Wrappers for:
- the metaMS R package by Ron Wehrens.
- the xcms package. 

Wrappers written by Pieter Lukasse. 


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

In R:
source("http://bioconductor.org/biocLite.R")
biocLite("metaMS")
biocLite("multtest")
#biocLite("R2HTML")
# for "multi-threading"  (actually starts multiple R processes for parallel processing):
install.packages("snow")
install.packages("Cairo")

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

E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>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:=================

E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>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:=================

E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>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:=================


E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>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

E:\workspace\PRIMS-metabolomics\python-tools\tools\metaMS>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:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


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
  
Cairo / no X11 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