Mercurial > repos > fgiacomoni > hmdb_ms_search
view hmdb/README.txt @ 0:9583f9772198 draft
Init and uploaded
author | fgiacomoni |
---|---|
date | Thu, 28 Jan 2016 10:52:26 -0500 |
parents | |
children |
line wrap: on
line source
## ****** HMDB environnemnt : ****** ## # version January 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' $ perl -e 'use LWP::Simple' $ perl -e 'use URI::URL' $ perl -e 'use SOAP::Lite' $ perl -e 'use HTML::Template' $ sudo perl -MCPAN -e shell cpan> install Text::CSV cpan> install LWP::Simple cpan> install URI::URL cpan> install SOAP::Lite cpan> install HTML::Template # libs pfem PERL : this lib were included in lib dir. use conf::conf qw( :ALL ) ; use formats::csv qw( :ALL ) ; -- ## --- 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 : -- ## --- ??? 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. --