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annotate README.txt @ 1:6d0a0f8f672a draft

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author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -0500
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1 ## ****** HMDB environnemnt : ****** ##
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2 # version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team
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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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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 Exporter ;
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13 use Data::Dumper ;
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14 use Getopt::Long ;
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15 use FindBin ;
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16 use Encode;
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18 # libs CPAN PERL :
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19 $ perl -e 'use Text::CSV' - OK
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20 use LWP::Simple; - OK
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21 use LWP::UserAgent; - OK
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22 use URI::URL; - OK
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23 use SOAP::Lite; - OK
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24 use HTML::Template ; - OK
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25 use XML::Twig ; - OK
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27 $ sudo perl -MCPAN -e shell
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28 cpan> install Text::CSV
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30 # libs pfem PERL : this lib were included in lib dir.
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31 use conf::conf qw( :ALL ) ;
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32 use formats::csv qw( :ALL ) ;
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33 --
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35 ## --- Conda compliant --- ##
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36 This tool and its PERL dependencies are "Conda compliant".
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37 The requirements section in the Xml file is still commented, waiting for "Conda" deployment improvement in Galaxy project.
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39 ## --- R bin and Packages : --- ##
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40 No interaction with R
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41 --
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43 ## --- Binary dependencies --- ##
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44 No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?)
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45 --
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47 ## --- Config : --- ##
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48 JS and CSS (used in HTML output format) are now hosted on cdn.rawgit.com server - no local config needed
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51 PS :If Galaxy can't find the file "hmdb.tmpl", perform this command line : perl -pi -e 's/\r//g' conf_hmdb.cfg
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52 --
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54 ## --- XML HELP PART --- ##
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55 one image :
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56 hmdb.png
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57 --
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59 ## --- DATASETS OR TUTORIAL --- ##
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60 Please find help on W4M: http://workflow4metabolomics.org/howto
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61 --
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63 ## --- ??? COMMENTS ??? --- ##
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64 If Galaxy can't find the file "hmdb.tmpl", perform this command line : " perl -pi -e 's/\r//g' " on the conf file "conf_hmdb.cfg".
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66 To use fully functionalities of HTML output format file :
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67 - check that sanitize_all_html option in universe_wsgi.ini file is uncomment and set to FALSE.
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68 --