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Commit message:
Uploaded perl file |
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added:
sm_dos2unix.pl |
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| diff -r fc7c00da3eeb -r 836946d90d26 sm_dos2unix.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sm_dos2unix.pl Tue Dec 12 09:30:48 2017 -0500 |
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| @@ -0,0 +1,39 @@ +#!/usr/bin/perl -w + +# usage : perl sm_FASTQ_qual.pl <file.fastq> +# 26/05/2015 +# Sarah Maman +# Copyright (C) 2014 INRA +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +# +use strict; +use File::Basename; +use Getopt::Long; +use lib "$ENV{'MY_GALAXY_DIR'}"; +use GalaxyPath; + + +my $input1 = $ARGV[0]; +my $output = $ARGV[1]; +my $cmd1 = ''; + +my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"} ); +my $DOS = $cfg->my_path( 'toolsPath', 'DOS' ); + +$cmd1 = "($DOS -n $input1 $output) >& ./out_dos2unix.log 2>&1"; +system $cmd1; +#Info pour les biologistes +print STDOUT "Command run on cluster : \n\n $cmd1 \n\n "; + +#Recuperation des fichiers par Galaxy |