Mercurial > repos > iuc > package_trnascan_1_3_1

comparison tool_dependencies.xml @ 0:2ddcff5d0fa2 draft

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author iuc
date Sun, 08 Sep 2013 07:13:55 -0400
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-1:000000000000 0:2ddcff5d0fa2
1 <tool_dependency>
2 <package name="tRNAscan-SE" version="1.3.1">
3 <install version="1.0">
4 <actions>
5 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
6 <action type="make_directory">$INSTALL_DIR/bin/</action>
7 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
8 <action type="make_directory">$INSTALL_DIR/man/</action>
9 <!-- replacing the hardcoded pathvariables with the real ones -->
10 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; sed 's%^BINDIR = .*%BINDIR = $INSTALL_DIR/bin/%' Makefile | sed 's%^LIBDIR = .*%LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/%' | sed 's%^MANDIR = .*%MANDIR = $INSTALL_DIR/man%' > Makefile_new</action>
11 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; rm Makefile &amp;&amp; mv Makefile_new Makefile</action>
12 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; make &amp;&amp; make install</action>
13
14 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
15 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
16 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
17 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
18 <action type="set_environment">
19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
20 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
21 </action>
22 </actions>
23 </install>
24 <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
25 </package>
26 </tool_dependency>