<?xml version="1.0"?>
<tool_dependency>
    <package name="sickle" version="1.21.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action>
                <action type="set_environment">
                    <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
                </action>
                <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action>
                <action type="shell_command">make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action>
                <action type="move_file">
                    <source>sickle</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source. It also requires zlib, which is included in this repo.
        </readme>
    </package>
</tool_dependency>