diff README.txt @ 1:6d0a0f8f672a draft

planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -0500
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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
+-- 
+
+## --- Binary dependencies --- ##
+No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?)
+--
+
+## --- 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
+--
+
+## --- XML HELP PART --- ##
+one image : 
+hmdb.png
+--
+
+## --- DATASETS OR TUTORIAL --- ##
+Please find help on W4M: http://workflow4metabolomics.org/howto 
+--
+
+## --- ??? 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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