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README.txt
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README.txt
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## ****** HMDB environnemnt : ****** ##
# version June 2022 M Landi / F Giacomoni - INRAE - 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.
--