Mercurial > repos > bjoern-gruening > trna_prediction
view tool_dependencies.xml @ 1:65d282ef088e draft
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author | bjoern-gruening |
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date | Tue, 19 Mar 2013 16:56:25 -0400 |
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children | 0fef99b5f63f |
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<tool_dependency> <package name="aragorn" version="1.2.36"> <install version="1.0"> <actions> <action type="download_by_url">http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz</action> <action type="make_directory">$INSTALL_DIR/bin/</action> <action type="shell_command">gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c</action> <action type="move_file"> <source>aragorn</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme>Compiling ARAGORN requires gcc.</readme> </package> <package name="tRNAscan-SE" version="1.3.1"> <install version="1.0"> <actions> <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action> <action type="make_directory">$INSTALL_DIR/bin/</action> <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action> <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && make</action> <!-- replacing the hardcoded pathvariables with the real ones --> <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> <action type="shell_command">sed -i 's%^our $bindir.*%our $bindir="$INSTALL_DIR/bin/";%' ./tRNAscan-SE-1.3.1/tRNAscan-SE</action> <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && cp trnascan-1.4 covels-SE coves-SE eufindtRNA tRNAscan-SE $INSTALL_DIR/bin/</action> <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && cp -R tRNAscanSE $INSTALL_DIR/bin/</action> <action type="shell_command">cd ./tRNAscan-SE-1.3.1 && cp TPCsignal Dsignal *.cm gcode.* $INSTALL_DIR/lib/tRNAscan-SE/</action> <!-- for some reason infernal needs to be directly unter the bin/ from tRNAScan --> <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action> <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action> <action type="shell_command">cd infernal-1.0.2 && ./configure --prefix=$INSTALL_DIR && make && make install</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable> </action> </actions> </install> <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme> </package> </tool_dependency>