Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison README.txt @ 1:6d0a0f8f672a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -0500
parents
children 8f7546d0b925
comparison
equal deleted inserted replaced
0:9583f9772198 1:6d0a0f8f672a
1 ## ****** HMDB environnemnt : ****** ##
2 # version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team
3
4 ## --- PERL compilator / libraries : --- ##
5 $ perl -v
6 This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi
7
8 # libs CORE PERL :
9 use strict ;
10 use warnings ;
11 use Carp qw (cluck croak carp) ;
12 use Exporter ;
13 use Data::Dumper ;
14 use Getopt::Long ;
15 use FindBin ;
16 use Encode;
17
18 # libs CPAN PERL :
19 $ perl -e 'use Text::CSV' - OK
20 use LWP::Simple; - OK
21 use LWP::UserAgent; - OK
22 use URI::URL; - OK
23 use SOAP::Lite; - OK
24 use HTML::Template ; - OK
25 use XML::Twig ; - OK
26
27 $ sudo perl -MCPAN -e shell
28 cpan> install Text::CSV
29
30 # libs pfem PERL : this lib were included in lib dir.
31 use conf::conf qw( :ALL ) ;
32 use formats::csv qw( :ALL ) ;
33 --
34
35 ## --- Conda compliant --- ##
36 This tool and its PERL dependencies are "Conda compliant".
37 The requirements section in the Xml file is still commented, waiting for "Conda" deployment improvement in Galaxy project.
38
39 ## --- R bin and Packages : --- ##
40 No interaction with R
41 --
42
43 ## --- Binary dependencies --- ##
44 No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?)
45 --
46
47 ## --- Config : --- ##
48 JS and CSS (used in HTML output format) are now hosted on cdn.rawgit.com server - no local config needed
49
50
51 PS :If Galaxy can't find the file "hmdb.tmpl", perform this command line : perl -pi -e 's/\r//g' conf_hmdb.cfg
52 --
53
54 ## --- XML HELP PART --- ##
55 one image :
56 hmdb.png
57 --
58
59 ## --- DATASETS OR TUTORIAL --- ##
60 Please find help on W4M: http://workflow4metabolomics.org/howto
61 --
62
63 ## --- ??? COMMENTS ??? --- ##
64 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".
65
66 To use fully functionalities of HTML output format file :
67 - check that sanitize_all_html option in universe_wsgi.ini file is uncomment and set to FALSE.
68 --