comparison README.txt @ 1:6d0a0f8f672a draft

planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471

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## ****** HMDB environnemnt : ****** ##
# version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team

## --- PERL compilator / libraries : --- ##
$ perl -v
This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi

# libs CORE PERL : 
use strict ;
use warnings ;
use Carp qw (cluck croak carp) ;
use Exporter ;
use Data::Dumper ;
use Getopt::Long ;
use FindBin ;
use Encode;

# libs CPAN PERL : 
$ perl -e 'use Text::CSV' 	- OK
use LWP::Simple;		- OK
use LWP::UserAgent;		- OK
use URI::URL;			- OK
use SOAP::Lite;			- OK
use HTML::Template ;		- OK
use XML::Twig ; 	- OK

$ sudo perl -MCPAN -e shell
cpan> install Text::CSV

# libs pfem PERL : this lib were included in lib dir.
use conf::conf  qw( :ALL ) ;
use formats::csv  qw( :ALL ) ;
--

## --- Conda compliant --- ##
This tool and its PERL dependencies are "Conda compliant".
The requirements section in the Xml file is still commented, waiting for "Conda" deployment improvement in Galaxy project.

## --- R bin and Packages : --- ##
No interaction with R
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## --- Binary dependencies --- ##
No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?)
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## --- Config : --- ##
JS and CSS (used in HTML output format) are now hosted on cdn.rawgit.com server - no local config needed


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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## --- XML HELP PART --- ##
one image : 
hmdb.png
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## --- DATASETS OR TUTORIAL --- ##
Please find help on W4M: http://workflow4metabolomics.org/howto 
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## --- ??? COMMENTS ??? --- ##
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".

To use fully functionalities of HTML output format file : 
  - check that sanitize_all_html option in universe_wsgi.ini file is uncomment and set to FALSE.
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