bitbucket.org/shenglinmei/chilin