Mercurial > repos > sarahinraauzeville > dos2unix

comparison sm_dos2unix.pl @ 1:836946d90d26 draft

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Uploaded perl file
author sarahinraauzeville
date Tue, 12 Dec 2017 09:30:48 -0500
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0:fc7c00da3eeb 1:836946d90d26
1 #!/usr/bin/perl -w
2
3 # usage : perl sm_FASTQ_qual.pl <file.fastq>
4 # 26/05/2015
5 # Sarah Maman
6 # Copyright (C) 2014 INRA
7 # This program is free software: you can redistribute it and/or modify
8 # it under the terms of the GNU General Public License as published by
9 # the Free Software Foundation, either version 3 of the License, or
10 # (at your option) any later version.
11 #
12 # This program is distributed in the hope that it will be useful,
13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 # GNU General Public License for more details.
16 #
17 # You should have received a copy of the GNU General Public License
18 # along with this program. If not, see <http://www.gnu.org/licenses/>.
19 #
20 use strict;
21 use File::Basename;
22 use Getopt::Long;
23 use lib "$ENV{'MY_GALAXY_DIR'}";
24 use GalaxyPath;
25
26
27 my $input1 = $ARGV[0];
28 my $output = $ARGV[1];
29 my $cmd1 = '';
30
31 my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"} );
32 my $DOS = $cfg->my_path( 'toolsPath', 'DOS' );
33
34 $cmd1 = "($DOS -n $input1 $output) >& ./out_dos2unix.log 2>&1";
35 system $cmd1;
36 #Info pour les biologistes
37 print STDOUT "Command run on cluster : \n\n $cmd1 \n\n ";
38
39 #Recuperation des fichiers par Galaxy