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annotate tool_dependencies.xml @ 10:08e9244aeab8

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Change dependency for kent (blat faToTwoBit) to latest since versions not available at UCSC
author Jim Johnson <jj@umn.edu>
date Thu, 06 Jun 2013 07:36:16 -0500
parents d9017e11cde5
children 19c48803a377
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="boost" version="1.53.0">
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4 <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="samtools" version="0.1.18">
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7 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="bowtie" version="1.0.0">
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10 <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="gmap" version="2013-05-09">
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13 <repository changeset_revision="03bb09b717ae" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="kent" version="latest">
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16 <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18 <package name="defuse" version="0.6.1">
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19 <install version="1.0">
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20 <actions>
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21 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action>
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22 <!-- populate the environment variables from the dependent repos -->
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23 <action type="set_environment_for_install">
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24 <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" >
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25 <package name="boost" version="1.53.0" />
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26 </repository>
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27 </action>
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28 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
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29 <action type="move_directory_files">
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30 <source_directory>.</source_directory>
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31 <destination_directory>$INSTALL_DIR</destination_directory>
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32 </action>
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33 <action type="set_environment">
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34 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</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 deFuse code
5545ec69acbd Defuse version 0.6.0
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40 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
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41 </readme>
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42 </package>
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44 </tool_dependency>