Mercurial > repos > fgiacomoni > hmdb_ms_search
diff README.txt @ 1:6d0a0f8f672a draft
planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
author | fgiacomoni |
---|---|
date | Wed, 23 Nov 2016 09:31:50 -0500 |
parents | |
children | 8f7546d0b925 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,68 @@ +## ****** 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. +-- \ No newline at end of file