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annotate tool_dependencies.xml @ 8:aad08b24baff default tip

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switched to git
author nilesh
date Mon, 15 Jul 2013 14:09:29 -0500
parents 6baaaaa1f858
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="zlib" version="1.2.8">
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4 <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="zlib" owner="nilesh" changeset_revision="28f618926504" />
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5 </package>
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6 <package name="bwa" version="0.7.5a">
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7 <install version="1.0">
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8 <actions>
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9 <action type="set_environment_for_install">
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10 <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" toolshed="http://testtoolshed.g2.bx.psu.edu">
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11 <package name="zlib" version="1.2.8" />
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12 </repository>
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13 </action>
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14 <action type="shell_command">git clone https://github.com/lh3/bwa.git</action>
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15 <action type="shell_command">cd ./bwa &amp;&amp; make LIBS="-L$ZLIB_PATH -lm -lz -lpthread"</action>
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16 <action type="move_file">
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17 <source>bwa/bwa</source>
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18 <destination>$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">$INSTALL_DIR/bin</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 </package>
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26 <set_environment version="1.0">
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27 <environment_variable name="RNASEQCPATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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28 </set_environment>
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29 </tool_dependency>