annotate tool_dependencies.xml @ 0:bb92d30b4f52 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
        <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="openbabel" version="2.3.2">
        <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="rdkit" version="2012_12_1">
        <repository changeset_revision="7c60f011c70c" name="package_rdkit_2012_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="silicos_it" version="1.0.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/bgruening/silicos-it_store/raw/master/strip-it/strip-it-1.0.2.tar.gz</action>

                <!-- populate the environment variables from the dependend repos 
                    $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR
                -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="openbabel" version="2.3.2" />
                    </repository>
                </action>

                <!--compiling strip-it -->
                <action type="shell_command">
                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                    make  &amp;&amp;
                    make install</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/strip-it/bin</environment_variable>
                </action>

                <!-- compiling align-it -->
                <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/align-it/align-it-1.0.3.tar.gz</action>
                <action type="shell_command">tar xfvz align-it-1.0.3.tar.gz &amp;&amp; 
                    cd align-it-1.0.3 &amp;&amp; 
                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                    make &amp;&amp; 
                    make install</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/align-it/bin</environment_variable>
                </action>

                <!-- compiling shape-it -->
                <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/shape-it/shape-it-1.0.1.tar.gz</action>
                <action type="shell_command">tar xfvz shape-it-1.0.1.tar.gz &amp;&amp; 
                    cd shape-it-1.0.1 &amp;&amp; 
                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                    make &amp;&amp; 
                    make install</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/shape-it/bin</environment_variable>
                </action>

            </actions>
        </install>
        <readme>Compiling silicos-it requires g++ and CMake 2.4+.</readme>
    </package>
</tool_dependency>