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4
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <set_environment version="1.0">
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4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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5 </set_environment>
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6 <package name="samtools" version="0.1.12">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/tool_shed_dependencies/bamedit/samtoolspkg.tar</action>
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10 <action type="shell_command">chmod ago+x samtools</action>
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11 <action type="shell_command">chmod ago+x maq2sam-long</action>
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12 <action type="move_file">
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13 <source>samtools</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="move_file">
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17 <source>maq2sam-long</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
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26 </package>
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27 </tool_dependency>
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