<?xml version="1.0"?>
<tool_dependency>
  <package name="sspace" version="2.0">
    <install version="1.0">
      <actions>
        <action type="download_by_url" target_filename="SSPACE-BASIC-2.0_linux-x86_64.zip">http://www.baseclear.com/download.php?file_id=1038</action>
        <!-- fix for Perl >= 5.16.0-->
        <action type="shell_command">sed -i -e 's/require "getopts.pl"/use Getopt::Std/' -e 's/&amp;Getopts/getopts/' SSPACE_Basic_v2.0.pl</action>
        <action type="move_directory_files">
          <source_directory>.</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
        </action>
        <action type="set_environment">
          <environment_variable name="SSPACE_SITE_OPTIONS" action="set_to">"-T 1"</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
Change the SSPACE_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in Bowtie alignment (-T).
    </readme>
  </package>
</tool_dependency>