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