<?xml version="1.0"?>
<tool_dependency>
    <package name="defuse" version="0.6.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
                <action type="shell_command">cd tools &amp;&amp; make</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
deFuse code
To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
        </readme>
    </package>

    <package name="samtools" version="0.1.18">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>misc/maq2sam-long</source>
                    <destination>$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>
Compiling SAMtools requires the ncurses and zlib development libraries.
        </readme>
    </package>


    <package name="bowtie" version="0.12.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bowtie</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie-build</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie-inspect</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>
            Compiling Bowtie requires libpthread to be present on your system.
        </readme>
    </package>

    <package name="gmap" version="2012-07-20">
        <install version="1.0">
            <actions>
	        <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action>
                <action type="shell_command">./configure</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>src/gmap</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/gmapindex</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/gsnap</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/uniqscan</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/iit_store</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/iit_get</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/atoiindex</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/snpindex</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/cmetindex</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>src/get-genome</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>util</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>

    <package name="blat" version="34x10">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
                <action type="shell_command">chmod 755 blat</action>
                <action type="move_file">
                    <source>blat</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>
This only handles blat for a non-commercial linux system.

Please note that the Blat source and executables are freely available for
academic, nonprofit and personal use. Commercial licensing information is
available on the Kent Informatics website (http://www.kentinformatics.com/).
        </readme>
    </package>

    <package name="fatotwobit" version="34x10">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
                <action type="shell_command">chmod 755 faToTwoBit</action>
                <action type="move_file">
                    <source>faToTwoBit</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>
This only handles faToTwoBit for a non-commercial linux system.

Please note that the source and executables are freely available for
academic, nonprofit and personal use. Commercial licensing information is
available on the Kent Informatics website (http://www.kentinformatics.com/).
        </readme>
    </package>

</tool_dependency>