comparison tool_dependencies.xml @ 0:833c4be8f4d4 draft default tip

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0:833c4be8f4d4

<?xml version="1.0"?>
<tool_dependency>
    <package name="pear" version="0.9.6">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-bin-64.tar.gz</action>
                    <action type="move_file">
                        <source>pear-0.9.6-bin-64</source>
                        <destination>$INSTALL_DIR/bin/</destination>
                    </action>
                    <action type="shell_command">mv $INSTALL_DIR/bin/pear-0.9.6-bin-64 $INSTALL_DIR/bin/pear</action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                   <action type="download_by_url">http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-src.tar.gz</action>
                    <action type="autoconf" />
                </actions>
                <action type="set_environment">
                    <environment_variable action="set_to" name="PEAR_ROOT_DIR">$INSTALL_DIR</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>PEAR - Paired-End reAd mergeR
        PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. 
        It is fully parallelized and can run with as low as just a few kilobytes of memory.

        PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input.
        In addition, it implements a statistical test for minimizing false-positive results.
        Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.
        </readme>
    </package>
</tool_dependency>