annotate tool_dependencies.xml @ 0:8dd538c6ebaf draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_piranha_1_2_1 commit 67caff6ff1cfac1f4f13d206611856ea7ca737c9

<?xml version="1.0"?>
<tool_dependency>
  <package name="gsl" version="1.16">
    <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="bamtools" version="2.3.0_2d7685d2ae">
    <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="piranha" version="1.2.1">
    <install version="1.0">
      <actions>
        <action type="download_by_url">http://smithlabresearch.org/downloads/piranha-1.2.1.tar.gz</action>
        <action type="set_environment_for_install">
          <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="gsl" version="1.16" />
          </repository>
          <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="bamtools" version="2.3.0_2d7685d2ae" />
          </repository>
        </action>
        <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-bam_tools_headers=$BAMTOOLS_ROOT_PATH/include/  --with-bam_tools_library=$BAMTOOLS_ROOT_PATH/lib/</action>
        <action type="shell_command">make all</action>
        <action type="shell_command">make install</action>
        <action type="move_directory_files">
            <source_directory>./bin/</source_directory>
            <destination_directory>$INSTALL_DIR/bin</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
          <environment_variable action="set_to" name="PIRANHA_ROOT_PATH">$INSTALL_DIR/</environment_variable>
        </action>
      </actions>
    </install>
    <readme>Piranha is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process. 
http://smithlabresearch.org/software/piranha/
</readme>
  </package>
</tool_dependency>