annotate tool_dependencies.xml @ 1:eb47f6bbd2e5 draft

Updated system dependencies to add numpy and bowtie2

<?xml version="1.0"?>
<tool_dependency>
    <package name="metaphlan" version="1.7.0">
        <install version="1.0">
            <actions>
                <action type="shell_command">hg clone https://bitbucket.org/nsegata/metaphlan</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="METAPHLAN_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>

            </actions>
        </install>
        <readme>
These links provide information for the metaphlan package:
http://huttenhower.sph.harvard.edu/metaphlan
https://groups.google.com/forum/#!forum/metaphlan-users
        </readme>
    </package>
    <package name="numpy" version="1.7">
        <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="bowtie2" version="2.1.0">
        <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
</tool_dependency>