<?xml version="1.0"?>
<tool_dependency>
    <package name="spades" version="2.5.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.0/SPAdes-2.5.0-Linux.tar.gz</action>
                <!-- Copying the whole bin folder -->
		<action type="make_directory">$INSTALL_DIR/bin</action>
		<action type="make_directory">$INSTALL_DIR/share</action>
		<action type="move_directory_files">
		  <source_directory>bin</source_directory>
		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
		</action>
                <action type="move_directory_files">
		  <source_directory>share</source_directory>
		  <destination_directory>$INSTALL_DIR/share</destination_directory>
		</action>
		<!-- This is required to have spades accept .dat files -->
		<action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
This installs SPAdes 2.5.0.

See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html
See also here http://bioinf.spbau.ru/en/spades
        </readme>
    </package>
</tool_dependency>