diff README.txt @ 0:86296c048e46 draft

Init repository for [hr2]

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+## ****** HR2 environnemnt : ****** ##
+# version sept 2014 M Landi / A LIEURADE, Cl LIONNET, P MARIJON, B RADISSON and L VARRAILHON / F Giacomoni
+
+## --- 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 Data::Dumper ;
+use Getopt::Long ;
+use FindBin ;
+
+# libs CPAN PERL : 
+$ perl -e 'use Text::CSV'
+$ sudo perl -MCPAN -e shell
+cpan> install Text::CSV
+
+# libs pfem PERL : already include in the package
+use lib::conf  qw( :ALL ) ;
+use lib::csv  qw( :ALL ) ;
+--
+
+## --- R bin and Packages : --- ##
+NA
+--
+
+## --- Binary dependencies --- ##
+Install folowing binaries :
+* HR2 :
+source : HR2_v1.04.cpp available in the tar ball at lib/HR2_v1.04.cpp
+lab : http://jhau.maliwi.de/sci/ms.html for initial project and http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/ for fork
+install : in /opt/prog/metabolomics/hr2 (you can change this path in conf file : conf_hr2.cfg
+compilation : g++ HR2_v1.04.cpp -o HR2-all-res_v1.04.exe
+
+The project is available on :
+http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/seven-golden-rules-supplement-v46.zip (the launch of the download may take some time)
+~/seven-golden-rules-supplement-v46.zip/supplement/HR2-formula-generator/HR2.zip/HR2.cpp
+OR
+http://sourceforge.net/projects/hires/ : This proposed binary is an fork of the HiRes initial project.
+--
+
+## --- Config : --- ##
+Edit the following lines in the config file : conf_hr2.cfg
+lancerHR2=/your_hr2_binary_path/HR2-all-res_v1.04.exe
+JS_GALAXY_PATH=http://YOUR_GALAXY_HOSTNAME/static/scripts/libs/outputs
+CSS_GALAXY_PATH=http://YOUR_GALAXY_HOSTNAME/static/style
+--
+
+## --- XML HELP PART --- ##
+one image : in the static/images dir
+hr2.png
+--
+
+## --- DATASETS --- ##
+No data set ! waiting for galaxy pages
+--
+
+## --- ??? COMMENTS ??? --- ##
+In the PFEM version, the HR2 source (HR2_v*.cpp) is modified to correct atom exact masses.
+For more information, please contact us.
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