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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="biopython" version="1.61">
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4 <repository changeset_revision="627c7b41b970" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="aragorn" version="1.2.36">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz</action>
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10 <action type="make_directory">$INSTALL_DIR/bin/</action>
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11 <action type="shell_command">gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c</action>
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12 <action type="move_file">
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13 <source>aragorn</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="set_environment">
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17 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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18 </action>
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19 </actions>
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20 </install>
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21 <readme>Compiling ARAGORN requires gcc.</readme>
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22 </package>
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23 <package name="tRNAscan-SE" version="1.3.1">
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24 <install version="1.0">
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25 <actions>
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26 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
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27 <action type="make_directory">$INSTALL_DIR/bin/</action>
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28 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
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29 <action type="make_directory">$INSTALL_DIR/man/</action>
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30 <!-- replacing the hardcoded pathvariables with the real ones -->
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31 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && sed 's%^BINDIR = .*%BINDIR = $INSTALL_DIR/bin/%' Makefile | sed 's%^LIBDIR = .*%LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/%' | sed 's%^MANDIR = .*%MANDIR = $INSTALL_DIR/man%' > Makefile_new</action>
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32 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && rm Makefile && mv Makefile_new Makefile</action>
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33 <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && make && make install</action>
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34
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35 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
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36 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
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37 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
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38 <action type="shell_command">cd infernal-1.0.2 && ./configure --prefix=$INSTALL_DIR && make && make install</action>
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39 <action type="set_environment">
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40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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41 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/bin/</environment_variable>
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42 </action>
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43 </actions>
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44 </install>
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45 <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
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46 </package>
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47 </tool_dependency>
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