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comparison VCF_to_VariantDB.pl @ 8:db44ff975de8 draft

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Corrected macro.xml handling of GALAXY_URL
author geert-vandeweyer
date Tue, 10 Jun 2014 06:01:18 -0400
parents 04e3bba317f4
children 3b27cae9b359
comparison
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7:04e3bba317f4 8:db44ff975de8
109 $result = system("mkdir $wd"); 109 $result = system("mkdir $wd");
110 110
111 111
112 ## link files 112 ## link files
113 $vcfurl = "$dd/data.vcf"; 113 $vcfurl = "$dd/data.vcf";
114 $vcfurl =~ s/\s//g;
114 system ("ln -s $vcfpath $wd/data.vcf"); 115 system ("ln -s $vcfpath $wd/data.vcf");
115 if (exists($opts{'b'})) { 116 if (exists($opts{'b'})) {
116 $bamurl = "$dd/data.bam"; 117 $bamurl = "$dd/data.bam";
118 $bamurl =~ s/\s//g;
117 $bamidxurl = "$dd/data.bai"; 119 $bamidxurl = "$dd/data.bai";
120 $bamidxurl =~ s/\s//g;
118 system ("ln -s $bampath $wd/data.bam"); 121 system ("ln -s $bampath $wd/data.bam");
119 system ("ln -s $baipath $wd/data.bai"); 122 system ("ln -s $baipath $wd/data.bai");
120 } 123 }
121 $sample = $opts{'n'}; 124 $sample = $opts{'n'};
122 $gender = $opts{'g'}; 125 $gender = $opts{'g'};