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