Mercurial > repos > iuc > package_trnascan_1_3_1
comparison 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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1:a3fb2752c340 | 2:a3c3535a61a5 |
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5 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action> | 5 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action> |
6 <action type="make_directory">$INSTALL_DIR/bin/</action> | 6 <action type="make_directory">$INSTALL_DIR/bin/</action> |
7 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action> | 7 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action> |
8 <action type="make_directory">$INSTALL_DIR/man/</action> | 8 <action type="make_directory">$INSTALL_DIR/man/</action> |
9 <!-- replacing the hardcoded pathvariables with the real ones --> | 9 <!-- replacing the hardcoded pathvariables with the real ones --> |
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> | 10 <action type="shell_command">sed -i.bak -e "s|^BINDIR = .*|BINDIR = $INSTALL_DIR/bin/|" Makefile</action> |
11 <action type="shell_command">rm Makefile && mv Makefile_new Makefile</action> | 11 <action type="shell_command">sed -i.bak -e "s|^LIBDIR = .*|LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/|" Makefile</action> |
12 <action type="shell_command">sed -i.bak -e "s|^MANDIR = .*|MANDIR = $INSTALL_DIR/man|" Makefile</action> | |
12 <action type="make_install"/> | 13 <action type="make_install"/> |
13 | 14 |
14 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan --> | 15 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan --> |
15 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action> | 16 <action type="download_file">ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action> |
16 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action> | 17 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action> |
17 <action type="shell_command">cd infernal-1.0.2 && ./configure --prefix=$INSTALL_DIR && make && make install</action> | 18 <action type="shell_command">cd infernal-1.0.2 && ./configure --prefix=$INSTALL_DIR && make && make install</action> |
18 <action type="set_environment"> | 19 <action type="set_environment"> |
19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 20 <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 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable> |