Wrappers for:
- the metaMS R package by Ron Wehrens (https://github.com/rwehrens/metaMS.git)
- the xcms package (https://xcmsonline.scripps.edu/, http://www.bioconductor.org/packages/release/bioc/html/xcms.html)
- the CAMERA tool ( http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html)

Wrappers written by Pieter Lukasse. 


=======Installation  (when updating: close all vignettes [i.e. pdfs/manuals] !)============

In R execute:
source("http://bioconductor.org/biocLite.R")
biocLite("metaMS")
biocLite("multtest")

# for "multi-threading"  (actually starts multiple R processes for parallel processing):
install.packages("snow")
install.packages("Cairo")

>> Running the wrappers: go to <this> directory and execute: 

======Run metaMS_cmd_pick_and_group.r with:=================

Rscript metaMS_cmd_pick_and_group.r test/extdata.zip test/example_settings.txt test/out/peakTable.txt test/out/xsAnnotatePrep.rdata positive test/out/html_peaks.html test/out 


======Run metaMS_cmd_annotate.r with:=================

Rscript metaMS_cmd_annotate.r test/LCDBtest.RData test/out/xsAnnotatePrep.rdata test/example_settings.txt test/out/annotationTable.txt "0" test/out/html_annot.html test/out


======Run xcms_differential_analysis.r with:=================

Rscript xcms_differential_analysis.r test/out/xsAnnotatePrep.rdata "CLASS1" "CLASS2" 10 test/out2/outtable.tsv test/out2/html/html.html test/out2/html


======Run xcms_get_eic.r with:=================


Rscript xcms_get_alignment_eic.r test/out/xsAnnotatePrep.rdata 10 300 3 STDmix_GC_01,STDmix_GC_02 test/out3/html/html.html test/out3/html

OR

Rscript xcms_get_mass_eic.r test/out/xsAnnotatePrep.rdata 10 3000 -1 -1 "77.98,231.96" 5 STDmix_GC_01,STDmix_GC_02 Yes raw test/out4/html/html.html test/out4/html



!!!!!!!!!!!!!!!!Troubleshooting:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


(1) NetCDF is required. If the following is found in the installation.log : 

	In file included from rnetCDF.c:2:0:
	rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
	compilation terminated.


then metaMS will not have been installed and running the tool will result in error: 
	
	<simpleError in library(metaMS): there is no package called 'metaMS'>

Possible solution:
	> Install the -dev of those packages to get the headers that are 
	  required to compile the package. In this case, you need libnetcdf-dev, udunits-bin and libudunits2-dev
	  (from http://stackoverflow.com/questions/11319698/how-to-install-r-packages-rnetcdf-and-ncdf-on-ubuntu)
So 
	>>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev
  
(2) Cairo / "no X11" (headless) mode is required. 

Possible solution:
	> install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.  
So 
	>>sudo apt-get install libcairo2-dev