Mercurial > repos > fgiacomoni > hmdb_ms_search
annotate README.txt @ 2:a3744fb3605c draft
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author | fgiacomoni |
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date | Fri, 25 Nov 2016 05:05:54 -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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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 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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17 |
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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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26 |
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27 $ sudo perl -MCPAN -e shell |
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28 cpan> install Text::CSV |
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29 |
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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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34 |
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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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38 |
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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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42 |
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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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46 |
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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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49 |
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50 |
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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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53 |
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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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58 |
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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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62 |
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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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65 |
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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 -- |