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comparison metaMS/README.txt @ 6:4393f982d18f

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reorganized sources
author pieter.lukasse@wur.nl
date Thu, 19 Mar 2015 12:22:23 +0100
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1 Wrappers for:
2 - the metaMS R package by Ron Wehrens.
3 - the xcms package.
4
5 Wrappers written by Pieter Lukasse.
6
7
8 Installation (when updating: close all vignettes [i.e. pdfs/manuals] !)
9
10 In R:
11 source("http://bioconductor.org/biocLite.R")
12 biocLite("metaMS")
13 biocLite("multtest")
14 #biocLite("R2HTML")
15 # for "multi-threading" (actually starts multiple R processes for parallel processing):
16 install.packages("snow")
17 install.packages("Cairo")
18
19 ======Run metaMS_cmd_pick_and_group.r with:=================
20
21 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
22
23
24 ======Run metaMS_cmd_annotate.r with:=================
25
26 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
27
28
29 ======Run xcms_differential_analysis.r with:=================
30
31 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
32
33
34 ======Run xcms_get_eic.r with:=================
35
36
37 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
38
39 OR
40
41 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
42
43
44
45 !!!!!!!!!!!!!!!!Troubleshooting:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
46
47
48 NetCDF is required. If the following is found in the installation.log
49
50 In file included from rnetCDF.c:2:0:
51 rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
52 compilation terminated.
53
54
55 then metaMS will not have been installed and running the tool will result in error:
56 <simpleError in library(metaMS): there is no package called 'metaMS'>
57
58 Possible solution:
59 > Install the -dev of those packages to get the headers that are
60 required to compile the package. In this case, you need libnetcdf-dev, udunits-bin and libudunits2-dev
61 (from http://stackoverflow.com/questions/11319698/how-to-install-r-packages-rnetcdf-and-ncdf-on-ubuntu)
62 So
63 >>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev
64
65 Cairo / no X11 mode is required.
66
67 Possible solution:
68 > install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
69 So
70 >>sudo apt-get install libcairo2-dev