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author fgiacomoni
date Thu, 19 Nov 2020 14:28:46 +0000
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1 INTRODUCTION
2 ============
3
4 This tool is part of the xcms/camera/XSeeker workflow, and it inserts
5 between camera and XSeeker. It takes in input a rdata producd by camera,
6 gather some data from mzxml original files, and create a database
7 containing all these informations organized in such a way that XSeeker
8 has just to display the data without manipulating them anymore, which
9 makes it a lot faster and easier to use.
10
11
12 PREREQUISITES
13 =============
14 There is not real preriquesite to understand how this tool works
15 and to modify it. There is a single R script - XSeekerPreparator.R - that do
16 all the work.
17
18 You can make this tool work alone, but you can integrate it with galaxy.
19 In this case, you need to have a galaxy instance you can configure.
20 It is also recomended to have access to the datatypes definitions (in
21 the python files) to make the outputs recognized by galaxy as XSeeker's
22 database files.
23
24
25 DESIGN
26 ======
27 This tool is very simple and does a little number of things, so there is
28 only a single file: XSeekerPreparator.R .
29 There is a test/test.sh file that can be used as an example to know how
30 to use this tool.
31
32 You will find the galaxy patches in the galaxy/ directory. These files
33 are not meant to be copy/paste-ed. The content of these files must be
34 added to the existing files of your galaxy instance
35
36
37 REQUIREMENT
38 =====
39
40 - R-4.0.0
41 - optparse
42 - xcms
43 - blob
44 - fst
45 - DBModelR
46 - stringr
47 - optparse
48 - galaxy (optional)
49
50 #### R 4.0.0
51 - `export R_MAJOR=4 R_VERSION=4.0.0 BUILD_TARGET_DIR=~/R/`
52 - `wget https://cran.rstudio.com/src/base/R-${R_MAJOR}/R-${R_VERSION}.tar.gz`
53 - `tar -xf "R-${R_VERSION}.tar.gz"`
54 - `cd ./R-${R_VERSION}/`
55 - `./configure --prefix="${BUILD_TARGET_DIR}" --with-readline="no" --with-x="no"`
56 - `export CC="gcc -fPIC"`
57 - `make`
58 - `make install`
59
60 #### Packages
61 ```bash
62 ~/R/bin/R -e "
63 install.packages(
64 c(
65 'optparse',
66 'blob',
67 'fst',
68 'stringr',
69 'optparse',
70 'RSQLite',
71 'remotes',
72 'BiocManager'
73 ), repos='https://cloud.r-project.org'
74 )" && \
75 ~/R/bin/R -e '
76 remotes::install_github("LainPavot/DBModelR", force=TRUE)
77 ' && \
78 ~/R/bin/R -e '
79 BiocManager::install("xcms")
80 '
81 ```
82
83 #### galaxy
84 ```bash
85 git clone https://github.com/galaxyproject/galaxy
86 ```
87
88 DEPLOY
89 =====
90
91 Install the tool in galaxy:
92 Open each file in the galaxy/ directory and copy their content to their
93 respective files in your galaxy instance.
94 Copy XSeekerPreparator.R in galaxy/tool/tools/LC-MSMS/
95
96 METADATA
97 --------
98
99 - **@name**: XSeekerPreparator
100 - **@version**: 1.1.2
101 - **@authors**: Lain Pavot
102 - **@date creation**: 15/09/2020
103
104 NOTES
105 -----
106 Developed and tested using:
107
108 - R 4.0.0
109 - optparse 1.6.6
110 - xcms 3.10.2
111 - blob 1.2.1
112 - fst 0.9.4
113 - DBModelR
114 - stringr 1.4.0
115 - galaxy 21.01