annotate tool_dependencies.xml @ 10:124e64eea35b draft default tip

Fix shell command

<?xml version="1.0"?>
<tool_dependency>
  <package name="kggseq" version="1.0_20180410">
    <install version="1.0">
      <actions>
        <action type="download_by_url" target_filename="kggseq_archive-v1.0_20180410.tar.gz">https://github.com/crs4/kggseq_archive/archive/v1.0_20180410.tar.gz</action>
        <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource-update --resource resources --buildver hg19 --vcf-file examples-lite/rare.disease.hg19.vcf</action>
        <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource-update --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac,gadexome,gadgenome --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict best  --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10  --vcf-file examples-lite/rare.disease.hg19.vcf</action>
        <action type="move_directory_files">
          <source_directory>.</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable name="KGGSEQ_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
        </action>
      </actions>
    </install>
  </package>
</tool_dependency>