Mercurial > repos > iuc > package_trnascan_1_3_1
view tool_dependencies.xml @ 2:a3c3535a61a5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author | iuc |
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date | Fri, 17 Jul 2015 14:18:37 -0400 |
parents | a3fb2752c340 |
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<tool_dependency> <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="make_directory">$INSTALL_DIR/man/</action> <!-- replacing the hardcoded pathvariables with the real ones --> <action type="shell_command">sed -i.bak -e "s|^BINDIR = .*|BINDIR = $INSTALL_DIR/bin/|" Makefile</action> <action type="shell_command">sed -i.bak -e "s|^LIBDIR = .*|LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/|" Makefile</action> <action type="shell_command">sed -i.bak -e "s|^MANDIR = .*|MANDIR = $INSTALL_DIR/man|" Makefile</action> <action type="make_install"/> <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan --> <action type="download_file">ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action> <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action> <action type="shell_command">cd infernal-1.0.2 && ./configure --prefix=$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>