comparison tool_dependencies.xml @ 25:09e6427d3e6a draft

Use repository dependency for samtools

24:6460f2ba6a60

for the local installation.  

        </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>
</tool_dependency>

25:09e6427d3e6a

for the local installation.  

        </readme>
    </package>
    <package name="samtools" version="0.1.18">
        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_samtools_0_1_18" owner="devteam" changeset_revision="a7936f4ea405" />
    </package>
</tool_dependency>