--- a/metaMS/README.txt	Thu Mar 19 15:04:56 2015 +0100
+++ b/metaMS/README.txt	Fri Mar 20 17:10:04 2015 +0100
@@ -1,70 +1,74 @@
 Wrappers for:
-- the metaMS R package by Ron Wehrens.
-- the xcms package. 
+- 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] !)
+=======Installation  (when updating: close all vignettes [i.e. pdfs/manuals] !)============
 
-In R:
+In R execute:
 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")
 
+>> Running the wrappers: go to <this> directory and execute: 
+
 ======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 
+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
+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
+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
+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
+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 
+(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.
+	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'>
+	
+	<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)
+	> 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
+	>>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev
   
-Cairo / no X11 mode is required. 
+(2) Cairo / "no X11" (headless) mode is required. 
 
 Possible solution:
-> install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.  
+	> install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.  
 So 
->>sudo apt-get install libcairo2-dev
+	>>sudo apt-get install libcairo2-dev