<?xml version="1.0"?>
<tool_dependency>
  <package name="muscle" version="3.8.31">
    <install version="1.0">
      <actions>
        <action type="download_by_url" target_filename="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action>
        <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile -->
        <action type="shell_command">sed -i 's/-static//g' src/mk</action>
        <action type="shell_command">make -C src/</action>
        <action type="move_file">
          <source>src/muscle</source>
          <destination>$INSTALL_DIR/bin</destination>
        </action>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
        </action>
        <action type="set_environment">
          <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources.
    </readme>
  </package>
</tool_dependency>