Mercurial > repos > devteam > package_tophat2_2_0_9

annotate tool_dependencies.xml @ 0:bac5f59d20d8 draft

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Imported from capsule None
author devteam
date Thu, 23 Jan 2014 12:30:34 -0500
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children 976fbb88df15
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="tophat2" version="2.0.9">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.9.Linux_x86_64.tar.gz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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11 </action>
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12 </actions>
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13 <actions architecture="x86_64" os="darwin">
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14 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/tophat/tophat-2.0.9.OSX_x86_64.tar.gz</action>
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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18 </action>
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19 </actions>
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20 <actions>
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21 <package name="samtools" version="0.1.18">
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22 <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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23 </package>
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24 <action type="download_by_url">http://tophat.cbcb.umd.edu/downloads/tophat-2.0.9.tar.gz</action>
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25 <action type="set_environment_for_install">
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26 <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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27 </action>
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28 <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-bam=$BAM_ROOT</action>
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29 <action type="shell_command">make &amp;&amp; make install</action>
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30 </actions>
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31 <action type="set_environment">
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32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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33 </action>
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34 </actions_group>
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35 </install>
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36 <readme />
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37 </package>
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38 </tool_dependency>