Mercurial > repos > niels > annovar_yaml_wrapper
changeset 19:0044b989f60f draft
Uploaded
| author | niels |
|---|---|
| date | Mon, 10 Jun 2019 09:21:03 -0400 |
| parents | ce16079341bf |
| children | 237d0eef2ad3 |
| files | annovar_yaml/YAML_annovar.yml annovar_yaml/YAML_arguments_annovar.yml annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml |
| diffstat | 2 files changed, 11 insertions(+), 1 deletions(-) [+] |
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--- 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 @@ -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 ( $alias !~ /^N\/A$/ ) {
--- 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>