annotate tool_dependencies.xml @ 1:65d282ef088e draft

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author bjoern-gruening
date Tue, 19 Mar 2013 16:56:25 -0400
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1 <tool_dependency>
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2 <package name="aragorn" version="1.2.36">
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3 <install version="1.0">
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4 <actions>
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5 <action type="download_by_url">http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz</action>
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6 <action type="make_directory">$INSTALL_DIR/bin/</action>
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7 <action type="shell_command">gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c</action>
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8 <action type="move_file">
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9 <source>aragorn</source>
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10 <destination>$INSTALL_DIR/bin</destination>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>Compiling ARAGORN requires gcc.</readme>
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18 </package>
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19 <package name="tRNAscan-SE" version="1.3.1">
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20 <install version="1.0">
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21 <actions>
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22 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
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23 <action type="make_directory">$INSTALL_DIR/bin/</action>
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24 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
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25 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; make</action>
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26 <!-- replacing the hardcoded pathvariables with the real ones -->
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27 <action type="shell_command">sed -i 's%^our $lib_dir.*%our $lib_dir="$INSTALL_DIR/lib/tRNAscan-SE/";%' ./tRNAscan-SE-1.3.1/tRNAscan-SE</action>
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28 <action type="shell_command">sed -i 's%^our $bindir.*%our $bindir="$INSTALL_DIR/bin/";%' ./tRNAscan-SE-1.3.1/tRNAscan-SE</action>
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29 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp trnascan-1.4 covels-SE coves-SE eufindtRNA tRNAscan-SE $INSTALL_DIR/bin/</action>
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30 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp -R tRNAscanSE $INSTALL_DIR/bin/</action>
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31 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp TPCsignal Dsignal *.cm gcode.* $INSTALL_DIR/lib/tRNAscan-SE/</action>
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32 <!-- for some reason infernal needs to be directly unter the bin/ from tRNAScan -->
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33 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
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34 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
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35 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
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36 <action type="set_environment">
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37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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38 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
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39 </action>
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40 </actions>
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41 </install>
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42 <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
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43 </package>
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44 </tool_dependency>