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1 ## ****** HR2 environnemnt : ****** ##
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2 # version sept 2014 M Landi / A LIEURADE, Cl LIONNET, P MARIJON, B RADISSON and L VARRAILHON / F Giacomoni
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3
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4 ## --- PERL compilator / libraries : --- ##
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5 $ perl -v
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6 This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
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7
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8 # libs CORE PERL :
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9 use strict ;
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10 use warnings ;
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11 use Carp qw (cluck croak carp) ;
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12 use Data::Dumper ;
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13 use Getopt::Long ;
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14 use FindBin ;
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15
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16 # libs CPAN PERL :
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17 $ perl -e 'use Text::CSV'
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18 $ sudo perl -MCPAN -e shell
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19 cpan> install Text::CSV
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20
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21 # libs pfem PERL : already include in the package
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22 use lib::conf qw( :ALL ) ;
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23 use lib::csv qw( :ALL ) ;
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24 --
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25
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26 ## --- R bin and Packages : --- ##
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27 NA
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28 --
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29
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30 ## --- Binary dependencies --- ##
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31 Install folowing binaries :
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32 * HR2 :
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33 source : HR2_v1.04.cpp available in the tar ball at lib/HR2_v1.04.cpp
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34 lab : http://jhau.maliwi.de/sci/ms.html for initial project and http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/ for fork
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35 install : in /opt/prog/metabolomics/hr2 (you can change this path in conf file : conf_hr2.cfg
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36 compilation : g++ HR2_v1.04.cpp -o HR2-all-res_v1.04.exe
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37
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38 The project is available on :
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39 http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/seven-golden-rules-supplement-v46.zip (the launch of the download may take some time)
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40 ~/seven-golden-rules-supplement-v46.zip/supplement/HR2-formula-generator/HR2.zip/HR2.cpp
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41 OR
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42 http://sourceforge.net/projects/hires/ : This proposed binary is an fork of the HiRes initial project.
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43 --
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44
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45 ## --- Config : --- ##
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46 Edit the following lines in the config file : conf_hr2.cfg
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47 lancerHR2=/your_hr2_binary_path/HR2-all-res_v1.04.exe
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48 JS_GALAXY_PATH=http://YOUR_GALAXY_HOSTNAME/static/scripts/libs/outputs
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49 CSS_GALAXY_PATH=http://YOUR_GALAXY_HOSTNAME/static/style
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50 --
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51
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52 ## --- XML HELP PART --- ##
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53 one image : in the static/images dir
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54 hr2.png
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55 --
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56
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57 ## --- DATASETS --- ##
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58 No data set ! waiting for galaxy pages
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59 --
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60
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61 ## --- ??? COMMENTS ??? --- ##
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62 In the PFEM version, the HR2 source (HR2_v*.cpp) is modified to correct atom exact masses.
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63 For more information, please contact us. |
