Mercurial > repos > bjoern-gruening > trna_prediction

comparison tool_dependencies.xml @ 2:0fef99b5f63f draft default tip

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apply patch from Nicola Soranzo
author bjoern-gruening
date Sun, 24 Mar 2013 14:35:48 -0400
parents 65d282ef088e
children
comparison
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1:65d282ef088e 2:0fef99b5f63f
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> 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>
28 <action type="shell_command">sed -i 's%^our $bindir.*%our $bindir="$INSTALL_DIR/bin/";%' ./tRNAscan-SE-1.3.1/tRNAscan-SE</action> 28 <action type="shell_command">sed -i 's%^our $bindir.*%our $bindir="$INSTALL_DIR/bin/";%' ./tRNAscan-SE-1.3.1/tRNAscan-SE</action>
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> 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>
30 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp -R tRNAscanSE $INSTALL_DIR/bin/</action> 30 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp -R tRNAscanSE $INSTALL_DIR/bin/</action>
31 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp TPCsignal Dsignal *.cm gcode.* $INSTALL_DIR/lib/tRNAscan-SE/</action> 31 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp TPCsignal Dsignal *.cm gcode.* $INSTALL_DIR/lib/tRNAscan-SE/</action>
32 <!-- for some reason infernal needs to be directly unter the bin/ from tRNAScan --> 32 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
33 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action> 33 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
34 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action> 34 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
35 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action> 35 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
36 <action type="set_environment"> 36 <action type="set_environment">
37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>