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#                                   #
# ChIPSeq Scoring                   #
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-- DEPENDENCIES

+ MACS 1.4
http://liulab.dfci.harvard.edu/MACS/Download

+ MACS 2
https://github.com/taoliu/MACS/downloads

+ SPP 1.10 [modified]
http://code.google.com/p/phantompeakqualtools/

+ IDR
https://sites.google.com/site/anshulkundaje/projects/idr

+ SJM 1.2.0
http://sourceforge.net/projects/hpcsjm/

+ R 2.15.1

+ SUN GRID ENGINE

-- INSTALLATION

Unpack scripts and add directory to $PYTHONPATH.  Modify globals.conf
configuration file to input the particulars of your system.  See wiki
(https://github.com/StanfordBioInformatics/Scoring/wiki) for details.

-- USAGE

Create control.conf and sample.conf configuration files.  Sample config
files are included.  Further details are available on the wiki
(https://github.com/StanfordBioInformatics/Scoring/wiki).  Use the config
files as input to pipeline.py

Usage:  pipeline.py [-f] [-p] [-h] [-s] [-a] [-m <email address>] 
[-l <directory>] [-n <run_name>] [-c <peakcaller>] <control_config_file>
 [<sample_config_file>]

Arguments:
	-c, --peakcaller <peakcaller>
	specify the peakcaller to be used.  Current options are peakseq, macs, 
	macs2, spp. Defaults to macs2.
	
	-a, --no_archive
	does not archive the control and sample results.  
	
	-f, --force
	forces running of pipeline, even if results already exist
	
	-p, --print
	prints the job commands, but does not dispatch them to the cluster
	
	-d, --no_duplicates
	runs cross correlation analysis assuming duplicated reads have
	already been filtered out of the mapped reads.  Uncommon, so
	defaults to false.
	
	-h, --help
	displays this usage information and exits
	
	-l <directory>, --log <directory>
	log directory, current working directory if not specified
	
	-n <run_name>, --name <run_name>
	name for the pipeline run
	
	-m <email_address>, --mail <email_address>
	email address to send summary and result location
	
	-s, --snap
	make a call to the SNAP LIMS after completion
	
	--filtchr <chromosome>
	SPP option to ignore a chromosome during analysis.  Used to fix bug that 
	chrs with low read counts causes SPP to fail. 
	
	--rmdups
	Filter out all duplicate reads in sample read files before peakcalling.  Use
	when PCR amplification errors are present.  (i.e., PBC value is low)
	
	<control_config_file>
	(required) configuration file for the experiment's control
	
	<sample_config_file>
	configuration file for the sample replicates in the experiment.  Optional, 
	but in most cases this is specified.