| Previous changeset 18:ce16079341bf (2019-06-10) Next changeset 20:237d0eef2ad3 (2019-06-10) |
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Commit message:
Uploaded |
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modified:
annovar_yaml/YAML_annovar.yml annovar_yaml/YAML_arguments_annovar.yml annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml |
| b |
| diff -r ce16079341bf -r 0044b989f60f annovar_yaml/annovar_yaml.pl --- a/annovar_yaml/annovar_yaml.pl Mon Jun 10 07:53:19 2019 -0400 +++ b/annovar_yaml/annovar_yaml.pl Mon Jun 10 09:21:03 2019 -0400 |
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| @@ -695,6 +695,16 @@ print "command3: $command\n"; system ( $command ); } + if ( $alias =~ /^Annotation$/ ) { + my $command = "ln -s $path_folder_symlinks/$species\_$database_detail\Mrna.fa $path_symlinks$species\_$alias\Mrna.fa"; + print "command4: $command\n"; + system ( $command ); + } + if ( $database_detail =~ /^clinvar/ ) { + my $command = "ln -s $path_folder_symlinks/$species\_$database_detail.txt.idx $path_symlinks$species\_$database_detail.txt.idx"; + print "command3: $command\n"; + system ( $command ); + } #Push all softlinks used in array if ( $alias !~ /^N\/A$/ ) { |
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| diff -r ce16079341bf -r 0044b989f60f annovar_yaml/annovar_yaml.xml --- a/annovar_yaml/annovar_yaml.xml Mon Jun 10 07:53:19 2019 -0400 +++ b/annovar_yaml/annovar_yaml.xml Mon Jun 10 09:21:03 2019 -0400 |
| [ |
| @@ -7,7 +7,7 @@ <requirement type="package" version="2.50">perl-getopt-long</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - perl $__tool_directory__/annovar_yaml.pl --paryml /data/annovar/YAML_arguments_annovar.yml --invcf $vcf --inyml $yaml --outvcf $output + perl $__tool_directory__/annovar_yaml.pl --invcf $vcf --inyml $yaml --outvcf $output ]]></command> <inputs> |