annotate tool_dependencies.xml @ 0:6bb02bb29819 draft default tip

Imported from capsule None

<?xml version="1.0"?>
<tool_dependency>
    <package name="stacks" version="1.18">
        <install version="1.0">
            <actions>
<!-- compile stacks -->
                <action type="download_by_url">http://creskolab.uoregon.edu/stacks/source/stacks-1.18.tar.gz</action>
		<action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
		<action type="shell_command">make</action>
                <action type="shell_command">make install</action>

		<!-- move binary into $INSTALL_dir -->
		<!--action type="move_file">
				     <source>ustacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>pstacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>estacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>cstacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>sstacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>hstacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>process_radtags</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>process_shortreads</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>kmer_filter</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>clone_filter</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>genotypes</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>populations</source>
				     <destination>$INSTALL_DIR</destination>
				</action>
		<action type="move_file">
				     <source>phasedstacks</source>
				     <destination>$INSTALL_DIR</destination>
				</action-->

		<!-- create env.sh -->
                <action type="set_environment">
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
                        <environment_variable name="INSTALL_DIR" action="set_to">$INSTALL_DIR/</environment_variable>
                </action>
 
           </actions>

        </install>
        <readme>
            This package installs STACKS from the sources available
        </readme>
    </package>
</tool_dependency>