Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tool_dependencies.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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children 977861cbcf10
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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4 <package name="cgatools17" version="1">
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5 <install version="1.0">
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6 <actions>
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7 <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action>
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8 <action type="shell_command"> chmod a+x bin/cgatools</action>
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9 <action type="move_file">
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10 <source>bin/cgatools</source>
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11 <destination>$INSTALL_DIR/bin</destination>
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12 </action>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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15 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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16 </action>
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17 </actions>
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18 </install>
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19 <readme>
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20 Downloads and installs the cgatools binary.
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21 </readme>
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22 </package>
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23
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24 <package name="vcf_to_listVariants" version="1.0.0">
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25 <install version="1.0">
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26 <actions>
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27 <!--
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28 <action type="move_file">
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29 <source>$REPOSITORY_INSTALL_DIR/cgatools_v17/bin/vcf_to_listVariants.py</source>
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30 <destination>$INSTALL_DIR/bin/</destination>
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31 </action>
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32 -->
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33
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34 <action type="shell_command">cp $REPOSITORY_INSTALL_DIR/cgatools_v17/tools/cgatools17/vcf_to_listVariants.py $INSTALL_DIR</action>
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35 <action type="chmod">
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36 <file mode="755">$INSTALL_DIR/vcf_to_listVariants.py</file>
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37 </action>
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38
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39 <action type="set_environment">
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40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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41 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17/bin</environment_variable>
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42 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/cgatools_v17</environment_variable>
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43 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR/bin</environment_variable>
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44 </action>
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45 </actions>
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46 </install>
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47 </package>
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48
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49 </tool_dependency>