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17
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="numpy" version="1.7.1">
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4 <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="ghostscript" version="9.07">
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7 <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9
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10 <package name="package_weblogo" version="3.3">
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11 <install version="1.0">
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12 <actions>
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13 <!-- populate the environment variables from the dependend repos -->
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14 <action type="download_by_url">http://weblogo.googlecode.com/files/weblogo-3.3.tar.gz</action>
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15 <action type="shell_command">echo `ls -lt` && echo `pwd`</action>
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16
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17 <action type="set_environment_for_install">
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18 <repository changeset_revision="c842299349c0" name="package_ghostscript_9_07" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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19 <package name="ghostscript" version="9.07" />
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20 </repository>
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21 <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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22 <package name="numpy" version="1.7.1" />
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23 </repository>
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24 </action>
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25 <!-- install weblogo -->
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26 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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27 <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &&
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28 python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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29 <action type="set_environment">
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30 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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31 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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32 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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34 <environment_variable action="set_to" name="WEBLOGO_PATH">$INSTALL_DIR/bin/weblogo</environment_variable>
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35 </action>
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36 </actions>
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37 </install>
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38 <readme>
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39 weblogo3 is a python version of the old weblogo2.8 or so. Requires numpy and ghostscript so these are installed if not already on your system - if that happens, please be patient
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40 while numpy compiles - especially if the ATLAS libraries are being installed - which is not at present.
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41 </readme>
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42 </package>
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43 </tool_dependency>
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