--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS/README.txt	Thu Mar 19 12:22:23 2015 +0100
@@ -0,0 +1,70 @@
+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