Merge pull request #22 from sartorlab/v0.2.0-beta

* Simplify project setup by adding parameters to init.R.
* Split methylSig analysis by chromosome to deal with memory issues for large WGBS runs (we will return to this solution in a future release).
* Implement simple classification for pulldown_compare.
* Refactor annotatr related code. Currently works with annotatr v0.99.5 and annotatr.data v0.99.4.
* Turn off random regions for cases where it is too computationally cumbersome.
* Remove *_align rules as prereqs for *_compare rules.
* Add intron/exon boundaries to default annotatr analyses.

README.md

@@ -1,6 +1,6 @@
 ## mint: Analysis, integration, classification, and annotation of DNA methylation and hydroxymethylation data
 
-v0.1.5
+v0.2.0
 
 ## Contents
 

init.R

@@ -5,14 +5,28 @@
 library(optparse)
 
 option_list = list(
-  make_option('--project', type='character'),
-  make_option('--genome', type='character'),
-  make_option('--datapath', type='character')
+	make_option('--project', type='character',
+		help='[Required] The name for the project. Corresponding to projects/[project]_annotation.txt file.'),
+	make_option('--genome', type='character',
+		help='[Required] The genome to be used for analyses.'),
+	make_option('--genomepath', type='character',
+		help='[Required] The absolute path to the reference genome.'),
+	make_option('--chrompath', type='character',
+		help='[Required] The absolute path to the chromosome length file.'),
+	make_option('--datapath', type='character',
+		help='[Required] The absolute path to the .fastq.gz sequencing data whose filenames match those in the sampleID column of the projects/[project]_annotation.txt file.')
 )
-opt = parse_args(OptionParser(option_list=option_list))
+option_parser = OptionParser(
+	usage = "usage: Rscript %prog [options]",
+	option_list = option_list,
+	add_help_option = TRUE,
+	prog = "init.R")
+opt = parse_args(option_parser)
 
 project = opt$project
 genome = opt$genome
+genomepath = opt$genomepath
+chrompath = opt$chrompath
 datapath = opt$datapath
 
 file_make = sprintf('projects/%s/makefile', project)