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view tool_dependencies.xml @ 2:24a2978f8ffc draft

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tool_dependencies with ftputil > 2.3 with statment bug fix
author mzeidler
date Tue, 24 Sep 2013 10:42:48 -0400
parents 3ba5983012cf
children bf1ce9b6e103
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<tool_dependency>
    <package name="virana_python" version="1.0">
        <install version="1.0">
            <actions>
                <action type="setup_virtualenv"> plumbum==1.3.0
                                                 pysam==0.7.5
                                                 ftputil==2.7</action>
            </actions>
        </install>
    </package>
 <package name="numpy" version="1.7.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable name="PYTHONPATH_NUMPY" action="set_to">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>
        <package name="freetype" version="2.4.11">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR/freetype/</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="append_to">$INSTALL_DIR/freetype/bin/</environment_variable>
                    <environment_variable name="FREETYPE_LIB_DIR" action="set_to">$INSTALL_DIR/freetype/lib/</environment_variable>
                    <environment_variable name="FREETYPE_INCLUDE_DIR" action="set_to">$INSTALL_DIR/freetype/include/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling freetype requires a C compiler (typically gcc).</readme>
    </package>

<package name="matplotlib" version="1.3.0">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.3.0/matplotlib-1.3.0.tar.gz</action>

                             
                <!-- install matplotlib -->
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">echo "### PYTHONPATH = $PYTHONPATH, PYTHONPATH_NUMPY = $PYTHONPATH_NUMPY"</action>
                <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &amp;&amp;
                                             export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/:$CPLUS_INCLUDE_PATH &amp;&amp; 
                                             export LIBRARY_PATH=$FREETYPE_LIB_DIR:$LIBRARY_PATH &amp;&amp;  
                                             python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_MATPLOTLIB">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling matplotlib requires a C compiler (typically gcc) and libpng.</readme>
    </package>
<package name="biopython" version="1.61">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
                    python setup.py install --install-lib $INSTALL_DIR/lib/python
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
    </package>
 <package name="htseq" version="0.5.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>
   
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
                    python setup.py install --install-lib $INSTALL_DIR/lib/python --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_HTSEQ">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
    </package>

    <package name="samtools" version="0.1.19">
        <install>
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</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>
    </package>
    <package name="bwa" version="0.7.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.4.tar.bz2 </action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bwa</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>
    </package>
    
    <package name="STAR" version="2.3.0" >
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action>
                <action type="move_file">
                    <source>STAR</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>
    
    </package>
    <package name="lastz" version="1.02.00" >
        <install version="1.0">
            <actions>
                <action type="download_by_url" target_filename="lastz-distrib-1.02.00.tar.gz">http://www.bx.psu.edu/miller_lab/dist/lastz-1.02.00.tar.gz</action>
                <action type="shell_command">sed -i 's/-Werror//g' src/Makefile</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                         <source>src/lastz</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                     <action type="move_file">
                         <source>src/lastz_D</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    </package>   
</tool_dependency>