Import the repository locally

git clone git@forgemia.inra.fr:bios4biol/bioinfo-utils.git

If you don't have an authentified access to the repository ask to join the project in GitLab.

Write your script

Your scripts should have a pod which display when script is called without parameters.
Here are mandatory pod !

Perl script example

use Getopt::Long;
use Pod::Usage;

my( $opt_help, $opt_man, $opt_full, $opt_admins, $opt_choose, $opt_createdb );

GetOptions(
    'help'                 =>      \$opt_help,
    'man'                  =>      \$opt_man,
)
or pod2usage( "Try '$0 --help' for more information.");

pod2usage( -verbose => 1 ) if $opt_help;
pod2usage( -verbose => 2 ) if $opt_man;

# Main
print "Coucou";

=pod

=head1 NAME

mon_script.pl

=head1 SYNOPSIS

mon_script.pl [options] > STDOUT

=head1 DESCRIPTION

First line must be explicit (will be in web site)
After write what you want

=head1 AUTHORS

Author

=head1 VERSION

1

=head1 DATE

05/2012

=head1 KEYWORDS

bidule bidou

=cut

Python script example

from optparse import *

__name__ = "mon_script.py"
__synopsis__ = "mon_script.py [OPTIONS] > STDOUT"
__date__ = "05/2012"
__authors__ = "Author"
__keywords__ = "bidule bidou"
__description__ = "mon_script.pl prints Coucou"
__version__ = '1.0'

Bash script example

##NAME = "mon_script.sh" 
##SYNOPSIS = "mon_script.sh [OPTIONS]" 
##DATE = "05/2012"
##AUTHORS = "Author"
##KEYWORDS = "bidule bidou"
##DESCRIPTION = "mon_script.sh prints Coucou"

Test your script

Go to your local directory and launch the following command to generate json.

/usr/local/bioinfo/Scripts/doc/bin/scripts_to_json.pl -f monscript.pl

You will find in wrong_scripts details about documentations errors. If it's ok, then commit your script.

Commit your script

git add YOUR_SCRIPT
git commit -m "YOUR MESSAGE" YOUR_SCRIPT
git push

Ask to admin to update repository on genotoul and to regenerate json documentation to update the page in the plateform website.

Generate all the documentation

Go to the directory BioinfoUtils/doc/ en launch the command to generate json.

cd /usr/local/bioinfo/Scripts/doc
./bin/scripts_to_json.pl -d ../bin

This script generate a file out.json in the current directory. This json is read by script.html in BioinfoUtils/doc directory. Open script.html to view the list of scripts.

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