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1 #!/usr/bin/perl -w
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2
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3 # usage : perl sm_FASTQ_qual.pl <file.fastq>
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4 # 26/05/2015
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5 # Sarah Maman
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6 # Copyright (C) 2014 INRA
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7 # This program is free software: you can redistribute it and/or modify
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8 # it under the terms of the GNU General Public License as published by
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9 # the Free Software Foundation, either version 3 of the License, or
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10 # (at your option) any later version.
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11 #
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12 # This program is distributed in the hope that it will be useful,
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13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 # GNU General Public License for more details.
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16 #
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17 # You should have received a copy of the GNU General Public License
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18 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 #
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20 use strict;
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21 use File::Basename;
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22 use Getopt::Long;
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23 use lib "$ENV{'MY_GALAXY_DIR'}";
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24 use GalaxyPath;
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25
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26
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27 my $input1 = $ARGV[0];
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28 my $output = $ARGV[1];
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29 my $cmd1 = '';
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30
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31 my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"} );
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32 my $DOS = $cfg->my_path( 'toolsPath', 'DOS' );
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33
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34 $cmd1 = "($DOS -n $input1 $output) >& ./out_dos2unix.log 2>&1";
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35 system $cmd1;
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36 #Info pour les biologistes
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37 print STDOUT "Command run on cluster : \n\n $cmd1 \n\n ";
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38
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39 #Recuperation des fichiers par Galaxy
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