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comparison metaMS/README.txt @ 14:346ff9ad8c7a

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fix for rankfilter, removed pfd read functional
author linda.bakker@wur.nl <linda.bakker@wur.nl>
date Fri, 20 Mar 2015 17:10:04 +0100
parents 4393f982d18f
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13:5a753524e525 14:346ff9ad8c7a
1 Wrappers for: 1 Wrappers for:
2 - the metaMS R package by Ron Wehrens. 2 - the metaMS R package by Ron Wehrens (https://github.com/rwehrens/metaMS.git)
3 - the xcms package. 3 - the xcms package (https://xcmsonline.scripps.edu/, http://www.bioconductor.org/packages/release/bioc/html/xcms.html)
4 - the CAMERA tool ( http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html)
4 5
5 Wrappers written by Pieter Lukasse. 6 Wrappers written by Pieter Lukasse.
6 7
7 8
8 Installation (when updating: close all vignettes [i.e. pdfs/manuals] !) 9 =======Installation (when updating: close all vignettes [i.e. pdfs/manuals] !)============
9 10
10 In R: 11 In R execute:
11 source("http://bioconductor.org/biocLite.R") 12 source("http://bioconductor.org/biocLite.R")
12 biocLite("metaMS") 13 biocLite("metaMS")
13 biocLite("multtest") 14 biocLite("multtest")
14 #biocLite("R2HTML") 15
15 # for "multi-threading" (actually starts multiple R processes for parallel processing): 16 # for "multi-threading" (actually starts multiple R processes for parallel processing):
16 install.packages("snow") 17 install.packages("snow")
17 install.packages("Cairo") 18 install.packages("Cairo")
18 19
20 >> Running the wrappers: go to <this> directory and execute:
21
19 ======Run metaMS_cmd_pick_and_group.r with:================= 22 ======Run metaMS_cmd_pick_and_group.r with:=================
20 23
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 24 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 25
23 26
24 ======Run metaMS_cmd_annotate.r with:================= 27 ======Run metaMS_cmd_annotate.r with:=================
25 28
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 29 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 30
28 31
29 ======Run xcms_differential_analysis.r with:================= 32 ======Run xcms_differential_analysis.r with:=================
30 33
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 34 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 35
33 36
34 ======Run xcms_get_eic.r with:================= 37 ======Run xcms_get_eic.r with:=================
35 38
36 39
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 40 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 41
39 OR 42 OR
40 43
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 44 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 45
43 46
44 47
45 !!!!!!!!!!!!!!!!Troubleshooting:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 48 !!!!!!!!!!!!!!!!Troubleshooting:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
46 49
47 50
48 NetCDF is required. If the following is found in the installation.log 51 (1) NetCDF is required. If the following is found in the installation.log :
49 52
50 In file included from rnetCDF.c:2:0: 53 In file included from rnetCDF.c:2:0:
51 rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory 54 rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
52 compilation terminated. 55 compilation terminated.
53 56
54 57
55 then metaMS will not have been installed and running the tool will result in error: 58 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'> 59
60 <simpleError in library(metaMS): there is no package called 'metaMS'>
57 61
58 Possible solution: 62 Possible solution:
59 > Install the -dev of those packages to get the headers that are 63 > 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 64 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) 65 (from http://stackoverflow.com/questions/11319698/how-to-install-r-packages-rnetcdf-and-ncdf-on-ubuntu)
62 So 66 So
63 >>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev 67 >>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev
64 68
65 Cairo / no X11 mode is required. 69 (2) Cairo / "no X11" (headless) mode is required.
66 70
67 Possible solution: 71 Possible solution:
68 > install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. 72 > install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
69 So 73 So
70 >>sudo apt-get install libcairo2-dev 74 >>sudo apt-get install libcairo2-dev