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annotate tool_dependencies.xml @ 12:62a1de8c8aae

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Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist
author lparsons
date Mon, 11 Mar 2013 12:44:45 -0400
parents 5d969cb56112
children 30bb8acb77a4
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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="1.6.2">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action>
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7 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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8 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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9 <action type="set_environment">
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10 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
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11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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12 </action>
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13 </actions>
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14 </install>
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15 <readme>
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16 </readme>
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17 </package>
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18
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19 <package name="htseq" version="0.5.4p1">
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20 <install version="1.0">
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21 <actions>
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22 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
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23 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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24 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
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25 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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26 <action type="set_environment">
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27 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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32 <readme>
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33 Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
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34 </readme>
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35 </package>
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36
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37 <package name="samtools" version="0.1.18">
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38 <install version="1.0">
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39 <actions>
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40 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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41 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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42 <action type="shell_command">make</action>
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43 <action type="move_file">
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44 <source>samtools</source>
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45 <destination>$INSTALL_DIR/bin</destination>
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46 </action>
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47 <action type="move_file">
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48 <source>misc/maq2sam-long</source>
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49 <destination>$INSTALL_DIR/bin</destination>
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50 </action>
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51 <action type="set_environment">
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52 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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53 </action>
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54 </actions>
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55 </install>
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56 <readme>
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57 Compiling SAMtools requires the ncurses and zlib development libraries.
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58 </readme>
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59 </package>
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60
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61 <package name="picard" version="1.56.0">
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62 <install version="1.0">
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63 <actions>
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64 <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
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65 <action type="move_directory_files">
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66 <source_directory>picard-tools-1.56</source_directory>
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67 <destination_directory>$INSTALL_DIR/jars</destination_directory>
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68 </action>
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69 <action type="set_environment">
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70 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
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71 </action>
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72 </actions>
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73 </install>
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74 <readme>
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75 </readme>
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76 </package>
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77 </tool_dependency>