Mercurial > repos > jdv > nanopolish

comparison nanopolish_variants.pl @ 4:bdd6c1ab07c5 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
author jdv
date Fri, 01 Dec 2017 21:22:01 -0500
parents a1d433401bc2
children 32cb27adeb34
comparison
equal deleted inserted replaced
3:a1d433401bc2 4:bdd6c1ab07c5
2 2
3 use strict; 3 use strict;
4 use warnings; 4 use warnings;
5 use 5.012; 5 use 5.012;
6 6
7 use Archive::Tar;
8 use Cwd qw/getcwd abs_path/; 7 use Cwd qw/getcwd abs_path/;
9 use File::Copy qw/copy/; 8 use File::Copy qw/copy/;
10 use Getopt::Long qw/:config pass_through/; 9 use Getopt::Long qw/:config pass_through/;
11 use threads; 10 use threads;
12 use threads::shared; 11 use threads::shared;
29 'consensus=s' => \$fn_consensus, 28 'consensus=s' => \$fn_consensus,
30 'fast5=s' => \$fn_fast5, 29 'fast5=s' => \$fn_fast5,
31 'reads=s' => \$fn_reads, 30 'reads=s' => \$fn_reads,
32 ); 31 );
33 32
33 my $ret;
34
34 my $tmp_dir = 'tmp_dir'; 35 my $tmp_dir = 'tmp_dir';
35 mkdir $tmp_dir; 36 mkdir $tmp_dir;
36 37
37 $fn_fast5 = abs_path($fn_fast5); 38 $fn_fast5 = abs_path($fn_fast5);
38 39
39 # extract FAST5 files to path where they are expected 40 # extract FAST5 files to path where they are expected
41 # use system 'tar' to transparently and safely handle absolute paths
40 my $fast5_dir = 'fast5'; 42 my $fast5_dir = 'fast5';
41 mkdir $fast5_dir; 43 mkdir $fast5_dir;
42 my $cwd = abs_path( getcwd() ); 44 my $cwd = abs_path( getcwd() );
43 chdir $fast5_dir; 45 chdir $fast5_dir;
44 my $tar = Archive::Tar->new(); 46 $ret = system(
45 $tar->read($fn_fast5); 47 'tar',
46 $tar->extract(); 48 '-xvf',
47 say "done extracting $fn_fast5 here"; 49 $fn_fast5
50 );
51 die "Failed to extract tarball: $!\n"
52 if ($ret);
48 chdir $cwd; 53 chdir $cwd;
49 54
50 55
51 # index reads 56 # index reads
52 my $ret = system( 57 $ret = system(
53 'nanopolish', 58 'nanopolish',
54 'index', 59 'index',
55 '--directory' => $fast5_dir, 60 '--directory' => $fast5_dir,
56 $fn_reads, 61 $fn_reads,
57 ); 62 );