Mercurial > repos > pieterlukasse > prims_metabolomics2

annotate metaMS/README.txt @ 16:fe4682eb938c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
small improvement
author pieter.lukasse@wur.nl
date Mon, 23 Mar 2015 08:40:42 +0100
parents 346ff9ad8c7a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
1 Wrappers for:
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
2 - the metaMS R package by Ron Wehrens (https://github.com/rwehrens/metaMS.git)
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
3 - the xcms package (https://xcmsonline.scripps.edu/, http://www.bioconductor.org/packages/release/bioc/html/xcms.html)
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
4 - the CAMERA tool ( http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html)
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
5
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
6 Wrappers written by Pieter Lukasse.
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
7
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
8
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
9 =======Installation (when updating: close all vignettes [i.e. pdfs/manuals] !)============
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
10
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
11 In R execute:
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
12 source("http://bioconductor.org/biocLite.R")
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
13 biocLite("metaMS")
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
14 biocLite("multtest")
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
15
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
16 # for "multi-threading" (actually starts multiple R processes for parallel processing):
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
17 install.packages("snow")
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
18 install.packages("Cairo")
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
19
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
20 >> Running the wrappers: go to <this> directory and execute:
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
21
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
22 ======Run metaMS_cmd_pick_and_group.r with:=================
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
23
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
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
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
25
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
26
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
27 ======Run metaMS_cmd_annotate.r with:=================
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
28
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
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
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
30
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
31
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
32 ======Run xcms_differential_analysis.r with:=================
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
33
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
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
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
35
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
36
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
37 ======Run xcms_get_eic.r with:=================
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
38
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
39
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
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
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
41
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
42 OR
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
43
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
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
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
45
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
46
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
47
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
48 !!!!!!!!!!!!!!!!Troubleshooting:!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
49
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
50
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
51 (1) NetCDF is required. If the following is found in the installation.log :
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
52
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
53 In file included from rnetCDF.c:2:0:
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
54 rnetCDF.h:1:20: fatal error: netcdf.h: No such file or directory
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
55 compilation terminated.
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
56
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
57
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
58 then metaMS will not have been installed and running the tool will result in error:
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
59
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
60 <simpleError in library(metaMS): there is no package called 'metaMS'>
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
61
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
62 Possible solution:
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
63 > Install the -dev of those packages to get the headers that are
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
64 required to compile the package. In this case, you need libnetcdf-dev, udunits-bin and libudunits2-dev
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
65 (from http://stackoverflow.com/questions/11319698/how-to-install-r-packages-rnetcdf-and-ncdf-on-ubuntu)
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
66 So
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
67 >>sudo apt-get install libnetcdf-dev, udunits-bin and libudunits2-dev
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
68
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
69 (2) Cairo / "no X11" (headless) mode is required.
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
70
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
71 Possible solution:
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
72 > install of cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
6
4393f982d18f reorganized sources
pieter.lukasse@wur.nl
parents:
diff changeset
73 So
14
346ff9ad8c7a fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents: 6
diff changeset
74 >>sudo apt-get install libcairo2-dev