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comparison libexec/callSomaticVariants.pl @ 9:0e8e6011082b

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Strelka Workflow 0.0.2
author mini
date Fri, 26 Sep 2014 15:51:35 +0200
parents 87568e5a7d4f
children
comparison
equal deleted inserted replaced
8:2cee4ed50058 9:0e8e6011082b
1 #!/usr/bin/env perl 1 #!/usr/bin/env perl
2 print "\n"; 2
3 print @INC;
4 print "\n";
5 =head1 LICENSE 3 =head1 LICENSE
6 4
7 Strelka Workflow Software 5 Strelka Workflow Software
8 Copyright (c) 2009-2013 Illumina, Inc. 6 Copyright (c) 2009-2013 Illumina, Inc.
9 7
36 use Pod::Usage; 34 use Pod::Usage;
37 35
38 my $baseDir; 36 my $baseDir;
39 my $libDir; 37 my $libDir;
40 BEGIN { 38 BEGIN {
41 print "\n";
42 print @INC;
43 print "\n";
44 39
45 my $thisDir=(File::Spec->splitpath($0))[1]; 40 my $thisDir=(File::Spec->splitpath($0))[1];
46 $baseDir=File::Spec->catdir($thisDir,File::Spec->updir()); 41 $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
47 $libDir=File::Spec->catdir($baseDir,'lib'); 42 $libDir=File::Spec->catdir($baseDir,'lib');
48 } 43 }
49 use lib $libDir; 44 use lib $libDir;
50 use Utils; 45 use Utils;
46 print "all imported call";
51 47
52 if(getAbsPath($baseDir)) { 48 if(getAbsPath($baseDir)) {
53 errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'"); 49 errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
54 } 50 }
55 my $libexecDir=File::Spec->catdir($baseDir,'libexec'); 51 my $libexecDir=File::Spec->catdir($baseDir,'libexec');
56 #my $optDir=File::Spec->catdir($baseDir,'opt');
57 52
58 53
59 my $scriptName=(File::Spec->splitpath($0))[2]; 54 my $scriptName=(File::Spec->splitpath($0))[2];
60 my $argCount=scalar(@ARGV); 55 my $argCount=scalar(@ARGV);
61 my $cmdline = join(' ',$0,@ARGV); 56 my $cmdline = join(' ',$0,@ARGV);
80 # 75 #
81 # check all fixed paths (not based on commandline arguments): 76 # check all fixed paths (not based on commandline arguments):
82 # 77 #
83 checkDir($baseDir); 78 checkDir($baseDir);
84 checkDir($libexecDir); 79 checkDir($libexecDir);
85 #checkDir($optDir);
86 80
87 my $strelkaBin=File::Spec->catdir($libexecDir,'strelka2'); 81 my $strelkaBin=File::Spec->catdir($libexecDir,'strelka2');
88 checkFile($strelkaBin,"strelka binary"); 82 checkFile($strelkaBin,"strelka binary");
89 #my $samtoolsBin = File::Spec->catfile($optDir,'samtools','samtools');
90 #checkFile($samtoolsBin,"samtools binary");
91 83
92 84
93 85
94 # 86 #
95 # read config and validate values 87 # read config and validate values