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Repository hmdb_ms_search

Name: hmdb_ms_search

Owner: fgiacomoni

Synopsis: [W4M][Metabolomics][LC-MS] HMDB database MS Search Package - Annotation - Returns annotation results (adducts and metabolites) from The Human Metabolome Database.

Detailed description:

Part of the W4M project: http://workflow4metabolomics.org / HMDB: http://www.hmdb.ca/. The wrapper script use the HMDB 'MS search' resource to annotate a list of m/z. The process returns outputs files (CSV and HTML formats) with links through metabocards.

Content homepage: http://workflow4metabolomics.org

Link to this repository: https://toolshed.g2.bx.psu.edu/view/fgiacomoni/hmdb_ms_search/29195cb5d378

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search

Type: unrestricted

Revision: 29:29195cb5d378

This revision can be installed: True

Times cloned / installed: 977

Repository README files - may contain important installation or license information

Readme files

## ****** 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.
--

Name	Description	Version	Minimum Galaxy Version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
HMDB MS search View tool metadata	search by masses on HMDB v5 online LCMS bank	1.7.6	16.01